Hey Benedict,

After successfully completing all the previous steps in a UNIX server environment (remote login) the make test stage results in Failure, with 10/17 errors.

Not entirely sure what might have gone wrong. Tried troubleshooting by performing all steps inside the environment first, no luck there, currently trying to see if setting the path shortcuts fixes the issue.

I ran marginAlign on nanopore data. Full disclosure: my database was Gencode transcripts, not genome, but it seemed to work just fine (the sam header was just really, really long).
But when I tried marginStats on the output, I kept getting this index out of range error. I played some with the code, but I can't seem to find the problem.

Minimal example input here:
marginStats test.sam test.fastq tx.fa --identity

Full error:

Traceback (most recent call last):
  File "/home/ubuntu/bin/marginAlign/src/margin/marginStats.py", line 97, in <module>
    main()
  File "/home/ubuntu/bin/marginAlign/src/margin/marginStats.py", line 70, in main
    referenceFastaFile, globalAlignment=not options.localAlignment)
  File "/home/ubuntu/bin/marginAlign/src/margin/utils.py", line 383, in getReadAlignmentStats
    refSequences[sam.getrname(aR.rname)], aR, globalAlignment), samIterator(sam))
  File "/home/ubuntu/bin/marginAlign/src/margin/utils.py", line 383, in <lambda>
    refSequences[sam.getrname(aR.rname)], aR, globalAlignment), samIterator(sam))
  File "/home/ubuntu/bin/marginAlign/src/margin/utils.py", line 312, in __init__
    for aP in AlignedPair.iterator(alignedRead, self.refSeq, self.readSeq):
  File "/home/ubuntu/bin/marginAlign/src/margin/utils.py", line 278, in iterator
    if aP.getReadBase().upper() != alignedSegment.query_alignment_sequence[readPos].upper():
IndexError: string index out of range

In tests/ there is test.py file. This needs to have tests each of the run configurations described in the readme with the provided test files.

Hi,
I tried to use marginAlign, but I got this error message (see below).
However marginAlign generated a sam file (BC01_margin.sam). I then generated a sam file using minimap2. I then covered the two sam files into bam and compared them. I found that they are identical.
So I wonder what is this error message, and shall I ignore it?

./marginAlign BC01.fastq NCBI.GRCh38.fa BC01_margin.sam --minimap2 --jobTree ./jobTree

`Got message from job at time: 1532483160.06 : Going to chain sam file: /Users/tarekmagdyshehatamohamed/marginAlign/jobTree/jobs/gTD0/tmp_n8m4A2PTD1/temp.sam
Got message from job at time: 1532483160.12 : Going to realign sam file: /Users/tarekmagdyshehatamohamed/marginAlign/jobTree/jobs/gTD1/tmp_hLKwfZylUn/temp.sam to create output sam file: BC01_margin.sam with match gamma 0.5 and gap gamma 0.0 and model /Users/tarekmagdyshehatamohamed/marginAlign/src/margin/mappers/last_hmm_20.txt
The job seems to have left a log file, indicating failure: /Users/tarekmagdyshehatamohamed/marginAlign/jobTree/jobs/t0/t1/t3/t3/t2/job
Reporting file: /Users/tarekmagdyshehatamohamed/marginAlign/jobTree/jobs/t0/t1/t3/t3/t2/log.txt
log.txt: ---JOBTREE SLAVE OUTPUT LOG---
log.txt: /bin/sh: line 1: 56616 Done echo "cigar: 2bb57717-77dd-4330-b20f-548cd1975eae 14 37946 + chr14 54392591 54430647 + 1 M 10 D 1 M 13 D 1 M 48 I 1 M 47 D 1 M 25 D 2 M 15 I 1 M 6 D 3 M 38 D 3 M 22 I 1 M 71 D 2 M 13 D 1 M 24 I 1 M 22 I 2 M 13 D 1 M 2 D 1 M 40 D 1 M 25 D 1 M 15 D 1 M 3 D 1 M 16 D 1 M 22 D 2 M 10 I 1 M 3 I 2 M 8 I 1 M 10 I 1 M 17 D 2 M 5 D 1 M 9 D 2 M 9 I 1 M 15 I 1 M 4 D 2 M 33 D 2 M 17 D 1 M 2 D 1 M 9 I 1 M 5 I 1 M 2 D 1 M 2 D 1 M 15 I 1 M 1 I 1 M 20 D 6 M 3 D 1 M 8 I 1 M 2 D 1 M 37 I 1 M 7 I 1 M 7 I 1 M 19 D 1 M 26 D 3 M 18 D 2 M 5 D 1 M 7 D 1 M 6 D 1 M 9 I 1 M 9 D 1 M 10 D 1 M 7 D 2 M 6 D 2 M 5 D 2 M 2 D 1 M 8 I 2 M 5 D 2 M 2 I 1 M 5 I 1 M 15 I 4 M 6 I 2 M 12 D 1 M 3 D 2 M 2 I 2 M 5 D 2 M 33 D 1 M 9 D 4 M 51 D 3 M 11 I 3 M 10 I 3 M 17 D 3 M 5 I 1 M 5 D 1 M 8 D 2 M 6 D 1 M 10 D 3 M 11 I 1 M 19 D 1 M 4 D 3 M 7 I 1 M 15 I 1 M 22 D 2 M 2 I 4 M 7 I 1 M 7 D 3 M 15 I 1 M 5 I 3 M 12 I 1 M 7 D 2 M 14 D 1 M 15 I 1 M 24 D 1 M 8 I 1 M 45 D 1 M 11 D 2 M 27 D 1 M 34 I 1 M 7 D 1 M 6 I 1 M 9 D 1 M 7 D 1 M 12 D 1 M 3 D 1 M 19 I 1 M 10 D 1 M 15 I 2 M 3 D 1 M 26 I 2 M 3 I 2 M 21 I 1 M 22 I 1 M 2 D 2 M 12 I 1 M 2 I 2 M 6 D 2 M 23 I 2 M 12 I 1 M 16 D 2 M 1 I 1 M 9 D 1 M 5 I 1 M 14 D 1 M 15 I 1 M 37 I 1 M 3 D 1 M 28 D 1 M 31 D 2 M 8 D 1 M 6 D 1 M 20 I 2 M 30 D 1 M 8 I 1 M 11 D 1 M 4 D 1 M 1 D 1 M 7 I 3 M 22 I 2 M 2 D 1 M 3 I 1 M 13 D 1 M 7 I 2 M 1 D 1 M 20 D 1 M 7 I 3 M 5 I 2 M 4 I 2 M 2 D 1 M 8 D 2 M 2 I 1 M 3 D 3 M 33 D 1 M 8 D 2 M 2 D 1 M 8 I 1 M 24 D 3 M 6 I 2 M 19 D 1 M 4 D 1 M 2 I 2 M 26 I 2 M 12 D 1 M 19 I 2 M 25 D 1 M 5 D 1 M 32 I 1 M 21 D 1 M 29 I 1 M 36 D 2 M 2 D 2 M 8 D 2 M 8 D 1 M 82 D 1 M 11 I 1 M 16 I 2 M 32 I 1 M 7 I 1 M 10 I 1 M 16 I 1 M 20 I 1 M 12 I 2 M 17 D 2 M 5 D 1 M 4 D 1 M 5 D 2 M 2 D 1 M 5 D 2 M 11 I 1 M 14 I 2 M 25 D 1 M 16 D 1 M 44 I 1 M 2 D 2 M 10 D 3 M 4 D 1 M 25 D 1 M 8 D 3 M 7 I 1 M 2 I 3 M 19 I 1 M 40 D 1 M 33 D 1 M 4 D 1 M 1 D 2 M 8 D 1 M 31 I 2 M 2 D 1 M 8 I 1 M 5 I 1 M 2 I 1 M 6 D 1 M 26 D 1 M 105 I 1 M 6 I 2 M 76 D 2 M 11 I 1 M 11 I 1 M 31 I 1 M 3 D 3 M 21 I 1 M 44 I 1 M 7 I 1 M 12 I 1 M 7 I 1 M 1 I 1 M 4 I 2 M 19 D 2 M 4 D 2 M 34 I 1 M 21 I 2 M 24 I 1 M 13 I 1 M 16 I 1 M 13 I 3 M 2 D 1 M 34 D 2 M 11 I 1 M 15 D 3 M 11 I 1 M 24 D 1 M 41 D 2 M 5 I 1 M 6 I 2 M 48 I 2 M 2 D 2 M 7 D 1 M 8 I 1 M 36 I 1 M 71 D 2 M 6 D 1 M 1 D 1 M 9 D 1 M 2 D 1 M 2 D 1 M 71 D 1 M 10 D 2 M 22 I 2 M 36 I 1 M 6 D 1 M 9 D 2 M 11 I 1 M 60 D 1 M 7 I 1 M 24 I 1 M 58 D 2 M 7 D 1 M 38 I 1 M 31 I 2 M 27 D 2 M 5 D 1 M 16 D 1 M 51 D 3 M 13 D 2 M 5 I 1 M 12 D 2 M 13 I 1 M 5 I 2 M 5 I 1 M 11 I 3 M 15 D 1 M 22 I 1 M 37 D 1 M 10 D 1 M 26 I 1 M 7 D 2 M 8 I 1 M 33 D 3 M 9 I 4 M 13 D 7 M 19 I 1 M 1 D 3 M 37 I 1 M 16 I 1 M 30 D 2 M 16 D 1 M 5 I 2 M 1 D 1 M 5 D 1 M 10 I 1 M 1 I 2 M 7 I 2 M 3 D 1 M 5 I 1 M 42 I 4 M 11 D 1 M 20 I 1 M 8 D 3 M 26 D 2 M 63 I 1 M 1 I 1 M 30 I 3 M 8 D 1 M 16 I 1 M 8 I 1 M 6 I 1 M 13 I 2 M 9 D 1 M 50 I 1 M 22 D 2 M 31 I 1 M 8 I 1 M 2 I 1 M 2 I 1 M 12 I 3 M 25 D 3 M 32 D 3 M 11 I 1 M 4 D 1 M 7 D 1 M 22 D 1 M 2 I 2 M 59 I 1 M 29 D 3 M 11 I 2 M 7 I 1 M 20 I 1 M 37 I 1 M 2 I 1 M 25 D 1 M 9 I 1 M 7 D 2 M 11 D 2 M 10 I 1 M 4 I 2 M 7 D 1 M 17 D 1 M 19 D 1 M 16 I 2 M 14 D 1 M 31 I 2 M 5 I 1 M 5 D 1 M 27 D 2 M 16 I 1 M 23 I 2 M 13 I 3 M 25 D 1 M 11 I 5 M 10 D 1 M 41 D 1 M 13 I 1 M 21 I 1 M 17 D 1 M 18 I 1 M 7 I 2 M 47 D 1 M 19 D 1 M 35 D 3 M 26 D 1 M 30 I 1 M 15 D 2 M 20 D 3 M 2 I 2 M 19 I 1 M 12 I 4 M 28 D 1 M 12 D 2 M 7 D 1 M 9 I 1 M 7 I 2 M 13 D 1 M 10 I 3 M 7 D 2 M 27 I 2 M 24 I 2 M 25 I 2 M 13 I 1 M 41 I 1 M 20 D 1 M 24 I 3 M 39 D 1 M 26 D 1 M 37 D 2 M 9 I 1 M 4 I 1 M 7 I 2 M 3 D 1 M 28 D 2 M 23 D 1 M 13 I 1 M 10 I 1 M 5 I 1 M 10 D 1 M 34 D 1 M 10 D 1 M 71 D 2 M 31 D 1 M 19 D 1 M 7 D 1 M 54 I 1 M 5 I 1 M 10 I 1 M 9 D 1 M 15 I 1 M 10 I 1 M 15 I 3 M 19 I 1 M 12 I 1 M 6 D 1 M 17 D 1 M 38 I 1 M 21 D 2 M 15 D 1 M 10 D 1 M 10 I 1 M 55 I 1 M 8 I 2 M 10 I 2 M 26 D 1 M 65 I 1 M 18 I 1 M 75 I 2 M 44 D 2 M 7 D 2 M 15 I 1 M 21 I 1 M 13 D 1 M 88 I 10 M 37 I 1 M 32 D 1 M 28 D 1 M 23 D 1 M 21 D 2 M 35 D 1 M 84 D 1 M 24 I 3 M 6 I 1 M 4 D 2 M 51 D 4 M 21 D 2 M 12 D 2 M 52 D 1 M 17 D 1 M 15 D 1 M 18 D 1 M 12 I 1 M 31 D 3 M 9 I 2 M 44 I 1 M 43 D 1 M 102 D 1 M 17 D 2 M 10 D 1 M 17 I 3 M 32 I 2 M 7 I 2 M 2 D 1 M 13 D 1 M 38 I 3 M 12 D 2 M 13 D 1 M 10 I 2 M 1 D 3 M 10 D 1 M 36 D 1 M 14 D 1 M 41 I 1 M 38 D 2 M 3 D 1 M 35 D 1 M 10 D 1 M 2 I 1 M 1 I 1 M 12 I 6 M 15 D 3 M 8 D 1 M 1 D 1 M 3 D 2 M 10 I 1 M 5 D 1 M 17 D 1 M 16 D 1 M 15 D 1 M 29 I 2 M 31 I 2 M 8 I 1 M 20 D 2 M 57 D 2 M 2 I 1 M 22 D 3 M 7 I 1 M 10 D 1 M 34 D 1 M 21 I 2 M 23 D 2 M 7 I 2 M 8 I 1 M 5 D 2 M 10 I 1 M 18 D 1 M 31 I 1 M 29 I 2 M 5 D 1 M 50 D 1 M 10 D 3 M 10 I 1 M 2 D 1 M 16 I 3 M 28 D 2 M 23 D 1 M 15 I 2 M 13 D 1 M 7 D 1 M 36 I 4 M 8 D 1 M 50 I 1 M 15 I 1 M 19 D 1 M 7 I 3 M 13 I 3 M 36 I 1 M 6 I 2 M 63 I 1 M 28 I 1 M 3 I 1 M 14 D 1 M 11 I 1 M 34 D 2 M 10 I 1 M 17 I 1 M 23 D 1 M 5 D 1 M 6 I 1 M 4 I 1 M 40 D 1 M 2 I 1 M 46 I 1 M 29 I 5 M 4 I 1 M 3 D 1 M 35 D 1 M 36 I 1 M 6 I 1 M 47 D 2 M 39 I 3 M 5 I 1 M 3 D 3 M 67 D 1 M 41 I 2 M 31 D 1 M 16 D 1 M 7 D 1 M 27 I 1 M 28 D 2 M 4 D 1 M 2 D 1 M 6 D 1 M 26 D 2 M 57 D 1 M 19 D 2 M 4 D 1 M 90 D 1 M 11 I 1 M 46 I 1 M 12 D 1 M 27 D 1 M 9 D 1 M 22 D 3 M 34 I 2 M 2 D 1 M 5 D 2 M 32 D 2 M 1 D 1 M 18 I 1 M 38 I 2 M 21 D 4 M 18 I 3 M 15 I 1 M 2 D 3 M 4 D 1 M 21 I 1 M 4 I 1 M 22 D 1 M 29 D 1 M 14 D 1 M 30 I 1 M 2 I 1 M 3 D 1 M 1 D 2 M 10 I 3 M 33 I 1 M 11 D 1 M 12 D 2 M 44 I 3 M 6 D 1 M 46 I 2 M 1 D 1 M 42 D 1 M 5 I 1 M 27 D 1 M 21 D 2 M 16 D 1 M 33 D 1 M 20 D 2 M 3 D 1 M 24 D 1 M 10 D 1 M 9 D 5 M 25 I 1 M 4 I 2 M 1 I 1 M 28 D 1 M 9 I 4 M 3 D 2 M 4 D 1 M 5 I 1 M 11 I 1 M 15 D 1 M 48 D 1 M 5 I 1 M 2 I 1 M 15 D 3 M 21 D 1 M 6 D 2 M 6 D 1 M 15 I 1 M 11 D 1 M 63 D 2 M 3 D 1 M 15 I 1 M 24 I 2 M 12 I 1 M 21 D 1 M 7 I 1 M 18 I 3 M 12 D 1 M 3 I 1 M 11 I 1 M 13 I 1 M 27 I 1 M 11 I 2 M 10 D 1 M 17 D 2 M 8 I 1 M 6 I 1 M 9 I 1 M 20 D 1 M 18 D 1 M 5 D 1 M 17 I 2 M 2 D 1 M 5 D 1 M 2 D 1 M 16 D 1 M 41 D 2 M 8 D 1 M 13 I 1 M 18 D 1 M 13 I 1 M 14 I 1 M 6 I 1 M 57 D 1 M 21 D 1 M 49 D 1 M 23 D 3 M 2 D 1 M 27 D 4 M 19 D 1 M 71 D 1 M 34 I 2 M 79 I 1 M 44 D 2 M 12 D 2 M 10 D 2 M 30 D 1 M 17 I 1 M 47 I 1 M 7 I 1 M 35 D 1 M 14 D 1 M 106 I 1 M 18 I 1 M 16 D 1 M 6 D 1 M 8 D 1 M 17 I 1 M 38 I 1 M 40 I 1 M 36 I 1 M 1 D 2 M 11 D 2 M 18 D 1 M 22 D 1 M 15 I 2 M 19 I 1 M 10 I 1 M 1 D 3 M 2 I 1 M 3 D 4 M 4 D 1 M 13 D 3 M 55 D 2 M 14 I 1 M 12 I 1 M 13 D 1 M 1 I 3 M 3 I 2 M 5 D 1 M 15 I 2 M 5 D 2 M 19 I 1 M 8 D 1 M 16 D 1 M 38 I 1 M 65 I 1 M 11 I 1 M 14 I 1 M 9 I 1 M 7 I 1 M 14 I 1 M 1 I 1 M 69 D 2 M 75 D 1 M 11 I 1 M 22 D 1 M 5 I 1 M 18 D 1 M 3 I 2 M 38 D 1 M 64 D 1 M 6 I 1 M 6 I 1 M 13 I 3 M 38 D 2 M 13 D 1 M 59 D 2 M 7 I 2 M 7 D 1 M 30 D 2 M 44 I 1 M 7 I 1 M 3 I 1 M 6 D 1 M 15 D 1 M 15 D 1 M 7 D 3 M 3 I 1 M 75 I 1 M 1 I 1 M 15 D 2 M 20 I 1 M 2 I 1 M 20 I 1 M 4 D 1 M 10 I 2 M 7 D 2 M 13 D 2 M 21 I 2 M 13 I 1 M 4 I 1 M 5 D 2 M 2 D 2 M 10 I 1 M 51 D 1 M 54 D 2 M 51 I 1 M 24 D 2 M 10 D 1 M 18 D 1 M 8 D 2 M 6 I 1 M 2 D 1 M 20 D 1 M 7 D 1 M 15 D 1 M 37 I 1 M 36 D 1 M 19 I 1 M 15 I 1 M 8 I 1 M 1 I 1 M 15 I 2 M 8 I 4 M 10 D 2 M 71 I 1 M 62 I 1 M 42 I 1 M 35 D 1 M 63 D 1 M 3 D 1 M 7 I 1 M 20 D 1 M 50 D 1 M 10 D 1 M 5 D 1 M 20 I 1 M 4 I 1 M 29 D 2 M 65 I 2 M 7 I 1 M 1 D 2 M 24 D 1 M 24 D 1 M 28 I 2 M 22 D 4 M 3 D 1 M 27 D 2 M 27 I 1 M 65 I 1 M 3 D 1 M 5 D 3 M 1 I 2 M 38 D 1 M 8 I 2 M 27 I 1 M 6 I 3 M 34 I 1 M 10 I 4 M 6 D 1 M 29 I 1 M 7 I 1 M 23 D 1 M 44 I 1 M 11 I 1 M 7 I 1 M 9 I 1 M 7 I 1 M 19 I 1 M 5 D 1 M 18 I 2 M 25 D 1 M 11 I 2 M 1 D 1 M 13 I 1 M 28 I 1 M 7 I 1 M 9 I 2 M 15 I 1 M 14 I 1 M 18 I 2 M 25 I 3 M 11 D 1 M 39 D 1 M 38 D 1 M 8 I 1 M 4 I 2 M 2 I 1 M 13 D 1 M 25 I 2 M 9 I 1 M 30 D 1 M 30 I 3 M 32 I 1 M 39 D 3 M 2 D 1 M 47 D 1 M 18 I 6 M 36 D 2 M 11 I 2 M 1 I 1 M 2 D 1 M 3 D 2 M 45 I 1 M 7 D 1 M 83 I 1 M 49 D 2 M 10 I 1 M 46 I 1 M 21 I 1 M 13 D 1 M 41 D 1 M 20 I 2 M 28 D 1 M 19 I 4 M 20 D 2 M 62 I 2 M 3 D 2 M 7 D 1 M 10 D 1 M 22 D 1 M 2 D 2 M 3 I 1 M 8 D 1 M 15 D 1 M 8 I 1 M 11 I 1 M 14 I 2 M 1 D 1 M 33 D 1 M 19 D 1 M 33 I 3 M 2 I 1 M 11 D 5 M 19 I 1 M 1 D 2 M 33 D 2 M 23 I 3 M 58 I 1 M 5 I 2 M 2 D 1 M 26 D 1 M 3 D 2 M 50 I 1 M 4 I 1 M 8 I 3 M 34 I 4 M 30 D 1 M 7 D 1 M 14 D 1 M 14 D 1 M 11 I 1 M 29 D 1 M 20 D 1 M 40 D 3 M 14 I 1 M 14 D 1 M 10 I 5 M 27 D 1 M 27 D 1 M 37 I 1 M 26 D 1 M 10 D 1 M 37 I 1 M 41 D 3 M 13 D 1 M 9 I 2 M 24 I 1 M 72 D 2 M 5 D 1 M 38 I 2 M 6 I 2 M 57 D 1 M 2 D 1 M 5 I 2 M 7 I 1 M 15 D 1 M 15 I 1 M 29 I 2 M 22 D 1 M 34 D 1 M 69 D 1 M 8 D 1 M 18 D 1 M 47 I 2 M 15 D 1 M 1 D 2 M 7 D 1 M 45 I 1 M 2 I 1 M 5 I 1 M 5 D 2 M 31 I 2 M 2 D 1 M 9 D 2 M 16 I 1 M 13 I 3 M 23 I 3 M 13 I 1 M 1 D 4 M 22 D 1 M 16 D 1 M 23 D 1 M 7 D 1 M 17 I 3 M 18 D 1 M 38 I 1 M 19 I 1 M 16 I 1 M 14 D 1 M 13 D 1 M 31 I 1 M 4 D 1 M 26 I 1 M 50 I 1 M 77 I 1 M 38 I 1 M 1 I 1 M 21 I 2 M 4 I 2 M 7 I 3 M 4 I 1 M 58 I 2 M 12 D 2 M 6 D 1 M 6 I 1 M 41 D 1 M 17 I 1 M 3 I 2 M 6 D 4 M 33 D 5 M 8 D 1 M 15 D 2 M 4 I 2 M 10 I 1 M 21 I 1 M 1 I 1 M 8 D 1 M 4 D 1 M 7 D 3 M 32 D 3 M 15 D 2 M 7 I 3 M 1 I 1 M 2 I 1 M 25 I 2 M 14 I 1 M 2 D 2 M 7 I 1 M 8 D 2 M 22 D 3 M 3 D 1 M 11 I 1 M 17 D 1 M 49 D 1 M 11 D 1 M 42 D 1 M 1 D 1 M 2 D 1 M 28 D 1 M 11 I 2 M 6 I 1 M 8 D 1 M 10 D 1 M 20 D 1 M 43 I 1 M 11 I 1 M 34 I 2 M 6 D 2 M 7 D 1 M 61 D 1 M 5 I 1 M 12 D 1 M 9 D 1 M 17 I 2 M 11 I 1 M 27 D 1 M 50 D 2 M 2 D 1 M 37 D 4 M 28 I 2 M 3 D 1 M 8 D 2 M 48 D 2 M 6 D 2 M 37 D 2 M 26 I 2 M 20 D 2 M 13 D 1 M 15 I 5 M 23 D 1 M 65 D 1 M 17 D 1 M 26 I 1 M 59 I 1 M 36 D 2 M 38 I 1 M 34 I 3 M 13 I 1 M 37 D 1 M 3 I 5 M 14 D 1 M 45 I 1 M 27 D 1 M 14 D 1 M 67 D 1 M 39 D 2 M 32 I 1 M 14 D 1 M 27 I 2 M 1 I 2 M 9 I 2 M 9 I 1 M 13 I 2 M 4 I 2 M 18 D 1 M 3 D 1 M 70 D 1 M 39 I 1 M 9 I 1 M 11 I 1 M 51 I 3 M 41 D 4 M 7 I 2 M 52 D 2 M 52 I 1 M 9 I 1 M 49 D 1 M 7 I 2 M 38 I 3 M 18 D 1 M 8 I 3 M 34 I 3 M 18 D 1 M 14 D 1 M 29 D 1 M 22 I 1 M 4 I 1 M 10 D 1 M 16 D 1 M 35 D 2 M 43 I 1 M 36 D 1 M 26 I 2 M 13 D 1 M 56 D 1 M 18 I 1 M 18 D 1 M 57 D 2 M 46 D 1 M 5 D 1 M 2 I 2 M 2 D 1 M 41 D 2 M 1 I 1 M 3 D 1 M 11 I 1 M 5 I 1 M 4 I 2 M 28 D 2 M 6 D 2 M 2 I 1 M 1 I 3 M 37 I 1 M 14 I 1 M 18 I 1 M 4 I 1 M 7 D 1 M 5 I 1 M 81 D 1 M 15 D 1 M 26 I 1 M 28 I 1 M 11 I 1 M 9 D 2 M 6 D 2 M 17 I 1 M 20 D 1 M 46 I 1 M 19 D 2 M 15 D 3 M 4 D 2 M 14 I 1 M 58 D 1 M 3 D 1 M 6 I 1 M 14 I 1 M 6 I 2 M 36 D 1 M 31 D 1 M 12 I 1 M 29 D 1 M 45 I 1 M 32 I 1 M 47 D 1 M 3 D 1 M 30 I 1 M 2 I 1 M 16 D 1 M 19 D 1 M 3 D 1 M 1 D 1 M 19 I 2 M 9 D 1 M 63 D 1 M 27 D 1 M 31 I 1 M 5 I 2 M 4 I 1 M 70 D 1 M 17 I 1 M 8 D 2 M 79 I 3 M 27 I 1 M 46 I 3 M 13 I 2 M 11 I 1 M 48 D 1 M 116 D 1 M 25 I 2 M 24 D 1 M 9 D 1 M 58 D 1 M 45 D 1 M 22 D 1 M 5 D 2 M 38 D 3 M 35 D 2 M 19 D 1 M 27 D 2 M 30 I 1 M 19 D 2 M 34 I 2 M 5 D 2 M 27 D 1 M 13 I 1 M 3 D 1 M 44 D 2 M 33 D 2 M 39 D 3 M 9 I 1 M 45 I 1 M 5 D 1 M 44 D 1 M 35 I 1 M 5 D 1 M 45 I 1 M 26 I 1 M 5 D 1 M 51 I 3 M 13 I 1 M 13 D 1 M 17 D 1 M 6 I 1 M 6 I 1 M 5 D 1 M 8 I 2 M 4 I 1 M 23 I 2 M 11 D 2 M 6 D 2 M 3 D 1 M 108 D 1 M 14 I 1 M 16 I 2 M 11 I 1 M 2 D 1 M 5 I 2 M 11 I 3 M 4 I 1 M 55 I 1 M 7 I 3 M 57 I 1 M 38 I 1 M 14 I 8 M 44 D 1 M 13 D 3 M 22 I 1 M 4 I 2 M 12 I 1 M 22 I 2 M 3 D 1 M 73 D 1 M 19 D 1 M 27 D 1 M 19 D 1 M 5 D 2 M 13 D 1 M 2 D 3 M 17 I 1 M 7 D 2 M 24 D 2 M 29 I 3 M 20 I 1 M 15 I 1 M 12 I 3 M 19 I 1 M 19 D 2 M 3 I 1 M 21 I 1 M 8 I 2 M 17 D 3 M 10 I 1 M 8 I 2 M 10 I 2 M 1 I 5 M 4 D 3 M 4 D 2 M 9 D 1 M 11 I 2 M 10 D 1 M 39 I 1 M 27 D 1 M 26 I 1 M 13 I 2 M 4 D 1 M 9 D 3 M 2 I 1 M 14 I 1 M 13 I 1 M 5 D 1 M 8 D 1 M 15 I 1 M 1 I 1 M 3 D 1 M 56 I 1 M 22 D 1 M 4 I 1 M 18 D 1 M 5 D 2 M 32 I 1 M 23 D 1 M 6 D 3 M 70 I 1 M 2 D 2 M 19 I 4 M 21 D 1 M 3 I 1 M 5 D 1 M 1 D 1 M 8 D 1 M 20 D 2 M 13 I 3 M 6 D 2 M 12 I 1 M 6 I 1 M 6 D 1 M 5 D 1 M 17 D 1 M 7 I 1 M 9 I 1 M 4 I 1 M 6 D 1 M 12 D 1 M 2 D 2 M 4 I 2 M 8 I 1 M 20 D 1 M 9 D 1 M 6 I 2 M 5 D 1 M 22 I 1 M 2 I 1 M 23 D 1 M 24 D 1 M 10 D 2 M 10 D 1 M 9 I 2 M 8 I 1 M 7 D 1 M 4 D 3 M 8 D 1 M 9 I 2 M 6 D 1 M 6 D 1 M 36 D 2 M 2 D 1 M 13 D 6 M 15 I 1 M 10 I 2 M 8 I 1 M 11 D 1 M 6 I 1 M 8 I 1 M 41 I 1 M 3 D 1 M 9 I 1 M 7 I 2 M 6 I 2 M 3 D 1 M 6 I 1 M 20 I 1 M 3 I 2 M 20 D 1 M 7 D 1 M 24 I 2 M 17 I 1 M 26 I 2 M 4 D 1 M 16 I 1 M 4 D 2 M 25 I 1 M 8 D 2 M 3 D 1 M 11 D 1 M 3 I 1 M 33 D 1 M 1 D 1 M 11 I 1 M 4 I 2 M 22 D 1 M 105 D 1 M 15 I 2 M 25 I 1 M 39 D 1 M 1 D 2 M 43 I 1 M 7 D 2 M 7 I 2 M 1 D 1 M 12 I 1 M 4 D 1 M 5 D 1 M 16 D 1 M 2 D 1 M 8 D 4 M 4 D 2 M 5 D 1 M 14 I 1 M 8 D 1 M 7 I 1 M 11 D 3 M 12 D 2 M 4 I 1 M 14 I 1 M 8 D 1 M 15 I 3 M 18 I 2 M 2 I 1 M 13 D 1 M 30 D 1 M 27 D 1 M 5 I 2 M 20 I 1 M 10 D 2 M 20 D 2 M 9 D 2 M 4 D 1 M 6 I 1 M 15 I 1 M 8 I 3 M 47 D 1 M 110 I 2 M 38 I 1 M 4 I 2 M 31 I 1 M 21 I 1 M 30 D 1 M 7 D 2 M 4 D 1 M 14 D 1 M 45 D 1 M 7 D 3 M 8 I 1 M 12 I 3 M 3 I 3 M 11 D 1 M 6 D 1 M 2 D 1 M 2 I 1 M 2 D 1 M 18 D 1 M 25 D 2 M 1 I 1 M 2 I 3 M 19 I 1 M 26 D 1 M 15 I 1 M 3 D 2 M 4 D 1 M 22 D 5 M 10 D 1 M 1 D 1 M 15 I 2 M 21 D 1 M 16 D 1 M 8 I 1 M 4 I 2 M 5 I 1 M 42 D 1 M 4 D 2 M 7 D 3 M 14 I 2 M 7 D 2 M 5 D 1 M 3 I 1 M 9 I 1 M 7 I 1 M 45 D 1 M 11 I 1 M 3 I 1 M 7 D 5 M 1 D 2 M 5 D 1 M 6 D 1 M 3 D 1 M 7 D 1 M 2 D 3 M 2 D 1 M 4 D 1 M 19 I 2 M 3 D 1 M 13 D 1 M 7 I 2 M 6 D 3 M 69 I 1 M 8 I 1 M 6 D 1 M 4 D 2 M 18 I 3 M 1 D 1 M 19 D 2 M 3 I 1 M 12 I 2 M 30 D 2 M 35 D 2 M 5 D 1 M 3 D 3 M 18 I 1 M 7 I 1 M 10 D 1 M 5 D 1 M 4 D 1 M 7 D 2 M 28 I 1 M 14 I 1 M 7 D 1 M 19 D 1 M 2 D 1 M 22 D 1 M 8 D 1 M 4 D 1 M 1 D 1 M 9 D 1 M 3 D 2 M 2 D 1 M 24 D 1 M 20 I 1 M 9 D 1 M 25 D 1 M 13 D 6 M 58 I 2 M 5 D 1 M 4 D 1 M 8 D 1 M 15 I 1 M 18 D 1 M 21 I 2 M 20 D 1 M 51 D 1 M 5 D 2 M 9 D 1 M 7 I 1 M 13 I 3 M 5 I 1 M 14 I 1 M 6 D 1 M 12 I 2 M 10 D 1 M 8 I 2 M 16 I 1 M 10 I 1 M 6 I 1 M 13 D 1 M 2 D 1 M 27 D 1 M 7 I 2 M 29 D 1 M 1 D 1 M 2 D 1 M 15 D 3 M 25 D 1 M 2 D 1 M 4 D 1 M 18 I 1 M 35 D 1 M 12 I 1 M 30 D 2 M 6 I 1 M 15 I 2 M 6 D 1 M 4 D 1 M 35 I 1 M 2 I 1 M 9 I 1 M 6 D 1 M 10 I 1 M 10 D 1 M 9 I 1 M 5 I 2 M 19 I 2 M 20 I 4 M 14 D 2 M 2 I 1 M 2 I 2 M 3 I 1 M 3 D 1 M 43 D 5 M 5 D 1 M 3 D 1 M 19 I 2 M 6 I 1 M 11 I 2 M 22 D 2 M 7 D 6 M 8 I 2 M 17 I 1 M 11 D 1 M 2 D 2 M 30 D 1 M 2 D 1 M 11 I 1 M 15 D 1 M 51 D 2 M 16 D 1 M 17 I 1 M 6 I 1 M 9 D 1 M 37 I 2 M 36 D 3 M 2 D 1 M 32 I 2 M 7 I 3 M 11 D 2 M 20 D 1 M 1 D 1 M 6 I 1 M 19 I 1 M 2 D 1 M 26 D 1 M 31 I 2 M 5 D 2 M 17 D 1 M 16 D 1 M 14 D 1 M 54 D 1 M 24 I 2 M 23 D 1 M 5 I 2 M 15 D 1 M 14 D 1 M 10 I 1 M 10 D 1 M 5 D 6 M 10 D 3 M 1 D 5 M 13 D 2 M 4 D 2 M 29 D 2 M 46 D 1 M 12 I 2 M 25 D 1 M 8 I 3 M 21 I 1 M 9 D 4 M 2 I 2 M 5 D 1 M 3 D 1 M 16 I 1 M 7 I 2 M 3 D 1 M 7 I 3 M 15 D 2 M 24 I 1 M 22 I 7 M 13 I 1 M 31 D 1 M 8 I 1 M 11 I 1 M 47 D 1 M 36 D 1 M 6 I 1 M 2 I 2 M 36 D 2 M 85 D 2 M 11 D 2 M 9 D 1 M 10 I 1 M 13 D 1 M 13 D 1 M 9 I 1 M 6 D 4 M 10 I 1 M 6 D 1 M 3 I 1 M 21 D 1 M 4 I 1 M 4 D 3 M 32 I 2 M 7 I 3 M 17 I 1 M 12 I 1 M 13 D 2 M 35 D 1 M 8 D 2 M 13 D 1 M 26 I 1 M 15 D 2 M 74 D 3 M 14 I 2 M 5 I 1 M 15 D 3 M 16 D 1 M 32 I 2 M 86 D 1 M 3 I 1 M 13 I 2 M 83 I 2 M 14 D 1 M 9 I 1 M 5 I 1 M 6 D 1 M 40 D 2 M 24 D 1 M 21 I 1 M 30 I 3 M 3 D 2 M 15 I 2 M 13 I 1 M 10 D 1 M 2 I 2 M 27 D 1 M 20 I 2 M 11 I 2 M 75 I 1 M 47 D 1 M 76 D 1 M 15 I 2 M 9 I 1 M 20 D 1 M 108 I 1 M 33 D 1 M 35 D 1 M 52 I 1 M 14 I 2 M 50 D 1 M 15 D 1 M 2 D 1 M 11 D 2 M 12 I 1 M 33 D 1 M 24 D 2 M 14 I 1 M 32 D 1 M 11 I 3 M 2 D 2 M 20 D 3 M 8 D 1 M 1 D 1 M 7 D 1 M 11 I 3 M 6 D 1 M 21 D 1 M 79 I 1 M 37 D 1 M 56 I 1 M 12 I 1 M 44 D 1 M 4 D 2 M 21 D 1 M 18 I 1 M 4 D 1 M 37 I 1 M 14 D 1 M 17 D 1 M 9 D 1 M 40 D 1 M 4 D 1 M 26 I 1 M 1 I 1 M 18 I 1 M 53 I 1 M 38 I 2 M 4 I 2 M 8 D 1 M 62 D 1 M 24 I 2 M 3 I 1 M 39 D 1 M 23 I 1 M 12 I 1 M 9 I 1 M 8 D 1 M 10 I 4 M 31 D 1 M 7 D 1 M 49 D 1 M 6 D 1 M 3 D 1 M 22 D 1 M 9 I 1 M 3 I 1 M 28 D 1 M 29 I 3 M 9 D 2 M 42 D 1 M 22 D 3 M 72 D 1 M 36 D 1 M 13 I 1 M 46 D 2 M 17 I 1 M 16 I 3 M 42 I 1 M 36 I 4 M 8 D 1 M 10 I 2 M 3 D 1 M 52 D 1 M 17 I 2 M 38 I 1 M 25 I 1 M 6 D 1 M 15 I 1 M 26 D 2 M 8 D 2 M 26 I 1 M 11 D 1 M 14 D 1 M 38 D 2 M 1 D 1 M 16 D 1 M 29 I 2 M 4 D 1 M 57 D 2 M 15 I 1 M 16 D 2 M 5 D 1 M 27 I 1 M 25 D 1 M 22 D 1 M 13 I 3 M 9 D 1 M 26 D 2 M 34 I 1 M 24 I 1 M 40 D 1 M 11 D 2 M 2 I 1 M 47 D 3 M 34 D 1 M 48 I 1 M 76 I 1 M 25 D 2 M 3 I 1 M 14 I 2 M 11 D 1 M 16 I 1 M 13 I 3 M 40 D 1 M 29 D 1 M 26 D 1 M 4 I 2 M 6 D 1 M 15 I 1 M 62 D 2 M 26 I 1 M 31 I 1 M 2 D 1 M 5 D 1 M 31 D 1 M 13 I 1 M 20 I 2 M 19 I 2 M 34 I 3 M 20 I 1 M 22 I 1 M 26 I 2 M 9 D 1 M 27 I 5 M 10 D 1 M 39 D 1 M 2 I 2 M 10 D 1 M 30 D 1 M 29 D 1 M 2 D 1 M 9 D 2 M 3 D 2 M 13 I 1 M 71 D 3 M 21 D 1 M 35 I 1 M 6 D 1 M 4 D 1 M 9 D 1 M 20 I 1 M 4 D 1 M 18 I 1 M 10 I 1 M 8 I 1 M 13 D 1 M 23 D 1 M 17 D 1 M 40 I 2 M 20 D 1 M 58 I 3 M 37 I 1 M 23 D 1 M 17 I 2 M 3 I 2 M 62 I 1 M 32 D 1 M 7 I 2 M 15 D 1 M 1 D 1 M 27 I 2 M 23 I 2 M 9 I 2 M 9 I 2 M 85 I 1 M 4 I 1 M 18 I 4 M 13 D 1 M 6 D 1 M 61 D 2 M 22 I 1 M 27 D 1 M 7 I 2 M 120 I 1 M 46 D 1 M 66 D 2 M 11 I 1 M 6 I 3 M 9 D 1 M 10 D 3 M 31 D 2 M 51 I 1 M 20 I 1 M 2 D 1 M 40 D 1 M 9 I 2 M 49 I 2 M 8 I 2 M 8 D 1 M 14 D 2 M 5 D 1 M 1 D 2 M 3 I 1 M 26 I 1 M 14 I 2 M 40 D 1 M 20 D 2 M 4 I 1 M 6 D 2 M 2 D 1 M 24 D 1 M 13 I 1 M 4 D 1 M 49 I 1 M 21 I 2 M 33 D 3 M 27 I 2 M 17 D 2 M 29 I 1 M 1 I 1 M 12 I 1 M 11 D 1 M 20 I 2 M 19 I 1 M 36 I 1 M 6 I 4 M 69 D 3 M 36 D 1 M 14 I 2 M 23 I 1 M 14 I 2 M 7 D 1 M 6 D 1 M 4 I 1 M 13 D 1 M 17 I 2 M 10 I 1 M 20 I 1 M 33 D 2 M 8 I 2 M 1 I 1 M 2 I 1 M 26 I 1 M 33 I 1 M 40 D 1 M 3 D 1 M 23 I 1 M 13 I 1 M 13 D 1 M 69 I 2 M 36 D 2 M 19"
log.txt: 56617 Segmentation fault: 11 | cPecanRealign /var/folders/pm/y6_x4m551tx4l6b0kwnbh_ch0000gp/T/tmpJMWZ6c/localTempDir/ref.fa /var/folders/pm/y6_x4m551tx4l6b0kwnbh_ch0000gp/T/tmpJMWZ6c/localTempDir/read.fa --diagonalExpansion=10 --splitMatrixBiggerThanThis=3000 --loadHmm /Users/tarekmagdyshehatamohamed/marginAlign/src/margin/mappers/last_hmm_20.txt --gapGamma=0.5 --matchGamma=0.0 >> /Users/tarekmagdyshehatamohamed/marginAlign/jobTree/jobs/gTD1/tmp_hLKwfZylUn/tempOutput_53.txt
log.txt: Traceback (most recent call last):
log.txt: File "/Users/tarekmagdyshehatamohamed/marginAlign/submodules/jobTree/src/jobTreeSlave.py", line 271, in main
log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth)
log.txt: File "/Users/tarekmagdyshehatamohamed/marginAlign/submodules/jobTree/scriptTree/stack.py", line 153, in execute
log.txt: self.target.run()
log.txt: File "/Users/tarekmagdyshehatamohamed/marginAlign/submodules/jobTree/scriptTree/target.py", line 197, in run
log.txt: func(*((self,) + tuple(self.args)), **self.kwargs)
log.txt: File "/Users/tarekmagdyshehatamohamed/marginAlign/src/margin/marginAlignLib.py", line 318, in realignCigarTargetFn
log.txt: options.gapGamma, options.matchGamma, outputCigarFile))
log.txt: File "/Users/tarekmagdyshehatamohamed/marginAlign/submodules/sonLib/bioio.py", line 184, in system
log.txt: raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts))
log.txt: RuntimeError: Command: echo "cigar: 2bb57717-77dd-4330-b20f-548cd1975eae 14 37946 + chr14 54392591 54430647 + 1 M 10 D 1 M 13 D 1 M 48 I 1 M 47 D 1 M 25 D 2 M 15 I 1 M 6 D 3 M 38 D 3 M 22 I 1 M 71 D 2 M 13 D 1 M 24 I 1 M 22 I 2 M 13 D 1 M 2 D 1 M 40 D 1 M 25 D 1 M 15 D 1 M 3 D 1 M 16 D 1 M 22 D 2 M 10 I 1 M 3 I 2 M 8 I 1 M 10 I 1 M 17 D 2 M 5 D 1 M 9 D 2 M 9 I 1 M 15 I 1 M 4 D 2 M 33 D 2 M 17 D 1 M 2 D 1 M 9 I 1 M 5 I 1 M 2 D 1 M 2 D 1 M 15 I 1 M 1 I 1 M 20 D 6 M 3 D 1 M 8 I 1 M 2 D 1 M 37 I 1 M 7 I 1 M 7 I 1 M 19 D 1 M 26 D 3 M 18 D 2 M 5 D 1 M 7 D 1 M 6 D 1 M 9 I 1 M 9 D 1 M 10 D 1 M 7 D 2 M 6 D 2 M 5 D 2 M 2 D 1 M 8 I 2 M 5 D 2 M 2 I 1 M 5 I 1 M 15 I 4 M 6 I 2 M 12 D 1 M 3 D 2 M 2 I 2 M 5 D 2 M 33 D 1 M 9 D 4 M 51 D 3 M 11 I 3 M 10 I 3 M 17 D 3 M 5 I 1 M 5 D 1 M 8 D 2 M 6 D 1 M 10 D 3 M 11 I 1 M 19 D 1 M 4 D 3 M 7 I 1 M 15 I 1 M 22 D 2 M 2 I 4 M 7 I 1 M 7 D 3 M 15 I 1 M 5 I 3 M 12 I 1 M 7 D 2 M 14 D 1 M 15 I 1 M 24 D 1 M 8 I 1 M 45 D 1 M 11 D 2 M 27 D 1 M 34 I 1 M 7 D 1 M 6 I 1 M 9 D 1 M 7 D 1 M 12 D 1 M 3 D 1 M 19 I 1 M 10 D 1 M 15 I 2 M 3 D 1 M 26 I 2 M 3 I 2 M 21 I 1 M 22 I 1 M 2 D 2 M 12 I 1 M 2 I 2 M 6 D 2 M 23 I 2 M 12 I 1 M 16 D 2 M 1 I 1 M 9 D 1 M 5 I 1 M 14 D 1 M 15 I 1 M 37 I 1 M 3 D 1 M 28 D 1 M 31 D 2 M 8 D 1 M 6 D 1 M 20 I 2 M 30 D 1 M 8 I 1 M 11 D 1 M 4 D 1 M 1 D 1 M 7 I 3 M 22 I 2 M 2 D 1 M 3 I 1 M 13 D 1 M 7 I 2 M 1 D 1 M 20 D 1 M 7 I 3 M 5 I 2 M 4 I 2 M 2 D 1 M 8 D 2 M 2 I 1 M 3 D 3 M 33 D 1 M 8 D 2 M 2 D 1 M 8 I 1 M 24 D 3 M 6 I 2 M 19 D 1 M 4 D 1 M 2 I 2 M 26 I 2 M 12 D 1 M 19 I 2 M 25 D 1 M 5 D 1 M 32 I 1 M 21 D 1 M 29 I 1 M 36 D 2 M 2 D 2 M 8 D 2 M 8 D 1 M 82 D 1 M 11 I 1 M 16 I 2 M 32 I 1 M 7 I 1 M 10 I 1 M 16 I 1 M 20 I 1 M 12 I 2 M 17 D 2 M 5 D 1 M 4 D 1 M 5 D 2 M 2 D 1 M 5 D 2 M 11 I 1 M 14 I 2 M 25 D 1 M 16 D 1 M 44 I 1 M 2 D 2 M 10 D 3 M 4 D 1 M 25 D 1 M 8 D 3 M 7 I 1 M 2 I 3 M 19 I 1 M 40 D 1 M 33 D 1 M 4 D 1 M 1 D 2 M 8 D 1 M 31 I 2 M 2 D 1 M 8 I 1 M 5 I 1 M 2 I 1 M 6 D 1 M 26 D 1 M 105 I 1 M 6 I 2 M 76 D 2 M 11 I 1 M 11 I 1 M 31 I 1 M 3 D 3 M 21 I 1 M 44 I 1 M 7 I 1 M 12 I 1 M 7 I 1 M 1 I 1 M 4 I 2 M 19 D 2 M 4 D 2 M 34 I 1 M 21 I 2 M 24 I 1 M 13 I 1 M 16 I 1 M 13 I 3 M 2 D 1 M 34 D 2 M 11 I 1 M 15 D 3 M 11 I 1 M 24 D 1 M 41 D 2 M 5 I 1 M 6 I 2 M 48 I 2 M 2 D 2 M 7 D 1 M 8 I 1 M 36 I 1 M 71 D 2 M 6 D 1 M 1 D 1 M 9 D 1 M 2 D 1 M 2 D 1 M 71 D 1 M 10 D 2 M 22 I 2 M 36 I 1 M 6 D 1 M 9 D 2 M 11 I 1 M 60 D 1 M 7 I 1 M 24 I 1 M 58 D 2 M 7 D 1 M 38 I 1 M 31 I 2 M 27 D 2 M 5 D 1 M 16 D 1 M 51 D 3 M 13 D 2 M 5 I 1 M 12 D 2 M 13 I 1 M 5 I 2 M 5 I 1 M 11 I 3 M 15 D 1 M 22 I 1 M 37 D 1 M 10 D 1 M 26 I 1 M 7 D 2 M 8 I 1 M 33 D 3 M 9 I 4 M 13 D 7 M 19 I 1 M 1 D 3 M 37 I 1 M 16 I 1 M 30 D 2 M 16 D 1 M 5 I 2 M 1 D 1 M 5 D 1 M 10 I 1 M 1 I 2 M 7 I 2 M 3 D 1 M 5 I 1 M 42 I 4 M 11 D 1 M 20 I 1 M 8 D 3 M 26 D 2 M 63 I 1 M 1 I 1 M 30 I 3 M 8 D 1 M 16 I 1 M 8 I 1 M 6 I 1 M 13 I 2 M 9 D 1 M 50 I 1 M 22 D 2 M 31 I 1 M 8 I 1 M 2 I 1 M 2 I 1 M 12 I 3 M 25 D 3 M 32 D 3 M 11 I 1 M 4 D 1 M 7 D 1 M 22 D 1 M 2 I 2 M 59 I 1 M 29 D 3 M 11 I 2 M 7 I 1 M 20 I 1 M 37 I 1 M 2 I 1 M 25 D 1 M 9 I 1 M 7 D 2 M 11 D 2 M 10 I 1 M 4 I 2 M 7 D 1 M 17 D 1 M 19 D 1 M 16 I 2 M 14 D 1 M 31 I 2 M 5 I 1 M 5 D 1 M 27 D 2 M 16 I 1 M 23 I 2 M 13 I 3 M 25 D 1 M 11 I 5 M 10 D 1 M 41 D 1 M 13 I 1 M 21 I 1 M 17 D 1 M 18 I 1 M 7 I 2 M 47 D 1 M 19 D 1 M 35 D 3 M 26 D 1 M 30 I 1 M 15 D 2 M 20 D 3 M 2 I 2 M 19 I 1 M 12 I 4 M 28 D 1 M 12 D 2 M 7 D 1 M 9 I 1 M 7 I 2 M 13 D 1 M 10 I 3 M 7 D 2 M 27 I 2 M 24 I 2 M 25 I 2 M 13 I 1 M 41 I 1 M 20 D 1 M 24 I 3 M 39 D 1 M 26 D 1 M 37 D 2 M 9 I 1 M 4 I 1 M 7 I 2 M 3 D 1 M 28 D 2 M 23 D 1 M 13 I 1 M 10 I 1 M 5 I 1 M 10 D 1 M 34 D 1 M 10 D 1 M 71 D 2 M 31 D 1 M 19 D 1 M 7 D 1 M 54 I 1 M 5 I 1 M 10 I 1 M 9 D 1 M 15 I 1 M 10 I 1 M 15 I 3 M 19 I 1 M 12 I 1 M 6 D 1 M 17 D 1 M 38 I 1 M 21 D 2 M 15 D 1 M 10 D 1 M 10 I 1 M 55 I 1 M 8 I 2 M 10 I 2 M 26 D 1 M 65 I 1 M 18 I 1 M 75 I 2 M 44 D 2 M 7 D 2 M 15 I 1 M 21 I 1 M 13 D 1 M 88 I 10 M 37 I 1 M 32 D 1 M 28 D 1 M 23 D 1 M 21 D 2 M 35 D 1 M 84 D 1 M 24 I 3 M 6 I 1 M 4 D 2 M 51 D 4 M 21 D 2 M 12 D 2 M 52 D 1 M 17 D 1 M 15 D 1 M 18 D 1 M 12 I 1 M 31 D 3 M 9 I 2 M 44 I 1 M 43 D 1 M 102 D 1 M 17 D 2 M 10 D 1 M 17 I 3 M 32 I 2 M 7 I 2 M 2 D 1 M 13 D 1 M 38 I 3 M 12 D 2 M 13 D 1 M 10 I 2 M 1 D 3 M 10 D 1 M 36 D 1 M 14 D 1 M 41 I 1 M 38 D 2 M 3 D 1 M 35 D 1 M 10 D 1 M 2 I 1 M 1 I 1 M 12 I 6 M 15 D 3 M 8 D 1 M 1 D 1 M 3 D 2 M 10 I 1 M 5 D 1 M 17 D 1 M 16 D 1 M 15 D 1 M 29 I 2 M 31 I 2 M 8 I 1 M 20 D 2 M 57 D 2 M 2 I 1 M 22 D 3 M 7 I 1 M 10 D 1 M 34 D 1 M 21 I 2 M 23 D 2 M 7 I 2 M 8 I 1 M 5 D 2 M 10 I 1 M 18 D 1 M 31 I 1 M 29 I 2 M 5 D 1 M 50 D 1 M 10 D 3 M 10 I 1 M 2 D 1 M 16 I 3 M 28 D 2 M 23 D 1 M 15 I 2 M 13 D 1 M 7 D 1 M 36 I 4 M 8 D 1 M 50 I 1 M 15 I 1 M 19 D 1 M 7 I 3 M 13 I 3 M 36 I 1 M 6 I 2 M 63 I 1 M 28 I 1 M 3 I 1 M 14 D 1 M 11 I 1 M 34 D 2 M 10 I 1 M 17 I 1 M 23 D 1 M 5 D 1 M 6 I 1 M 4 I 1 M 40 D 1 M 2 I 1 M 46 I 1 M 29 I 5 M 4 I 1 M 3 D 1 M 35 D 1 M 36 I 1 M 6 I 1 M 47 D 2 M 39 I 3 M 5 I 1 M 3 D 3 M 67 D 1 M 41 I 2 M 31 D 1 M 16 D 1 M 7 D 1 M 27 I 1 M 28 D 2 M 4 D 1 M 2 D 1 M 6 D 1 M 26 D 2 M 57 D 1 M 19 D 2 M 4 D 1 M 90 D 1 M 11 I 1 M 46 I 1 M 12 D 1 M 27 D 1 M 9 D 1 M 22 D 3 M 34 I 2 M 2 D 1 M 5 D 2 M 32 D 2 M 1 D 1 M 18 I 1 M 38 I 2 M 21 D 4 M 18 I 3 M 15 I 1 M 2 D 3 M 4 D 1 M 21 I 1 M 4 I 1 M 22 D 1 M 29 D 1 M 14 D 1 M 30 I 1 M 2 I 1 M 3 D 1 M 1 D 2 M 10 I 3 M 33 I 1 M 11 D 1 M 12 D 2 M 44 I 3 M 6 D 1 M 46 I 2 M 1 D 1 M 42 D 1 M 5 I 1 M 27 D 1 M 21 D 2 M 16 D 1 M 33 D 1 M 20 D 2 M 3 D 1 M 24 D 1 M 10 D 1 M 9 D 5 M 25 I 1 M 4 I 2 M 1 I 1 M 28 D 1 M 9 I 4 M 3 D 2 M 4 D 1 M 5 I 1 M 11 I 1 M 15 D 1 M 48 D 1 M 5 I 1 M 2 I 1 M 15 D 3 M 21 D 1 M 6 D 2 M 6 D 1 M 15 I 1 M 11 D 1 M 63 D 2 M 3 D 1 M 15 I 1 M 24 I 2 M 12 I 1 M 21 D 1 M 7 I 1 M 18 I 3 M 12 D 1 M 3 I 1 M 11 I 1 M 13 I 1 M 27 I 1 M 11 I 2 M 10 D 1 M 17 D 2 M 8 I 1 M 6 I 1 M 9 I 1 M 20 D 1 M 18 D 1 M 5 D 1 M 17 I 2 M 2 D 1 M 5 D 1 M 2 D 1 M 16 D 1 M 41 D 2 M 8 D 1 M 13 I 1 M 18 D 1 M 13 I 1 M 14 I 1 M 6 I 1 M 57 D 1 M 21 D 1 M 49 D 1 M 23 D 3 M 2 D 1 M 27 D 4 M 19 D 1 M 71 D 1 M 34 I 2 M 79 I 1 M 44 D 2 M 12 D 2 M 10 D 2 M 30 D 1 M 17 I 1 M 47 I 1 M 7 I 1 M 35 D 1 M 14 D 1 M 106 I 1 M 18 I 1 M 16 D 1 M 6 D 1 M 8 D 1 M 17 I 1 M 38 I 1 M 40 I 1 M 36 I 1 M 1 D 2 M 11 D 2 M 18 D 1 M 22 D 1 M 15 I 2 M 19 I 1 M 10 I 1 M 1 D 3 M 2 I 1 M 3 D 4 M 4 D 1 M 13 D 3 M 55 D 2 M 14 I 1 M 12 I 1 M 13 D 1 M 1 I 3 M 3 I 2 M 5 D 1 M 15 I 2 M 5 D 2 M 19 I 1 M 8 D 1 M 16 D 1 M 38 I 1 M 65 I 1 M 11 I 1 M 14 I 1 M 9 I 1 M 7 I 1 M 14 I 1 M 1 I 1 M 69 D 2 M 75 D 1 M 11 I 1 M 22 D 1 M 5 I 1 M 18 D 1 M 3 I 2 M 38 D 1 M 64 D 1 M 6 I 1 M 6 I 1 M 13 I 3 M 38 D 2 M 13 D 1 M 59 D 2 M 7 I 2 M 7 D 1 M 30 D 2 M 44 I 1 M 7 I 1 M 3 I 1 M 6 D 1 M 15 D 1 M 15 D 1 M 7 D 3 M 3 I 1 M 75 I 1 M 1 I 1 M 15 D 2 M 20 I 1 M 2 I 1 M 20 I 1 M 4 D 1 M 10 I 2 M 7 D 2 M 13 D 2 M 21 I 2 M 13 I 1 M 4 I 1 M 5 D 2 M 2 D 2 M 10 I 1 M 51 D 1 M 54 D 2 M 51 I 1 M 24 D 2 M 10 D 1 M 18 D 1 M 8 D 2 M 6 I 1 M 2 D 1 M 20 D 1 M 7 D 1 M 15 D 1 M 37 I 1 M 36 D 1 M 19 I 1 M 15 I 1 M 8 I 1 M 1 I 1 M 15 I 2 M 8 I 4 M 10 D 2 M 71 I 1 M 62 I 1 M 42 I 1 M 35 D 1 M 63 D 1 M 3 D 1 M 7 I 1 M 20 D 1 M 50 D 1 M 10 D 1 M 5 D 1 M 20 I 1 M 4 I 1 M 29 D 2 M 65 I 2 M 7 I 1 M 1 D 2 M 24 D 1 M 24 D 1 M 28 I 2 M 22 D 4 M 3 D 1 M 27 D 2 M 27 I 1 M 65 I 1 M 3 D 1 M 5 D 3 M 1 I 2 M 38 D 1 M 8 I 2 M 27 I 1 M 6 I 3 M 34 I 1 M 10 I 4 M 6 D 1 M 29 I 1 M 7 I 1 M 23 D 1 M 44 I 1 M 11 I 1 M 7 I 1 M 9 I 1 M 7 I 1 M 19 I 1 M 5 D 1 M 18 I 2 M 25 D 1 M 11 I 2 M 1 D 1 M 13 I 1 M 28 I 1 M 7 I 1 M 9 I 2 M 15 I 1 M 14 I 1 M 18 I 2 M 25 I 3 M 11 D 1 M 39 D 1 M 38 D 1 M 8 I 1 M 4 I 2 M 2 I 1 M 13 D 1 M 25 I 2 M 9 I 1 M 30 D 1 M 30 I 3 M 32 I 1 M 39 D 3 M 2 D 1 M 47 D 1 M 18 I 6 M 36 D 2 M 11 I 2 M 1 I 1 M 2 D 1 M 3 D 2 M 45 I 1 M 7 D 1 M 83 I 1 M 49 D 2 M 10 I 1 M 46 I 1 M 21 I 1 M 13 D 1 M 41 D 1 M 20 I 2 M 28 D 1 M 19 I 4 M 20 D 2 M 62 I 2 M 3 D 2 M 7 D 1 M 10 D 1 M 22 D 1 M 2 D 2 M 3 I 1 M 8 D 1 M 15 D 1 M 8 I 1 M 11 I 1 M 14 I 2 M 1 D 1 M 33 D 1 M 19 D 1 M 33 I 3 M 2 I 1 M 11 D 5 M 19 I 1 M 1 D 2 M 33 D 2 M 23 I 3 M 58 I 1 M 5 I 2 M 2 D 1 M 26 D 1 M 3 D 2 M 50 I 1 M 4 I 1 M 8 I 3 M 34 I 4 M 30 D 1 M 7 D 1 M 14 D 1 M 14 D 1 M 11 I 1 M 29 D 1 M 20 D 1 M 40 D 3 M 14 I 1 M 14 D 1 M 10 I 5 M 27 D 1 M 27 D 1 M 37 I 1 M 26 D 1 M 10 D 1 M 37 I 1 M 41 D 3 M 13 D 1 M 9 I 2 M 24 I 1 M 72 D 2 M 5 D 1 M 38 I 2 M 6 I 2 M 57 D 1 M 2 D 1 M 5 I 2 M 7 I 1 M 15 D 1 M 15 I 1 M 29 I 2 M 22 D 1 M 34 D 1 M 69 D 1 M 8 D 1 M 18 D 1 M 47 I 2 M 15 D 1 M 1 D 2 M 7 D 1 M 45 I 1 M 2 I 1 M 5 I 1 M 5 D 2 M 31 I 2 M 2 D 1 M 9 D 2 M 16 I 1 M 13 I 3 M 23 I 3 M 13 I 1 M 1 D 4 M 22 D 1 M 16 D 1 M 23 D 1 M 7 D 1 M 17 I 3 M 18 D 1 M 38 I 1 M 19 I 1 M 16 I 1 M 14 D 1 M 13 D 1 M 31 I 1 M 4 D 1 M 26 I 1 M 50 I 1 M 77 I 1 M 38 I 1 M 1 I 1 M 21 I 2 M 4 I 2 M 7 I 3 M 4 I 1 M 58 I 2 M 12 D 2 M 6 D 1 M 6 I 1 M 41 D 1 M 17 I 1 M 3 I 2 M 6 D 4 M 33 D 5 M 8 D 1 M 15 D 2 M 4 I 2 M 10 I 1 M 21 I 1 M 1 I 1 M 8 D 1 M 4 D 1 M 7 D 3 M 32 D 3 M 15 D 2 M 7 I 3 M 1 I 1 M 2 I 1 M 25 I 2 M 14 I 1 M 2 D 2 M 7 I 1 M 8 D 2 M 22 D 3 M 3 D 1 M 11 I 1 M 17 D 1 M 49 D 1 M 11 D 1 M 42 D 1 M 1 D 1 M 2 D 1 M 28 D 1 M 11 I 2 M 6 I 1 M 8 D 1 M 10 D 1 M 20 D 1 M 43 I 1 M 11 I 1 M 34 I 2 M 6 D 2 M 7 D 1 M 61 D 1 M 5 I 1 M 12 D 1 M 9 D 1 M 17 I 2 M 11 I 1 M 27 D 1 M 50 D 2 M 2 D 1 M 37 D 4 M 28 I 2 M 3 D 1 M 8 D 2 M 48 D 2 M 6 D 2 M 37 D 2 M 26 I 2 M 20 D 2 M 13 D 1 M 15 I 5 M 23 D 1 M 65 D 1 M 17 D 1 M 26 I 1 M 59 I 1 M 36 D 2 M 38 I 1 M 34 I 3 M 13 I 1 M 37 D 1 M 3 I 5 M 14 D 1 M 45 I 1 M 27 D 1 M 14 D 1 M 67 D 1 M 39 D 2 M 32 I 1 M 14 D 1 M 27 I 2 M 1 I 2 M 9 I 2 M 9 I 1 M 13 I 2 M 4 I 2 M 18 D 1 M 3 D 1 M 70 D 1 M 39 I 1 M 9 I 1 M 11 I 1 M 51 I 3 M 41 D 4 M 7 I 2 M 52 D 2 M 52 I 1 M 9 I 1 M 49 D 1 M 7 I 2 M 38 I 3 M 18 D 1 M 8 I 3 M 34 I 3 M 18 D 1 M 14 D 1 M 29 D 1 M 22 I 1 M 4 I 1 M 10 D 1 M 16 D 1 M 35 D 2 M 43 I 1 M 36 D 1 M 26 I 2 M 13 D 1 M 56 D 1 M 18 I 1 M 18 D 1 M 57 D 2 M 46 D 1 M 5 D 1 M 2 I 2 M 2 D 1 M 41 D 2 M 1 I 1 M 3 D 1 M 11 I 1 M 5 I 1 M 4 I 2 M 28 D 2 M 6 D 2 M 2 I 1 M 1 I 3 M 37 I 1 M 14 I 1 M 18 I 1 M 4 I 1 M 7 D 1 M 5 I 1 M 81 D 1 M 15 D 1 M 26 I 1 M 28 I 1 M 11 I 1 M 9 D 2 M 6 D 2 M 17 I 1 M 20 D 1 M 46 I 1 M 19 D 2 M 15 D 3 M 4 D 2 M 14 I 1 M 58 D 1 M 3 D 1 M 6 I 1 M 14 I 1 M 6 I 2 M 36 D 1 M 31 D 1 M 12 I 1 M 29 D 1 M 45 I 1 M 32 I 1 M 47 D 1 M 3 D 1 M 30 I 1 M 2 I 1 M 16 D 1 M 19 D 1 M 3 D 1 M 1 D 1 M 19 I 2 M 9 D 1 M 63 D 1 M 27 D 1 M 31 I 1 M 5 I 2 M 4 I 1 M 70 D 1 M 17 I 1 M 8 D 2 M 79 I 3 M 27 I 1 M 46 I 3 M 13 I 2 M 11 I 1 M 48 D 1 M 116 D 1 M 25 I 2 M 24 D 1 M 9 D 1 M 58 D 1 M 45 D 1 M 22 D 1 M 5 D 2 M 38 D 3 M 35 D 2 M 19 D 1 M 27 D 2 M 30 I 1 M 19 D 2 M 34 I 2 M 5 D 2 M 27 D 1 M 13 I 1 M 3 D 1 M 44 D 2 M 33 D 2 M 39 D 3 M 9 I 1 M 45 I 1 M 5 D 1 M 44 D 1 M 35 I 1 M 5 D 1 M 45 I 1 M 26 I 1 M 5 D 1 M 51 I 3 M 13 I 1 M 13 D 1 M 17 D 1 M 6 I 1 M 6 I 1 M 5 D 1 M 8 I 2 M 4 I 1 M 23 I 2 M 11 D 2 M 6 D 2 M 3 D 1 M 108 D 1 M 14 I 1 M 16 I 2 M 11 I 1 M 2 D 1 M 5 I 2 M 11 I 3 M 4 I 1 M 55 I 1 M 7 I 3 M 57 I 1 M 38 I 1 M 14 I 8 M 44 D 1 M 13 D 3 M 22 I 1 M 4 I 2 M 12 I 1 M 22 I 2 M 3 D 1 M 73 D 1 M 19 D 1 M 27 D 1 M 19 D 1 M 5 D 2 M 13 D 1 M 2 D 3 M 17 I 1 M 7 D 2 M 24 D 2 M 29 I 3 M 20 I 1 M 15 I 1 M 12 I 3 M 19 I 1 M 19 D 2 M 3 I 1 M 21 I 1 M 8 I 2 M 17 D 3 M 10 I 1 M 8 I 2 M 10 I 2 M 1 I 5 M 4 D 3 M 4 D 2 M 9 D 1 M 11 I 2 M 10 D 1 M 39 I 1 M 27 D 1 M 26 I 1 M 13 I 2 M 4 D 1 M 9 D 3 M 2 I 1 M 14 I 1 M 13 I 1 M 5 D 1 M 8 D 1 M 15 I 1 M 1 I 1 M 3 D 1 M 56 I 1 M 22 D 1 M 4 I 1 M 18 D 1 M 5 D 2 M 32 I 1 M 23 D 1 M 6 D 3 M 70 I 1 M 2 D 2 M 19 I 4 M 21 D 1 M 3 I 1 M 5 D 1 M 1 D 1 M 8 D 1 M 20 D 2 M 13 I 3 M 6 D 2 M 12 I 1 M 6 I 1 M 6 D 1 M 5 D 1 M 17 D 1 M 7 I 1 M 9 I 1 M 4 I 1 M 6 D 1 M 12 D 1 M 2 D 2 M 4 I 2 M 8 I 1 M 20 D 1 M 9 D 1 M 6 I 2 M 5 D 1 M 22 I 1 M 2 I 1 M 23 D 1 M 24 D 1 M 10 D 2 M 10 D 1 M 9 I 2 M 8 I 1 M 7 D 1 M 4 D 3 M 8 D 1 M 9 I 2 M 6 D 1 M 6 D 1 M 36 D 2 M 2 D 1 M 13 D 6 M 15 I 1 M 10 I 2 M 8 I 1 M 11 D 1 M 6 I 1 M 8 I 1 M 41 I 1 M 3 D 1 M 9 I 1 M 7 I 2 M 6 I 2 M 3 D 1 M 6 I 1 M 20 I 1 M 3 I 2 M 20 D 1 M 7 D 1 M 24 I 2 M 17 I 1 M 26 I 2 M 4 D 1 M 16 I 1 M 4 D 2 M 25 I 1 M 8 D 2 M 3 D 1 M 11 D 1 M 3 I 1 M 33 D 1 M 1 D 1 M 11 I 1 M 4 I 2 M 22 D 1 M 105 D 1 M 15 I 2 M 25 I 1 M 39 D 1 M 1 D 2 M 43 I 1 M 7 D 2 M 7 I 2 M 1 D 1 M 12 I 1 M 4 D 1 M 5 D 1 M 16 D 1 M 2 D 1 M 8 D 4 M 4 D 2 M 5 D 1 M 14 I 1 M 8 D 1 M 7 I 1 M 11 D 3 M 12 D 2 M 4 I 1 M 14 I 1 M 8 D 1 M 15 I 3 M 18 I 2 M 2 I 1 M 13 D 1 M 30 D 1 M 27 D 1 M 5 I 2 M 20 I 1 M 10 D 2 M 20 D 2 M 9 D 2 M 4 D 1 M 6 I 1 M 15 I 1 M 8 I 3 M 47 D 1 M 110 I 2 M 38 I 1 M 4 I 2 M 31 I 1 M 21 I 1 M 30 D 1 M 7 D 2 M 4 D 1 M 14 D 1 M 45 D 1 M 7 D 3 M 8 I 1 M 12 I 3 M 3 I 3 M 11 D 1 M 6 D 1 M 2 D 1 M 2 I 1 M 2 D 1 M 18 D 1 M 25 D 2 M 1 I 1 M 2 I 3 M 19 I 1 M 26 D 1 M 15 I 1 M 3 D 2 M 4 D 1 M 22 D 5 M 10 D 1 M 1 D 1 M 15 I 2 M 21 D 1 M 16 D 1 M 8 I 1 M 4 I 2 M 5 I 1 M 42 D 1 M 4 D 2 M 7 D 3 M 14 I 2 M 7 D 2 M 5 D 1 M 3 I 1 M 9 I 1 M 7 I 1 M 45 D 1 M 11 I 1 M 3 I 1 M 7 D 5 M 1 D 2 M 5 D 1 M 6 D 1 M 3 D 1 M 7 D 1 M 2 D 3 M 2 D 1 M 4 D 1 M 19 I 2 M 3 D 1 M 13 D 1 M 7 I 2 M 6 D 3 M 69 I 1 M 8 I 1 M 6 D 1 M 4 D 2 M 18 I 3 M 1 D 1 M 19 D 2 M 3 I 1 M 12 I 2 M 30 D 2 M 35 D 2 M 5 D 1 M 3 D 3 M 18 I 1 M 7 I 1 M 10 D 1 M 5 D 1 M 4 D 1 M 7 D 2 M 28 I 1 M 14 I 1 M 7 D 1 M 19 D 1 M 2 D 1 M 22 D 1 M 8 D 1 M 4 D 1 M 1 D 1 M 9 D 1 M 3 D 2 M 2 D 1 M 24 D 1 M 20 I 1 M 9 D 1 M 25 D 1 M 13 D 6 M 58 I 2 M 5 D 1 M 4 D 1 M 8 D 1 M 15 I 1 M 18 D 1 M 21 I 2 M 20 D 1 M 51 D 1 M 5 D 2 M 9 D 1 M 7 I 1 M 13 I 3 M 5 I 1 M 14 I 1 M 6 D 1 M 12 I 2 M 10 D 1 M 8 I 2 M 16 I 1 M 10 I 1 M 6 I 1 M 13 D 1 M 2 D 1 M 27 D 1 M 7 I 2 M 29 D 1 M 1 D 1 M 2 D 1 M 15 D 3 M 25 D 1 M 2 D 1 M 4 D 1 M 18 I 1 M 35 D 1 M 12 I 1 M 30 D 2 M 6 I 1 M 15 I 2 M 6 D 1 M 4 D 1 M 35 I 1 M 2 I 1 M 9 I 1 M 6 D 1 M 10 I 1 M 10 D 1 M 9 I 1 M 5 I 2 M 19 I 2 M 20 I 4 M 14 D 2 M 2 I 1 M 2 I 2 M 3 I 1 M 3 D 1 M 43 D 5 M 5 D 1 M 3 D 1 M 19 I 2 M 6 I 1 M 11 I 2 M 22 D 2 M 7 D 6 M 8 I 2 M 17 I 1 M 11 D 1 M 2 D 2 M 30 D 1 M 2 D 1 M 11 I 1 M 15 D 1 M 51 D 2 M 16 D 1 M 17 I 1 M 6 I 1 M 9 D 1 M 37 I 2 M 36 D 3 M 2 D 1 M 32 I 2 M 7 I 3 M 11 D 2 M 20 D 1 M 1 D 1 M 6 I 1 M 19 I 1 M 2 D 1 M 26 D 1 M 31 I 2 M 5 D 2 M 17 D 1 M 16 D 1 M 14 D 1 M 54 D 1 M 24 I 2 M 23 D 1 M 5 I 2 M 15 D 1 M 14 D 1 M 10 I 1 M 10 D 1 M 5 D 6 M 10 D 3 M 1 D 5 M 13 D 2 M 4 D 2 M 29 D 2 M 46 D 1 M 12 I 2 M 25 D 1 M 8 I 3 M 21 I 1 M 9 D 4 M 2 I 2 M 5 D 1 M 3 D 1 M 16 I 1 M 7 I 2 M 3 D 1 M 7 I 3 M 15 D 2 M 24 I 1 M 22 I 7 M 13 I 1 M 31 D 1 M 8 I 1 M 11 I 1 M 47 D 1 M 36 D 1 M 6 I 1 M 2 I 2 M 36 D 2 M 85 D 2 M 11 D 2 M 9 D 1 M 10 I 1 M 13 D 1 M 13 D 1 M 9 I 1 M 6 D 4 M 10 I 1 M 6 D 1 M 3 I 1 M 21 D 1 M 4 I 1 M 4 D 3 M 32 I 2 M 7 I 3 M 17 I 1 M 12 I 1 M 13 D 2 M 35 D 1 M 8 D 2 M 13 D 1 M 26 I 1 M 15 D 2 M 74 D 3 M 14 I 2 M 5 I 1 M 15 D 3 M 16 D 1 M 32 I 2 M 86 D 1 M 3 I 1 M 13 I 2 M 83 I 2 M 14 D 1 M 9 I 1 M 5 I 1 M 6 D 1 M 40 D 2 M 24 D 1 M 21 I 1 M 30 I 3 M 3 D 2 M 15 I 2 M 13 I 1 M 10 D 1 M 2 I 2 M 27 D 1 M 20 I 2 M 11 I 2 M 75 I 1 M 47 D 1 M 76 D 1 M 15 I 2 M 9 I 1 M 20 D 1 M 108 I 1 M 33 D 1 M 35 D 1 M 52 I 1 M 14 I 2 M 50 D 1 M 15 D 1 M 2 D 1 M 11 D 2 M 12 I 1 M 33 D 1 M 24 D 2 M 14 I 1 M 32 D 1 M 11 I 3 M 2 D 2 M 20 D 3 M 8 D 1 M 1 D 1 M 7 D 1 M 11 I 3 M 6 D 1 M 21 D 1 M 79 I 1 M 37 D 1 M 56 I 1 M 12 I 1 M 44 D 1 M 4 D 2 M 21 D 1 M 18 I 1 M 4 D 1 M 37 I 1 M 14 D 1 M 17 D 1 M 9 D 1 M 40 D 1 M 4 D 1 M 26 I 1 M 1 I 1 M 18 I 1 M 53 I 1 M 38 I 2 M 4 I 2 M 8 D 1 M 62 D 1 M 24 I 2 M 3 I 1 M 39 D 1 M 23 I 1 M 12 I 1 M 9 I 1 M 8 D 1 M 10 I 4 M 31 D 1 M 7 D 1 M 49 D 1 M 6 D 1 M 3 D 1 M 22 D 1 M 9 I 1 M 3 I 1 M 28 D 1 M 29 I 3 M 9 D 2 M 42 D 1 M 22 D 3 M 72 D 1 M 36 D 1 M 13 I 1 M 46 D 2 M 17 I 1 M 16 I 3 M 42 I 1 M 36 I 4 M 8 D 1 M 10 I 2 M 3 D 1 M 52 D 1 M 17 I 2 M 38 I 1 M 25 I 1 M 6 D 1 M 15 I 1 M 26 D 2 M 8 D 2 M 26 I 1 M 11 D 1 M 14 D 1 M 38 D 2 M 1 D 1 M 16 D 1 M 29 I 2 M 4 D 1 M 57 D 2 M 15 I 1 M 16 D 2 M 5 D 1 M 27 I 1 M 25 D 1 M 22 D 1 M 13 I 3 M 9 D 1 M 26 D 2 M 34 I 1 M 24 I 1 M 40 D 1 M 11 D 2 M 2 I 1 M 47 D 3 M 34 D 1 M 48 I 1 M 76 I 1 M 25 D 2 M 3 I 1 M 14 I 2 M 11 D 1 M 16 I 1 M 13 I 3 M 40 D 1 M 29 D 1 M 26 D 1 M 4 I 2 M 6 D 1 M 15 I 1 M 62 D 2 M 26 I 1 M 31 I 1 M 2 D 1 M 5 D 1 M 31 D 1 M 13 I 1 M 20 I 2 M 19 I 2 M 34 I 3 M 20 I 1 M 22 I 1 M 26 I 2 M 9 D 1 M 27 I 5 M 10 D 1 M 39 D 1 M 2 I 2 M 10 D 1 M 30 D 1 M 29 D 1 M 2 D 1 M 9 D 2 M 3 D 2 M 13 I 1 M 71 D 3 M 21 D 1 M 35 I 1 M 6 D 1 M 4 D 1 M 9 D 1 M 20 I 1 M 4 D 1 M 18 I 1 M 10 I 1 M 8 I 1 M 13 D 1 M 23 D 1 M 17 D 1 M 40 I 2 M 20 D 1 M 58 I 3 M 37 I 1 M 23 D 1 M 17 I 2 M 3 I 2 M 62 I 1 M 32 D 1 M 7 I 2 M 15 D 1 M 1 D 1 M 27 I 2 M 23 I 2 M 9 I 2 M 9 I 2 M 85 I 1 M 4 I 1 M 18 I 4 M 13 D 1 M 6 D 1 M 61 D 2 M 22 I 1 M 27 D 1 M 7 I 2 M 120 I 1 M 46 D 1 M 66 D 2 M 11 I 1 M 6 I 3 M 9 D 1 M 10 D 3 M 31 D 2 M 51 I 1 M 20 I 1 M 2 D 1 M 40 D 1 M 9 I 2 M 49 I 2 M 8 I 2 M 8 D 1 M 14 D 2 M 5 D 1 M 1 D 2 M 3 I 1 M 26 I 1 M 14 I 2 M 40 D 1 M 20 D 2 M 4 I 1 M 6 D 2 M 2 D 1 M 24 D 1 M 13 I 1 M 4 D 1 M 49 I 1 M 21 I 2 M 33 D 3 M 27 I 2 M 17 D 2 M 29 I 1 M 1 I 1 M 12 I 1 M 11 D 1 M 20 I 2 M 19 I 1 M 36 I 1 M 6 I 4 M 69 D 3 M 36 D 1 M 14 I 2 M 23 I 1 M 14 I 2 M 7 D 1 M 6 D 1 M 4 I 1 M 13 D 1 M 17 I 2 M 10 I 1 M 20 I 1 M 33 D 2 M 8 I 2 M 1 I 1 M 2 I 1 M 26 I 1 M 33 I 1 M 40 D 1 M 3 D 1 M 23 I 1 M 13 I 1 M 13 D 1 M 69 I 2 M 36 D 2 M 19" | cPecanRealign /var/folders/pm/y6_x4m551tx4l6b0kwnbh_ch0000gp/T/tmpJMWZ6c/localTempDir/ref.fa /var/folders/pm/y6_x4m551tx4l6b0kwnbh_ch0000gp/T/tmpJMWZ6c/localTempDir/read.fa --diagonalExpansion=10 --splitMatrixBiggerThanThis=3000 --loadHmm /Users/tarekmagdyshehatamohamed/marginAlign/src/margin/mappers/last_hmm_20.txt --gapGamma=0.5 --matchGamma=0.0 >> /Users/tarekmagdyshehatamohamed/marginAlign/jobTree/jobs/gTD1/tmp_hLKwfZylUn/tempOutput_53.txt exited with non-zero status 139
log.txt: Exiting the slave because of a failed job on host FSMD25VN00GJ1GN
log.txt: Due to failure we are reducing the remaining retry count of job /Users/tarekmagdyshehatamohamed/marginAlign/jobTree/jobs/t0/t1/t3/t3/t2/job to 0
log.txt: We have set the default memory of the failed job to 2147483648 bytes
Job: /Users/tarekmagdyshehatamohamed/marginAlign/jobTree/jobs/t0/t1/t3/t3/t2/job is completely failed
^Z
[1]+ Stopped ./marginAlign BC01.fastq NCBI.GRCh38.fa BC01_margin.sam --minimap2 --jobTree ./jobTree

`

Currently the code depends on pysam and numpy. These dependencies should be managed by virtual env.

Hi,
I was wondering if you might be able to help me decrypt this error message?
I am have the most recent release version 0.1. This job was run with the command

marginAlign input.fastq ref.fa marginAlign.sam --em --outputModel output.hmm \
    --jobTree ./jobTree --maxThreads=16

It was run on a cluster node with 50GB memory allocated and 16 CPUs. The job failed with message:

---JOBTREE SLAVE OUTPUT LOG---
Traceback (most recent call last):
  File "/nfs/research1/zi/mbhall/Software/marginAlign/submodules/jobTree/src/jobTreeSlave.py", line 271, in main
    defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth)
  File "/nfs/research1/zi/mbhall/Software/marginAlign/submodules/jobTree/scriptTree/stack.py", line 153, in execute
    self.target.run()
  File "/nfs/research1/zi/mbhall/Software/marginAlign/src/margin/mappers/last.py", line 35, in run
    Last.run(self)
  File "/nfs/research1/zi/mbhall/Software/marginAlign/src/margin/mappers/last.py", line 20, in run
    fastaWrite(fH, name, seq)
  File "/nfs/research1/zi/mbhall/Software/marginAlign/submodules/sonLib/bioio.py", line 746, in fastaWrite
    fileHandle.write("%s\n" % seq[i:i+chunkSize])
IOError: [Errno 28] No space left on device
Exiting the slave because of a failed job on host hx-noah-02-04.ebi.ac.uk
Due to failure we are reducing the remaining retry count of job /hps/nobackup/research/zi/mbhall/Aligner_test/jobTree/jobs/job to 0
We have set the default memory of the failed job to 2147483648.0 bytes

I am assuming IOError: [Errno 28] No space left on device is the clue. Just not sure if it is alluding to memory or disk space? I could throw more memory at it if need be but 50GB seems like a fair bit already. There's also more than enough disk space on the cluster for the job so I am assuming this is not the case.
Cheers.

Hi there,

Attempting to run marginCall on a .sam produced by minimap2. Built according to readme (using a venv) and all tests passed.

Getting the below error, any ideas?

The job seems to have left a log file, indicating failure: /rds/project/who1000/rds-who1000-wgs10k/WGS10K/data/projects/nanopore/us/analysis/PromethION_temp/NND/G008984/variant_calling/marginCaller/jobTree/jobs/job
Reporting file: /rds/project/who1000/rds-who1000-wgs10k/WGS10K/data/projects/nanopore/us/analysis/PromethION_temp/NND/G008984/variant_calling/marginCaller/jobTree/jobs/log.txt
log.txt: ---JOBTREE SLAVE OUTPUT LOG---
log.txt: Traceback (most recent call last):
log.txt: File "/home/ng384/software/builds/marginAlign/submodules/jobTree/src/jobTreeSlave.py", line 271, in main
log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth)
log.txt: File "/home/ng384/software/builds/marginAlign/submodules/jobTree/scriptTree/stack.py", line 153, in execute
log.txt: self.target.run()
log.txt: File "/home/ng384/software/builds/marginAlign/submodules/jobTree/scriptTree/target.py", line 197, in run
log.txt: func(*((self,) + tuple(self.args)), **self.kwargs)
log.txt: File "/home/ng384/software/builds/marginAlign/src/margin/utils.py", line 171, in paralleliseSamProcessingTargetFn
log.txt: tempExonerateFileHandle.write(getExonerateCigarFormatString(aR, sam) + "\n")
log.txt: File "/home/ng384/software/builds/marginAlign/src/margin/utils.py", line 50, in getExonerateCigarFormatString
log.txt: assert sum([ op.length for op in pA.operationList if op.type ==
log.txt: AttributeError: 'NoneType' object has no attribute 'operationList'
log.txt: Exiting the slave because of a failed job on host login-l-1
log.txt: Due to failure we are reducing the remaining retry count of job /rds/project/who1000/rds-who1000-wgs10k/WGS10K/data/projects/nanopore/us/analysis/PromethION_temp/NND/G008984/variant_calling/marginCaller/jobTree/jobs/job to 0
log.txt: We have set the default memory of the failed job to 2147483648 bytes
Job: /rds/project/who1000/rds-who1000-wgs10k/WGS10K/data/projects/nanopore/us/analysis/PromethION_temp/NND/G008984/variant_calling/marginCaller/jobTree/jobs/job is completely failed
Traceback (most recent call last):
File "/home/ng384/software/builds/marginAlign/src/margin/marginCaller.py", line 63, in
main()
File "/home/ng384/software/builds/marginAlign/src/margin/marginCaller.py", line 59, in main
raise RuntimeError("Got failed jobs")
RuntimeError: Got failed jobs

To test if margin call is working as expected, it would be good if the test data included some known snps, and the test checked to see if they are recovered. Ideally the tests should report a precision/recall value, similar to that given in the original paper.

After I run make test, it is reported that there is no vcf module

File "./tests/tests.py", line 4, in
from margin.marginCallerLib import vcfRead
File "/data/ltwang/software/marginAlign/src/margin/marginCallerLib.py", line 1, in
import pysam, sys, os, collections, vcf, datetime
ImportError: No module named vcf
Makefile:5: recipe for target 'test' failed
make: *** [test] Error 1

how can I solve this problem?

---JOBTREE SLAVE OUTPUT LOG---
/bin/sh: line 1: 24546 Done echo cigar: channel_439_read_57 0 1122 + DNA_CS 0 3
559 + 1 D 1838 I 1 M 7 D 1 M 3 I 2 M 6 D 1 M 13 I 1 M 2 I 1 M 7 I 1 M 16 D 1 M 35 D 1 M 47 I 1 M 1
I 2 M 11 D 3 M 45 I 2 M 26 I 1 M 2 I 1 M 18 D 2 M 17 I 1 M 36 D 2 M 4 D 1 M 8 I 2 M 7 D 1 M 9 I 1
M 52 D 1 M 8 D 1 M 9 D 3 M 29 D 1 M 18 D 3 M 12 D 1 M 19 I 2 M 103 D 1 M 18 D 1 M 8 D 1 M 14 I 1
M 9 D 1 M 10 I 1 M 3 D 1 M 5 D 1 M 9 I 2 M 14 D 1 M 14 D 1 M 2 I 1 M 4 I 1 M 46 D 1 M 2 I 1 M 66 I
1 M 1 I 1 M 17 I 2 M 5 D 1 M 20 I 1 M 12 D 1 M 71 I 1 M 15 I 2 M 9 D 2 M 23 I 1 M 6 D 1 M 6 D 1 M
6 D 1 M 19 D 2 M 26 I 1 M 36 I 1 M 9 D 605 I 10
24547 Segmentation fault (core dumped) | cPecanRealign /scratch/tmp/tmpivbY_w/localTempD
ir/ref.fa /scratch/tmp/tmpivbY_w/localTempDir/read.fa --diagonalExpansion=10 --splitMatrixBiggerTh
anThis=3000 --loadHmm /hive/users/miten/pipeline_full_runs/stats_marginAlign/margin/src/margin/map
pers/last_hmm_20.txt --gapGamma=0.5 --matchGamma=0.0 >> /hive/users/miten/pipeline_full_runs/stats
marginAlign/margin/jobTreeM13NoEM/jobs/gTD1/tmp_zsbGhgPBdH/tempOutput_1814.txt
Traceback (most recent call last):
File "/hive/users/miten/pipeline_full_runs/stats_marginAlign/margin/submodules/jobTree/src/jobTr
eeSlave.py", line 271, in main
defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth)
File "/hive/users/miten/pipeline_full_runs/stats_marginAlign/margin/submodules/jobTree/scriptTre
e/stack.py", line 153, in execute
self.target.run()
File "/hive/users/miten/pipeline_full_runs/stats_marginAlign/margin/submodules/jobTree/scriptTre
e/target.py", line 197, in run
func(((self,) + tuple(self.args)), *_self.kwargs)
File "/hive/users/miten/pipeline_full_runs/stats_marginAlign/margin/src/margin/marginAlignLib.py
", line 319, in realignCigarTargetFn
options.gapGamma, options.matchGamma, outputCigarFile))
File "/hive/users/miten/pipeline_full_runs/stats_marginAlign/margin/submodules/sonLib/bioio.py",
line 184, in system
raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts))
RuntimeError: Command: echo cigar: channel_439_read_57 0 1122 + DNA_CS 0 3559 + 1 D 1838 I 1 M 7 D
1 M 3 I 2 M 6 D 1 M 13 I 1 M 2 I 1 M 7 I 1 M 16 D 1 M 35 D 1 M 47 I 1 M 1 I 2 M 11 D 3 M 45 I 2 M
26 I 1 M 2 I 1 M 18 D 2 M 17 I 1 M 36 D 2 M 4 D 1 M 8 I 2 M 7 D 1 M 9 I 1 M 52 D 1 M 8 D 1 M 9 D
3 M 29 D 1 M 18 D 3 M 12 D 1 M 19 I 2 M 103 D 1 M 18 D 1 M 8 D 1 M 14 I 1 M 9 D 1 M 10 I 1 M 3 D 1
M 5 D 1 M 9 I 2 M 14 D 1 M 14 D 1 M 2 I 1 M 4 I 1 M 46 D 1 M 2 I 1 M 66 I 1 M 1 I 1 M 17 I 2 M 5
D 1 M 20 I 1 M 12 D 1 M 71 I 1 M 15 I 2 M 9 D 2 M 23 I 1 M 6 D 1 M 6 D 1 M 6 D 1 M 19 D 2 M 26 I 1
M 36 I 1 M 9 D 605 I 10 | cPecanRealign /scratch/tmp/tmpivbY_w/localTempDir/ref.fa /scratch/tmp/t
mpivbY_w/localTempDir/read.fa --diagonalExpansion=10 --splitMatrixBiggerThanThis=3000 --lo
adHmm /hive/users/miten/pipeline_full_runs/stats_marginAlign/margin/src/margin/mappers/last_hmm_20
.txt --gapGamma=0.5 --matchGamma=0.0 >> /hive/users/miten/pipeline_full_runs/stats_marginAlign/mar
gin/jobTreeM13NoEM/jobs/gTD1/tmp_zsbGhgPBdH/tempOutput_1814.txt exited with non-zero status 139
Exiting the slave because of a failed job on host juggernaut
Due to failure we are reducing the remaining retry count of job /hive/users/miten/pipeline_full_ru
ns/stats_marginAlign/margin/jobTreeM13NoEM/jobs/t3/t3/t3/t4/t2/t0/job to 0
We have set the default memory of the failed job to 2147483648 bytes

Hi,
I managed to map my FASTQ file with human genome with marginAlign. When trying with reference fasta file I created, it did not work. This file contains IUPAC code beside A; T; G; C. I just wonder if that's the problem.
Cheers

Hello,

I am running marginAlign and used --maxThreads 90, however the process lastal is only using one thread. Is this normal?

What parts of marginAlign are parallelized, and is the = necessary between --maxThreads and the argument?

Thanks!

Hi,

I'm using Ubuntu 16.04 LTS on virtualbox. I got the following error when running marginAlign for Nanopore reads.

---JOBTREE SLAVE OUTPUT LOG---
Traceback (most recent call last):
File "/home/ewc/marginAlign/submodules/jobTree/src/jobTreeSlave.py", line 271, in main
defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth)
File "/home/ewc/marginAlign/submodules/jobTree/scriptTree/stack.py", line 153, in execute
self.target.run()
File "/home/ewc/marginAlign/src/margin/mappers/last.py", line 35, in run
Last.run(self)
File "/home/ewc/marginAlign/src/margin/mappers/last.py", line 19, in run
for name, seq, quals in fastqRead(self.readFastqFile):
File "/home/ewc/marginAlign/submodules/sonLib/bioio.py", line 769, in fastqRead
raise RuntimeError("Got a qual value out of range %s (range is 33 to 126)" % i)
RuntimeError: Got a qual value out of range 13 (range is 33 to 126)
Exiting the slave because of a failed job on host ewc-VirtualBox
Due to failure we are reducing the remaining retry count of job /media/sf_MinION_Pipeline/jobTree/jobs/job to 0
We have set the default memory of the failed job to 2147483648.0 bytes

Then, I also got the following error when running marginCaller for SAM file (aligned using BWA-MEM).

---JOBTREE SLAVE OUTPUT LOG---
Traceback (most recent call last):
File "/home/ewc/marginAlign/submodules/jobTree/src/jobTreeSlave.py", line 271, in main
defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth)
File "/home/ewc/marginAlign/submodules/jobTree/scriptTree/stack.py", line 153, in execute
self.target.run()
File "/home/ewc/marginAlign/submodules/jobTree/scriptTree/target.py", line 197, in run
func(*((self,) + tuple(self.args)), **self.kwargs)
File "/home/ewc/marginAlign/src/margin/marginCallerLib.py", line 211, in variantCallSamFileTargetFn
evolutionarySubstitutionMatrix, errorSubstitutionMatrix)
File "/home/ewc/marginAlign/src/margin/marginCallerLib.py", line 89, in calcBasePosteriorProbs
observedBase))*baseObservations[observedBase], BASES)), BASES)
File "/home/ewc/marginAlign/src/margin/marginCallerLib.py", line 86, in
math.log(getProb(evolutionarySubstitionMatrix, refBase.upper(), missingBase)) +
File "/home/ewc/marginAlign/src/margin/marginCallerLib.py", line 79, in getProb
return subMatrix[(start, end)]
KeyError: ('N', 'A')
Exiting the slave because of a failed job on host ewc-VirtualBox
Due to failure we are reducing the remaining retry count of job /media/sf_MinION_Pipeline/jobTree/jobs/job to 0
We have set the default memory of the failed job to 2147483648 bytes
ount of job /media/sf_MinION_Pipeline/jobTree/jobs/job to 0
We have set the default memory of the failed job to 2147483648 bytes

What should i do to solve the issues?

Thanks.

Hi,
I installed marginAlign, I did a test run (make test) and it was successful, please see below the final part of the test run result.
However, when I try to call marginAlign it returns
-bash: marginAlign: command not found

`.AverageReadIdentity 0.795369618446
MedianReadIdentity 0.795369618446
MinReadIdentity 0.720926843486
MaxReadIdentity 0.869812393405
ValuesReadIdentity 0.869812393405 0.720926843486
AverageAlignmentIdentity 0.509266537938
MedianAlignmentIdentity 0.509266537938
MinAlignmentIdentity 0.417804478427
MaxAlignmentIdentity 0.60072859745
ValuesAlignmentIdentity 0.417804478427 0.60072859745
AverageReadCoverage 0.901063009589
MedianReadCoverage 0.901063009589
MinReadCoverage 0.860682016905
MaxReadCoverage 0.941444002274
ValuesReadCoverage 0.941444002274 0.860682016905
AverageMismatchesPerAlignedBase 0.119232100001
MedianMismatchesPerAlignedBase 0.119232100001
MinMismatchesPerAlignedBase 0.0760869565217
MaxMismatchesPerAlignedBase 0.162377243481
ValuesMismatchesPerAlignedBase 0.0760869565217 0.162377243481
AverageDeletionsPerReadBase 0.0574880045021
MedianDeletionsPerReadBase 0.0574880045021
MinDeletionsPerReadBase 0.0458937198068
MaxDeletionsPerReadBase 0.0690822891974
ValuesDeletionsPerReadBase 0.0458937198068 0.0690822891974
AverageInsertionsPerReadBase 0.0392299405665
MedianInsertionsPerReadBase 0.0392299405665
MinInsertionsPerReadBase 0.0386048086692
MaxInsertionsPerReadBase 0.0398550724638
ValuesInsertionsPerReadBase 0.0398550724638 0.0386048086692
.

Ran 19 tests in 72.898s

OK
`

Hello,

I am trying to use MarginAlign with the last release of Minimap2 (2.15-r908-dirty) and I had several issues:

1. I had this mysterious PySam error, that has not yet been mentionned in any issues (I think).
   I did the following sequence of commands to install MarginAlign and get the last release of Minimap2:

git clone https://github.com/benedictpaten/marginAlign.git
cd marginAlign
git pull
git submodule init
git submodule update
make
virtualenv --python=/usr/bin/python2 --no-site-packages --distribute env && source env/bin/activate && pip install -r requirements.txt
make test

Everything went fine, both on the make test and using a toy dataset (20 reads against a small database).
But when I used a bigger fastq file (against the same database) an error appeared, apparently coming from the getLastNonClippedPositionInRead function (utils.py file). The alignedSegment.query_alignment_end was crashing and returning a "SystemError: error return without exception set" (I checked the 2 other variables, they seemed fine).
I found a PySam issue mentionning a similar thing, but in a different context (pysam-developers/pysam#176), so I fixed this by installing pysam==0.9.0 instead of the version mentionned in the requirement.txt
I don't know, maybe I did something wrong, or maybe it is linked with the use of the last version of Minimap2 ?

2. Moreover, trying to use the --em option, to run the EM learning followed by the realignement, I realized that MarginAlign was always loading the HMM file "last_hmm_20.txt". So I had to comment the line options.inputModel = os.path.join(pathToBaseNanoporeDir(), "src", "margin", "mappers", "last_hmm_20.txt") in the marginAlign.py file.
   I guess this is linked with the fact that LAST is set as the default aligner, but maybe there is something to fix here?
   
   

Thanks in advance for your answer and many thanks for implementing Minimap2 into MarginAlign!
Felix.

I'm doing some test runs - it would be much quicker to split up the input fastq files to speed up last/bwa

Hi, I was trying to run the basic command line: marginAlign fastqfile fastaRef test.sam --jobTree ./jobTree but ran into the following error message and the program stalled.
Process Process-1:
Traceback (most recent call last):
File "/usr/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
self.run()
File "/usr/lib/python2.7/multiprocessing/process.py", line 114, in run
self._target(*self._args, **self._kwargs)
File "/home/username/exp/marginAlign/submodules/jobTree/batchSystems/singleMachine.py", line 51, in worker
slaveMain()
File "/home/username/exp/marginAlign/submodules/jobTree/src/jobTreeSlave.py", line 103, in main
fileHandle = open(getEnvironmentFileName(jobTreePath), 'r')
IOError: [Errno 2] No such file or directory: '/media/username/Seagate/environ.pickle'
I could not understand the error message becuase I was running the program at this location '/media/username/Seagate Backup Plus Drive/ONTreads/experiment1207/testmargin/' and I can see the jobTree folder created there. But the program seems to be looking for environ.pickle at '/media/username/Seagate/'.
How can I fix this problem? Thank you so much for your help!

When trying to call SNVs with marginCaller the programme crashes and I get the following output (I am only posting one instance of many identical messages):

Mac OS X (El Capitan):
$ marginCaller input.sam reference.fasta output.vcf
/Users/sam/software/marginAlign/src/margin/mappers/last_hmm_20.txt
0.3
The job seems to have left a log file, indicating failure: /Users/sam/jobTree/jobs/t3/t2/job
Reporting file: /Users/sam/jobTree/jobs/t3/t2/log.txt
log.txt: ---JOBTREE SLAVE OUTPUT LOG---
log.txt: /bin/sh: 939732440: command not found
log.txt: /bin/sh: gb: command not found
log.txt: /bin/sh: CP011343.2: command not found
log.txt: /bin/sh: 2403236: command not found
log.txt: Traceback (most recent call last):
log.txt: File "/Users/sam/software/marginAlign/submodules/jobTree/src/jobTreeSlave.py", line 271, in main
log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth)
log.txt: File "/Users/sam/software/marginAlign/submodules/jobTree/scriptTree/stack.py", line 153, in execute
log.txt: self.target.run()
log.txt: File "/Users/sam/software/marginAlign/submodules/jobTree/scriptTree/target.py", line 197, in run
log.txt: func(_((self,) + tuple(self.args)), *_self.kwargs)
log.txt: File "/Users/sam/software/marginAlign/src/margin/marginCallerLib.py", line 61, in posteriorProbabilityCalculationTargetFn
log.txt: map(lambda x : map(float, x.split()), open(tempPosteriorProbsFile, 'r')):
log.txt: IOError: [Errno 2] No such file or directory: '/var/folders/lr/ws3f8_kd2p343vqcrj36w7z40000gn/T/tmpomTYBS/localTempDir/posteriorProbs.txt'
log.txt: Exiting the slave because of a failed job on host Macbook
log.txt: Due to failure we are reducing the remaining retry count of job /Users/sam/jobTree/jobs/t3/t2/job to 0
log.txt: We have set the default memory of the failed job to 2147483648 bytes
Job: /Users/sam/jobTree/jobs/t3/t2/job is completely failed

Linux (Red Hat Enterprise Linux Server release 6.3 (Santiago)):
$ marginCaller output.sam referenceBC01.fasta output.vcf
/home/coml-nmsi/sdemharter/software/marginAlign/src/margin/mappers/last_hmm_20.txt
0.3
The job seems to have left a log file, indicating failure: /data/coml-nmsi/sdemharter/ont/jobTree/jobs/t0/t0/t1/job
Reporting file: /data/coml-nmsi/sdemharter/ont/jobTree/jobs/t0/t0/t1/log.txt
log.txt: ---JOBTREE SLAVE OUTPUT LOG---
log.txt: /bin/sh: gb: command not found
log.txt: /bin/sh: 173474: command not found
log.txt: /bin/sh: CP011343.2: command not found
log.txt: /bin/sh: 939732440: command not found
log.txt: Traceback (most recent call last):
log.txt: File "/home/coml-nmsi/sdemharter/software/marginAlign/submodules/jobTree/src/jobTreeSlave.py", line 271, in main
log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth)
log.txt: File "/home/coml-nmsi/sdemharter/software/marginAlign/submodules/jobTree/scriptTree/stack.py", line 153, in execute
log.txt: self.target.run()
log.txt: File "/home/coml-nmsi/sdemharter/software/marginAlign/submodules/jobTree/scriptTree/target.py", line 197, in run
log.txt: func(_((self,) + tuple(self.args)), *_self.kwargs)
log.txt: File "/home/coml-nmsi/sdemharter/software/marginAlign/src/margin/marginCallerLib.py", line 62, in posteriorProbabilityCalculationTargetFn
log.txt: map(lambda x : map(float, x.split()), open(tempPosteriorProbsFile, 'r')):
log.txt: IOError: [Errno 2] No such file or directory: '/tmp/tmpX__aXV/localTempDir/posteriorProbs.txt'
log.txt: Exiting the slave because of a failed job on host login3
log.txt: Due to failure we are reducing the remaining retry count of job /data/coml-nmsi/sdemharter/ont/jobTree/jobs/t0/t0/t1/job to 0
log.txt: We have set the default memory of the failed job to 2147483648 bytes
Job: /data/coml-nmsi/sdemharter/ont/jobTree/jobs/t0/t0/t1/job is completely failed

Hello! After running the marginAlign code as directly stated, I received several long error messages, such as "The job seems to have left a log file, indicating failure: /path/to/directory/jobTree/jobs/job" and "raise RuntimeError("Invalid FASTA character, ASCII code = '%d', found in input sequence %s" % (ord(i), name))". Could you please provide suggestions on how I could fix this? Thanks!

Hi,
after starting marginAlign and running for several hours I got this error message. But I could not interpret what it meant.

mStart --logInfo --stats --maxThreads=28 --minimap2
Logging set at level: INFO
Logging to file: None
Logging set at level: INFO
Logging to file: None
The job tree appears to already exist, so we'll reload it
Written the config file
Setting up the thread pool with 28 threads given the max threads 28 and the max cpus 9223372036854775807
Using the single machine batch system
Reloaded the jobtree
Written the environment for the jobs to the environment file
Got parameters,rescue jobs frequency: 5400.0 max job duration: 9.22337203685e+18
Checked batch system has no running jobs and no updated jobs
Found 1 jobs to start and 0 parent jobs with children to run
Starting the main loop
The job seems to have left a log file, indicating failure: /home/flo/marginAlign/jobTree/jobs/job
Reporting file: /home/flo/marginAlign/jobTree/jobs/log.txt
log.txt: ---JOBTREE SLAVE OUTPUT LOG---
log.txt: Parsed arguments and set up logging
log.txt: Traceback (most recent call last):
log.txt: File "/home/flo/marginAlign/submodules/jobTree/src/jobTreeSlave.py", line 271, in main
log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth)
log.txt: File "/home/flo/marginAlign/submodules/jobTree/scriptTree/stack.py", line 153, in execute
log.txt: self.target.run()
log.txt: File "/home/flo/marginAlign/submodules/jobTree/scriptTree/target.py", line 197, in run
log.txt: func(*((self,) + tuple(self.args)), **self.kwargs)
log.txt: File "/home/flo/marginAlign/src/margin/marginAlignLib.py", line 355, in realignSamFile3TargetFn
log.txt: sum(map(lambda (type, length) : length if type in (0,1,4) else 0, aR.cigar))
log.txt: AssertionError
log.txt: Exiting the slave because of a failed job on host ONT-Workstation
log.txt: Due to failure we are reducing the remaining retry count of job /home/flo/marginAlign/jobTree/jobs/job to 0
log.txt: We have set the default memory of the failed job to 2147483648 bytes
Job: /home/flo/marginAlign/jobTree/jobs/job is completely failed
Only failed jobs and their dependents (1 total) are remaining, so exiting.
Finished the main loop
Waiting for stats collator process to finish
Stats finished collating in 0.486446142197 seconds
Traceback (most recent call last):
File "./src/margin/marginAlign.py", line 109, in
main()
File "/home/flo/marginAlign/src/margin/marginAlign.py", line 105, in main
raise RuntimeError("Got failed jobs")
RuntimeError: Got failed jobs

Could anyone see, what's the problem and how I can solve it.
Thanks in advance!

Best
Florian

To write this up we need to record runtimes for how long it takes (wall and processing time) to process a minion dataset, both for marginAlign and marginCaller.

I think it would be good to do this on EC2, and to use docker to create a container that would run on EC2 as a push button process - that way an outside group without compute could use a beefy EC2 instance to process minion datasets with our tool set - perhaps they could pipe direct from the Metrichor process to our processing pipeline. Let's discuss this in person.

Hi,
I used marginAlign to align my reads which was successful. I then used marginCaller to call SNPs, mariginCaller took long time (it ran for more than 12 hours)
How can I solve this?

./marginAlign BC05.fastq NCBI.GRCh38.fa BC05_noalignchain.sam --minimap2 --jobTree ./jobTree --noChain --noRealign

./marginCaller BC01_noalignchain.sam NCBI.GRCh38.fa BC01.vcf --noMargin --jobTree ./jobTree

/projects/b1042/BurridgeLab/slc28a3_resequencing/marginAlign/src/margin/mappers/last_hmm_20.txt
0.3
The job seems to have left a log file, indicating failure: /projects/b1042/BurridgeLab/slc28a3_resequencing/marginAlign/jobTree/jobs/job
Reporting file: /projects/b1042/BurridgeLab/slc28a3_resequencing/marginAlign/jobTree/jobs/log.txt
log.txt: ---JOBTREE SLAVE OUTPUT LOG---
log.txt: Traceback (most recent call last):
log.txt: File "/projects/b1042/BurridgeLab/slc28a3_resequencing/marginAlign/submodules/jobTree/src/jobTreeSlave.py", line 271, in main
log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth)
log.txt: File "/projects/b1042/BurridgeLab/slc28a3_resequencing/marginAlign/submodules/jobTree/scriptTree/stack.py", line 153, in execute
log.txt: self.target.run()
log.txt: File "/projects/b1042/BurridgeLab/slc28a3_resequencing/marginAlign/submodules/jobTree/scriptTree/target.py", line 197, in run
log.txt: func(*((self,) + tuple(self.args)), **self.kwargs)
log.txt: File "/projects/b1042/BurridgeLab/slc28a3_resequencing/marginAlign/src/margin/marginCallerLib.py", line 211, in variantCallSamFileTargetFn
log.txt: evolutionarySubstitutionMatrix, errorSubstitutionMatrix)
log.txt: File "/projects/b1042/BurridgeLab/slc28a3_resequencing/marginAlign/src/margin/marginCallerLib.py", line 89, in calcBasePosteriorProbs
log.txt: observedBase))*baseObservations[observedBase], BASES)), BASES)
log.txt: File "/projects/b1042/BurridgeLab/slc28a3_resequencing/marginAlign/src/margin/marginCallerLib.py", line 86, in
log.txt: math.log(getProb(evolutionarySubstitionMatrix, refBase.upper(), missingBase)) +
log.txt: File "/projects/b1042/BurridgeLab/slc28a3_resequencing/marginAlign/src/margin/marginCallerLib.py", line 79, in getProb
log.txt: return subMatrix[(start, end)]
log.txt: KeyError: ('N', 'A')
log.txt: Exiting the slave because of a failed job on host qnode5161
log.txt: Due to failure we are reducing the remaining retry count of job /projects/b1042/BurridgeLab/slc28a3_resequencing/marginAlign/jobTree/jobs/job to 0
log.txt: We have set the default memory of the failed job to 2147483648 bytes
Job: /projects/b1042/BurridgeLab/slc28a3_resequencing/marginAlign/jobTree/jobs/job is completely failed
Traceback (most recent call last):
File "./src/margin/marginCaller.py", line 63, in
main()
File "/projects/b1042/BurridgeLab/slc28a3_resequencing/marginAlign/src/margin/marginCaller.py", line 59, in main
raise RuntimeError("Got failed jobs")
RuntimeError: Got failed jobs

Thanks

Hi all,
I have an issue when I run marginAlign. The first sam file contains the mapping quality (all of them are 255) while the last sam file all the quality goes to 0. how can I fix this problem? are you thinking to fix in a next release?

thanks
Luigi

Hi,

Thanks for the marginAlign suite. It is great.

I was wondering if there was a way to have marginStats (or other approach) go through alignments and spit out the read name and identity instead of stats. E.g.:

Read1  0.676691729323   
Read2  0.724295506474   
Read3  0.421308655158   
Read4  0.735033943633   
.
.
.
etc

I tried:

 marginStats --printValuePerReadAlignment --identity output.sam temp.fastq lambdaGenomeSequence.fa

which as you know outputs something like:

AverageIdentity 0.608038446759
MedianIdentity 0.742990654206
MinIdentity 0.015294021428
MaxIdentity 0.809134432064
ValuesIdentity 0.676691729323   0.724295506474  0.421308655158  0.735033943633  0.751218026797  0.750067805804  0.753963593658  0.776012530768  0.757202247895  0.698859626314  0.773887646932  0.809134432064  0.176849567696  0.262163438829  0.740789473684  0.015294021428  0.785557986871  0.787041036717  0.137452502891  0.742990654206  0.356559785803  0.696320949897  0.119196988708  0.0338850369045 0.488094798627  0.787056367432  0.793948126801  0.0889133492326 0.730844793713  0.769590643275  0.756786102063  0.771119294722  0.306422170594  0.069472739201  0.776006539955  0.76849861836   0.714887218045  0.762810678122  0.756357185098  0.769752358491  0.741569492594  0.774193548387  0.770156438026  0.740225118483  0.755319148936  0.745851528384  0.767524401065  0.762261014131  0.787345385347  0.65625 0.704954954955  0.400684931507  0.0273635442305

Are the values here in the same order that reads appear in the SAM file?

best,

John

Hello,

I am trying to use marginStats to collect alignment stats from minimap2 aligned data of a direct RNA sample, this error is reported:

...
Detected a discrepancy between the absolute read                     sequence and the aligned read sequence. Bases: U A,                     read-position: 107, is reversed: True, absolute read offset: -118,                     length absolute read sequence 924, length aligned read sequence 118,                     length aligned read sequence plus soft clipping 118, read name: 7caac1dc-f0c6-4ee8-9cd4-d52e29d4e9ed,                     cigar string 805H20M1I2M3I3M1I8M1D37M1D31M2D12M1H
Traceback (most recent call last):
  File "./src/margin/marginStats.py", line 111, in <module>
    main()
  File "./src/margin/marginStats.py", line 78, in main
    referenceFastaFile, globalAlignment=not options.localAlignment)
  File "/home/ubuntu/marginAlign/src/margin/utils.py", line 382, in getReadAlignmentStats
    refSequences[sam.getrname(aR.rname)], aR, globalAlignment), samIterator(sam))
  File "/home/ubuntu/marginAlign/src/margin/utils.py", line 382, in <lambda>
    refSequences[sam.getrname(aR.rname)], aR, globalAlignment), samIterator(sam))
  File "/home/ubuntu/marginAlign/src/margin/utils.py", line 308, in __init__
    for aP in AlignedPair.iterator(alignedRead, self.refSeq, self.readSeq):
  File "/home/ubuntu/marginAlign/src/margin/utils.py", line 262, in iterator
    assert len(alignedSegment.query_sequence) <= len(readSeq)
TypeError: object of type 'NoneType' has no len()

Hi there,

I used marginAlign and marginCaller to analyse my data. I just wonder if the VCF format generated by marginCaller can be converted into normal format. That will make it easier for downstream analysis. Thank you.

K

Hi,

I am running into problem when trying to execute marginAlign. Has anybody got any idea about the error message I got? I am new in this community. This is what I ran:

(env) Nadas-MBP:marginAlign nadakubikova$ ./marginAlign /Users/nadakubikova/Documents/Sequenced\ Data/fastq_First\ Nanopore\ Run/downloads/PASS/BC01/BC01_trimmed.fastq /Users/nadakubikova/Documents/Sequenced\ Data/fastq_First\ Nanopore\ Run/downloads/PASS/BC01/chr1.fa /Users/nadakubikova/Documents/Sequenced\ Data/fastq_First\ Nanopore\ Run/downloads/PASS/BC01/BC01_trimmed.sam --jobTree ./jobTree
Traceback (most recent call last):
File "./src/margin/marginAlign.py", line 109, in
main()
File "/Users/nadakubikova/marginAlign/src/margin/marginAlign.py", line 72, in main
raise RuntimeError("Expected three arguments, got: %s" % " ".join(args))
RuntimeError: Expected three arguments, got: /Users/nadakubikova/Documents/Sequenced Data/fastq_First Nanopore Run/downloads/PASS/BC01/BC01_trimmed.fastq /Users/nadakubikova/Documents/Sequenced Data/fastq_First Nanopore Run/downloads/PASS/BC01/chr1.fa /Users/nadakubikova/Documents/Sequenced Data/fastq_First Nanopore Run/downloads/PASS/BC01/BC01_trimmed.sam

I would be grateful for any suggestions.
Thanks,
N

There is a script in the nanopore pipeline for creating a custom track + assembly hub for a given sam file and reference. Please add to scripts.

As a simple test of correctness, it would be helpful if each test in tests/test.py that creates a sam file were to report the avg. identity / avg. coverage / total number of alignments in the sam file.

Good day,

I am receiving an error when trying to run marginAlign with the default parameters. Below the command that I ran as well as the error report. Please let me know if you need any other information, thank you very much!

alan@zoidberg:~/projects/minion/lambda-burn-in/filtered-data/lambda-burn-in$ /opt/bioinformatics-software/minion-software/margin/marginAlign first-run.passed.fastq ../../lamda-phage.fasta first.passed.sam
Got message from job at time: 1429552015.62 : Going to chain sam file: /home/alan/projects/minion/lambda-burn-in/filtered-data/lambda-burn-in/jobTree/jobs/gTD0/tmp_4vbY30VFrP/temp.sam
Got message from job at time: 1429552015.62 : Going to realign sam file: /home/alan/projects/minion/lambda-burn-in/filtered-data/lambda-burn-in/jobTree/jobs/gTD1/tmp_pxHowcXufF/temp.sam to create output sam file: first.passed.sam     with match gamma 0.5 and gap gamma 0.0 and model /opt/bioinformatics-software/minion-software/margin/src/margin/mappers/last_hmm_20.txt
The job seems to have left a log file, indicating failure: /home/alan/projects/minion/lambda-burn-in/filtered-data/lambda-burn-in/jobTree/jobs/job
Reporting file: /home/alan/projects/minion/lambda-burn-in/filtered-data/lambda-burn-in/jobTree/jobs/log.txt
log.txt:        ---JOBTREE SLAVE OUTPUT LOG---
log.txt:        Traceback (most recent call last):
log.txt:          File "/opt/bioinformatics-software/minion-software/margin/submodules/jobTree/src/jobTreeSlave.py", line 271, in main
log.txt:            defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth)
log.txt:          File "/opt/bioinformatics-software/minion-software/margin/submodules/jobTree/scriptTree/stack.py", line 153, in execute
log.txt:            self.target.run()
log.txt:          File "/opt/bioinformatics-software/minion-software/margin/submodules/jobTree/scriptTree/target.py", line 197, in run
log.txt:            func(*((self,) + tuple(self.args)), **self.kwargs)
log.txt:          File "/opt/bioinformatics-software/minion-software/margin/src/margin/marginAlignLib.py", line 345, in realignSamFile3TargetFn
log.txt:            ops += map(lambda op : (op.type, op.length), pA.operationList)
log.txt:        AttributeError: 'NoneType' object has no attribute 'operationList'
log.txt:        Exiting the slave because of a failed job on host zoidberg
log.txt:        Due to failure we are reducing the remaining retry count of job /home/alan/projects/minion/lambda-burn-in/filtered-data/lambda-burn-in/jobTree/jobs/job to 0
log.txt:        We have set the default memory of the failed job to 2147483648 bytes
Job: /home/alan/projects/minion/lambda-burn-in/filtered-data/lambda-burn-in/jobTree/jobs/job is completely failed
Traceback (most recent call last):
  File "/opt/bioinformatics-software/minion-software/margin/src/margin/marginAlign.py", line 91, in <module>
    main()
  File "/opt/bioinformatics-software/minion-software/margin/src/margin/marginAlign.py", line 87, in main
    raise RuntimeError("Got failed jobs")
RuntimeError: Got failed jobs

Hello,

I keep getting this error when using the make command . Any ideas on how to fix this? Thanks!

NOTE: a missing vtable usually means the first non-inline virtual member function has no definition.
  "vtable for std::__cxx11::basic_istringstream<char, std::char_traits<char>, std::allocator<char> >", referenced from:
      cbrc::MultiSequence::readFastaName(std::basic_istream<char, std::char_traits<char> >&) in MultiSequence.o
      cbrc::CyclicSubsetSeed::fromStream(std::basic_istream<char, std::char_traits<char> >&, bool, unsigned char const*) in CyclicSubsetSeed.o
      cbrc::CyclicSubsetSeed::fromString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, unsigned char const*) in CyclicSubsetSeed.o
      cbrc::SubsetSuffixArray::fromFiles(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, unsigned char const*) in SubsetSuffixArray.o
      void cbrc::unstringifySize<unsigned long>(unsigned long&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) in LastdbArguments.o
      void cbrc::unstringify<unsigned int>(unsigned int&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) in LastdbArguments.o
      void cbrc::unstringify<cbrc::sequenceFormat::Enum>(cbrc::sequenceFormat::Enum&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) in LastdbArguments.o
      ...
  NOTE: a missing vtable usually means the first non-inline virtual member function has no definition.
  "vtable for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >", referenced from:
      std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > cbrc::stringify<unsigned long>(unsigned long const&) in MultiSequence.o
      std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > cbrc::stringify<unsigned char>(unsigned char const&) in CyclicSubsetSeed.o
      std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > cbrc::stringify<unsigned long>(unsigned long const&) in SubsetSuffixArray.o
      cbrc::LastdbArguments::fromArgs(int, char**) in LastdbArguments.o
      std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > cbrc::stringify<unsigned long>(unsigned long const&) in fileMap.o
      std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > cbrc::stringify<int>(int const&) in MultiSequenceQual.o
      cbrc::MultiSequence::appendFromPrb(std::basic_istream<char, std::char_traits<char> >&, unsigned int, unsigned int, unsigned char const*) in MultiSequenceQual.o
      ...
  NOTE: a missing vtable usually means the first non-inline virtual member function has no definition.
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
make[3]: *** [lastdb] Error 1
make[2]: *** [all] Error 2
make[1]: *** [all.last] Error 2
make: *** [all] Error 2

Performance to calculate runtime is way too slow.

It's difficult to install this system wide in a cluster environment because it doesn't have a proper version. Right now I'm just using versions like marginalign/git-2369dafd with the commit hash for our environment modules.

In line 87 of marginCallerLib.py you'll see where we want to write out a VCF file of the SNV calls. Please add this output (there is some other missing stuff, but I can get that done over the weekend).

link to hub: http://hgwdev.soe.ucsc.edu/~miten/ecoli_hub/hub.txt
link to assembly hub on browser: http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=miten&hgS_otherUserSessionName=Test_hub_40127_E.coli_K12
link to hub on hgwdev: /cluster/home/miten/public_html/ecoli_hub

marginAlign should output alignment quality scores, like BAQ, using the posterior probs it calculates.

I am attempting to install marginAlign into a cluster environment utilising the lmod modules system (so I suppose I am also echoing alanorth's request to please tag your releases in git).

I have satisfied each of the dependencies listed in the requirements.txt and am able to import them successfully into the system python.

However, running any of the executables results in an import error related to pysam:

./marginAlign
Traceback (most recent call last):
  File "./src/margin/marginAlign.py", line 7, in <module>
    from margin.mappers.last import Last, LastChain, LastRealign
  File "/usr/local/installed/marginalign/0.1/src/margin/mappers/last.py", line 1, in <module>
    from margin.mappers.abstractMapper import AbstractMapper
  File "/usr/local/installed/marginalign/0.1/src/margin/mappers/abstractMapper.py", line 2, in <module>
    from margin.marginAlignLib import chainSamFile, realignSamFileTargetFn
  File "/usr/local/installed/marginalign/0.1/src/margin/marginAlignLib.py", line 1, in <module>
    import pysam, sys, os
ImportError: No module named pysam

./marginCaller
Traceback (most recent call last):
  File "./src/margin/marginCaller.py", line 7, in <module>
    from margin.utils import pathToBaseNanoporeDir
  File "/usr/local/installed/marginalign/0.1/src/margin/utils.py", line 1, in <module>
    import pysam, sys, os, random
ImportError: No module named pysam

./marginStats
Traceback (most recent call last):
  File "./src/margin/marginStats.py", line 5, in <module>
    from margin.utils import ReadAlignmentStats
  File "/usr/local/installed/marginalign/0.1/src/margin/utils.py", line 1, in <module>
    import pysam, sys, os, random
ImportError: No module named pysam

Is there any other requirement related to pysam that needs to be satisfied in order to be able to run marginAlign against the system python?

I get the following compilation error on Ubuntu 14.04:

... cp CuTest.h ../../lib/ make[4]: Leaving directory/opt/marginAlign/submodules/sonLib/externalTools/cutest'
make[3]: Leaving directory /opt/marginAlign/submodules/sonLib/externalTools' make[2]: Leaving directory/opt/marginAlign/submodules/sonLib'
make[1]: *** [all.sonLib] Error 2
make[1]: *** Waiting for unfinished jobs....
impl/pairwiseAligner.c:15:20: fatal error: bioioC.h: No such file or directory
#include "bioioC.h"
^
compilation terminated.
CA_code/lambda_calculator.c: In function 'Find_JP':
CA_code/lambda_calculator.c:371:17: warning: 'flag_sign' may be used uninitialized in this function [-Wmaybe-uninitialized]
Sum_local = Nail_lambda(mat_b, flag_sign, lambda_min, lambda_max, p,q, &lambda_final);
^
gcc -Wall -O2 -o last-merge-batches last-merge-batches.o
bwashm.c: In function 'bwa_shm_stage':
bwashm.c:29:11: warning: ignoring return value of 'ftruncate', declared with attribute warn_unused_result [-Wunused-result]
ftruncate(shmid, BWA_CTL_SIZE);
^
bwashm.c:66:11: warning: ignoring return value of 'ftruncate', declared with attribute warn_unused_result [-Wunused-result]
ftruncate(shmid, idx->l_mem);
^
impl/stateMachine.c:13:20: fatal error: bioioC.h: No such file or directory
#include "bioioC.h"
^
compilation terminated.
make[2]: Leaving directory /opt/marginAlign/submodules/cPecan' make[2]: *** [../sonLib/lib/cPecanLib.a] Error 1 make[1]: *** [all.cPecan] Error 2 g++ -O3 -o lastdb Alphabet.o MultiSequence.o CyclicSubsetSeed.o SubsetSuffixArray.o LastdbArguments.o io.o fileMap.o SubsetSuffixArraySort.o MultiSequenceQual.o lastdb.o g++ -O3 -o lastex Alphabet.o LastexArguments.o io.o ScoreMatrix.o lastex.o gumbel_params/mcf_local_alignment_evaluer.o gumbel_params/njn_dynprogprob.o gumbel_params/njn_dynprogproblim.o gumbel_params/njn_dynprogprobproto.o gumbel_params/njn_ioutil.o gumbel_params/njn_localmaxstat.o gumbel_params/njn_localmaxstatmatrix.o gumbel_params/njn_localmaxstatutil.o gumbel_params/njn_matrix.o gumbel_params/random_gen.o gumbel_params/sls_alp.o gumbel_params/sls_alp_data.o gumbel_params/sls_alp_regression.o gumbel_params/sls_alp_sim.o gumbel_params/sls_pvalues.o g++ -O3 -o last-split Alphabet.o MultiSequence.o fileMap.o split/cbrc_linalg.o split/last-split.o split/cbrc_split_aligner.o split/last-split-main.o split/cbrc_unsplit_alignment.o g++ -O3 -o lastal Alphabet.o MultiSequence.o CyclicSubsetSeed.o SubsetSuffixArray.o LastalArguments.o io.o fileMap.o ScoreMatrix.o DiagonalTable.o SegmentPair.o Alignment.o GappedXdropAligner.o SegmentPairPot.o AlignmentPot.o GeneralizedAffineGapCosts.o Centroid.o LambdaCalculator.o TwoQualityScoreMatrix.o OneQualityScoreMatrix.o QualityPssmMaker.o GeneticCode.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.o AlignmentWrite.o MultiSequenceQual.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o lastal.o CA_code/lambda_calculator.o make[3]: Leaving directory/opt/marginAlign/submodules/last/src'
make[2]: Leaving directory /opt/marginAlign/submodules/last' ar -csru libbwa.a utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o gcc -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS QSufSort.o bwt_gen.o bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o is.o bwtindex.o bwape.o kopen.o pemerge.o maxk.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread -lrt make[2]: Leaving directory/opt/marginAlign/submodules/bwa'
make[1]: Leaving directory /opt/marginAlign/submodules' make: *** [all] Error 2

Any suggestions how to fix this?

Refactoring has removed some methods from utils that are needed for the plots code (this is my bad) - they should be added back.

Hi,

the error seems to be thrown when a very long read/alignment (90kb) is processed. Please find the lines from my log file below:

cigar: 1ec35c6d-fed6-4814-8ef1-eaeb5e34c360 162178 253472 + chr17 21851107 21942767 + 1.000000 M 5 D 12 I 12 M 5 D 8 I 7 M 2 D 24 I 25 M 3 D 121 I 142 M 2 D 104 I 110 M 3 D 170 I 151 M 1 D 7 I 6 M 5 D 17 I 20 M 3 D 7 I 6 M 2 D 165 I 182 M 1 D 653 I 668 M 7 D 513 I 541 M 2 D 378 I 394 M 1 D 74 I 78 M 1 D 579 I 568 M 2 D 272 I 279 M 4 D 9 I 9 M 2 D 2 I 2 M 1 D 94 I 114 M 5 D 164 I 185 M 1 D 3 I 2 M 5 D 189 I 184 M 4 D 163 I 163 M 3 D 7 I 8 M 1 D 65 I 69 M 3 D 666 I 712 M 3 D 69 I 86 M 8 D 338 I 335 M 4 D 4 I 4 M 6 D 28 I 28 M 1 D 469 I 433 M 4 D 20 I 18 M 6 D 174 I 173 M 7 D 12 I 9 M 3 D 2 I 2 M 2 D 72 I 80 M 3 D 7 I 8 M 3 D 324 I 314 M 3 D 112 I 105 M 1 D 74 I 68 M 8 D 92 I 97 M 3 D 8 I 7 M 5 D 238 I 238 M 6 D 5 I 3 M 1 D 32 I 25 M 8 D 63 I 65 M 5 D 5 I 6 M 2 D 510 I 525 M 3 D 198 I 162 M 1 D 167 I 140 M 1 D 96 I 90 M 5 D 87 I 77 M 5 D 14 I 14 M 1 D 60 I 64 M 1 D 103 I 96 M 6 D 99 I 93 M 1 D 2 I 2 M 1 D 65 I 61 M 6 D 9 I 7 M 7 D 132 I 124 M 3 D 224 I 217 M 5 D 119 I 120 M 3 D 261 I 237 M 13 D 189 I 173 M 3 D 105 I 90 M 2 D 30 I 27 M 4 D 26 I 23 M 2 D 173 I 149 M 2 D 1 I 1 M 3 D 9 I 8 M 5 D 529 I 498 M 6 D 21 I 17 M 2 D 253 I 249 M 4 D 261 I 240 M 6 D 7 I 7 M 2 D 3 I 3 M 2 D 235 I 240 M 1 D 165 I 178 M 2 D 2 I 2 M 2 D 38 I 34 M 5 D 105 I 91 M 4 D 231 I 226 M 2 D 23 I 19 M 1 D 244 I 230 M 1 D 237 I 248 M 2 D 98 I 104 M 3 D 279 I 286 M 1 D 36 I 32 M 1 D 7 I 5 M 1 D 633 I 635 M 6 D 122 I 133 M 3 D 19 I 14 M 3 D 17 I 14 M 1 D 282 I 248 M 3 D 464 I 455 M 4 D 98 I 91 M 5 D 42 I 39 M 3 D 13 I 9 M 1 D 24 I 24 M 1 D 1 I 1 M 2 D 31 I 32 M 5 D 34 I 35 M 5 D 35 I 34 M 7 D 20 I 26 M 1 D 272 I 259 M 4 D 665 I 636 M 1 D 169 I 174 M 4 D 62 I 48 M 2 D 162 I 163 M 1 D 219 I 204 M 14 D 136 I 123 M 2 D 8 I 6 M 6 D 132 I 117 M 3 D 208 I 167 M 2 D 8 I 7 M 2 D 17 I 17 M 5 D 114 I 110 M 5 D 12 I 9 M 2 D 112 I 114 M 2 D 238 I 227 M 8 D 422 I 410 M 1 D 14 I 14 M 1 D 35 I 47 M 1 D 115 I 127 M 1 D 2 I 2 M 2 D 269 I 280 M 1 D 10 I 10 M 4 D 370 I 380 M 4 D 55 I 66 M 1 D 75 I 88 M 4 D 281 I 289 M 4 D 4 I 4 M 2 D 79 I 75 M 2 D 123 I 149 M 11 D 160 I 184 M 1 D 6 I 7 M 5 D 188 I 190 M 2 D 163 I 164 M 2 D 7 I 5 M 2 D 70 I 69 M 9 D 28 I 28 M 9 D 228 I 268 M 3 D 3 I 3 M 3 D 159 I 156 M 1 D 248 I 274 M 2 D 83 I 66 M 6 D 41 I 39 M 4 D 57 I 69 M 8 D 69 I 69 M 6 D 194 I 197 M 2 D 81 I 75 M 2 D 4 I 4 M 3 D 276 I 305 M 3 D 20 I 16 M 1 D 39 I 31 M 1 D 219 I 213 M 2 D 412 I 377 M 3 D 473 I 431 M 5 D 235 I 214 M 2 D 253 I 220 M 1 D 6 I 6 M 2 D 418 I 439 M 1 D 1 I 1 M 5 D 4 I 3 M 1 D 428 I 355 M 3 D 222 I 189 M 2 D 137 I 142 M 3 D 23 I 21 M 7 D 78 I 91 M 3 D 6 I 6 M 3 D 130 I 157 M 5 D 40 I 37 M 3 D 403 I 395 M 8 D 17 I 19 M 3 D 257 I 289 M 10 D 44 I 38 M 3 D 688 I 707 M 1 D 65 I 65 M 6 D 142 I 154 M 2 D 7 I 6 M 3 D 28 I 25 M 3 D 5 I 2 M 3 D 27 I 24 M 1 D 22 I 23 M 1 D 107 I 89 M 3 D 38 I 32 M 8 D 238 I 228 M 9 D 235 I 248 M 4 D 69 I 81 M 5 D 68 I 74 M 11 D 9 I 8 M 7 D 121 I 103 M 3 D 59 I 54 M 3 D 51 I 65 M 4 D 7 I 6 M 1 D 11 I 7 M 4 D 49 I 43 M 3 D 4 I 3 M 3 D 100 I 91 M 8 D 87 I 68 M 1 D 229 I 213 M 3 D 304 I 286 M 4 D 7 I 7 M 3 D 106 I 113 M 3 D 159 I 157 M 2 D 1 I 1 M 3 D 159 I 194 M 2 D 51 I 49 M 3 D 50 I 49 M 5 D 18 I 18 M 1 D 88 I 89 M 2 D 17 I 13 M 3 D 471 I 463 M 2 D 47 I 47 M 1 D 70 I 85 M 2 D 356 I 376 M 1 D 138 I 144 M 2 D 113 I 103 M 7 D 99 I 99 M 1 D 74 I 69 M 4 D 14 I 11 M 3 D 69 I 69 M 1 D 177 I 188 M 3 D 453 I 452 M 1 D 4 I 5 M 2 D 124 I 141 M 1 D 338 I 350 M 1 D 614 I 678 M 6 D 18 I 20 M 4 D 100 I 98 M 3 D 4 I 5 M 3 D 307 I 274 M 1 D 8 I 5 M 7 D 3 I 4 M 7 D 8 I 7 M 3 D 113 I 110 M 1 D 43 I 46 M 3 D 156 I 164 M 6 D 80 I 71 M 3 D 77 I 78 M 2 D 257 I 271 M 1 D 234 I 251 M 2 D 6 I 6 M 2 D 210 I 194 M 3 D 62 I 67 M 4 D 188 I 175 M 2 D 235 I 229 M 4 D 7 I 5 M 2 D 104 I 100 M 21 D 68 I 72 M 6 D 2 I 2 M 7 D 294 I 320 M 13 D 33 I 34 M 2 D 1 I 1 M 3 D 8 I 7 M 8 D 4 I 2 M 5 D 33 I 22 M 2 D 341 I 290 M 3 D 4 I 5 M 1 D 433 I 404 M 2 D 445 I 466 M 4 D 124 I 118 M 1 D 134 I 132 M 6 D 25 I 19 M 5 D 47 I 37 M 4 D 1 I 1 M 2 D 85 I 78 M 7 D 98 I 88 M 3 D 37 I 30 M 1 D 5 I 5 M 9 D 3 I 3 M 3 D 278 I 261 M 1 D 3 I 2 M 4 D 30 I 32 M 5 D 206 I 225 M 1 D 46 I 47 M 6 D 57 I 66 M 3 D 191 I 220 M 4 D 34 I 35 M 1 D 274 I 264 M 4 D 7 I 8 M 6 D 16 I 14 M 4 D 7 I 7 M 1 D 34 I 27 M 2 D 256 I 248 M 4 D 888 I 897 M 4 D 56 I 66 M 1 D 210 I 193 M 3 D 48 I 41 M 4 D 7 I 8 M 8 D 11 I 12 M 2 D 2 I 2 M 2 D 5 I 4 M 7 D 118 I 111 M 5 D 103 I 116 M 3 D 29 I 33 M 2 D 59 I 66 M 2 D 2 I 2 M 3 D 28 I 25 M 2 D 276 I 276 M 7 D 48 I 58 M 2 D 13 I 10 M 6 D 235 I 237 M 2 D 808 I 814 M 1 D 162 I 148 M 2 D 45 I 51 M 1 D 44 I 41 M 4 D 779 I 802 M 3 D 225 I 228 M 2 D 2 I 2 M 11 D 231 I 217 M 6 D 7 I 6 M 2 D 32 I 27 M 3 D 418 I 411 M 8 D 109 I 101 M 2 D 4 I 3 M 7 D 138 I 145 M 4 D 4 I 2 M 6 D 5 I 3 M 1 D 88 I 95 M 1 D 21 I 26 M 4 D 43 I 57 M 3 D 13 I 13 M 2 D 168 I 149 M 2 D 277 I 263 M 1 D 14 I 11 M 2 D 133 I 144 M 2 D 179 I 174 M 5 D 156 I 128 M 4 D 94 I 99 M 2 D 2 I 2 M 2 D 33 I 27 M 3 D 481 I 496 M 8 D 4 I 2 M 8 D 142 I 169 M 2 D 317 I 358 M 7 D 1 I 1 M 1 D 150 I 153 M 3 D 7 I 7 M 3 D 71 I 86 M 3 D 44 I 61 M 1 D 229 I 272 M 1 D 319 I 352 M 1 D 626 I 679 M 7 D 95 I 107 M 2 D 142 I 163 M 1 D 158 I 163 M 3 D 126 I 116 M 4 D 68 I 79 M 1 D 22 I 22 M 3 D 78 I 82 M 15 D 71 I 70 M 3 D 149 I 151 M 1 D 1 I 1 M 2 D 418 I 430 M 4 D 2 I 2 M 3 D 28 I 40 M 4 D 90 I 87 M 3 D 50 I 58 M 3 D 243 I 236 M 2 D 307 I 320 M 2 D 89 I 107 M 3 D 9 I 5 M 1 D 90 I 74 M 6 D 6 I 7 M 2 D 96 I 80 M 2 D 123 I 111 M 2 D 50 I 41 M 1 D 261 I 280 M 2 D 1 I 1 M 4 D 35 I 39 M 3 D 78 I 81 M 5 D 131 I 115 M 1 D 139 I 141 M 8 D 6 I 7 M 1 D 193 I 171 M 2 D 7 I 5 M 9 D 11 I 11 M 6 D 387 I 362 M 4 D 833 I 919 M 1 D 9 I 7 M 12 D 143 I 145 M 2 D 2 I 2 M 2 D 54 I 65 M 1 D 523 I 537 M 2 D 286 I 294 M 6 D 4 I 3 M 7 D 107 I 91 M 8 D 284 I 285 M 2 D 5 I 4 M 2 D 290 I 303 M 3 D 16 I 19 M 3 D 245 I 298 M 6 D 48 I 47 M 2 D 48 I 43 M 6 D 76 I 82 M 6 D 47 I 54 M 1 D 23 I 18 M 1 D 290 I 310 M 1 D 5 I 5 M 1 D 448 I 534 M 1 D 152 I 190 M 3 D 12 I 9 M 8 D 151 I 147 M 6 D 13 I 10 M 7 D 2 I 2 M 11 D 44 I 40 M 6 D 71 I 77 M 4 D 41 I 34 M 7 D 33 I 35 M 3 D 213 I 202 M 5 D 127 I 110 M 5 D 255 I 218 M 3 D 377 I 370 M 8 D 6 I 4 M 1 D 3 I 3 M 7 D 8 I 10 M 3 D 282 I 265 M 3 D 231 I 229 M 1 D 28 I 33 M 2 D 65 I 68 M 1 D 166 I 155 M 10 D 67 I 61 M 2 D 221 I 230 M 4 D 269 I 237 M 2 D 84 I 74 M 2 D 197 I 178 M 6 D 14 I 12 M 1 D 98 I 99 M 1 D 1 I 1 M 1 D 42 I 35 M 4 D 35 I 25 M 2 D 2 I 2 M 5 D 187 I 181 M 7 D 1 I 1 M 1 D 247 I 232 M 5 D 5 I 5 M 5 D 352 I 323 M 1 D 134 I 111 M 1 D 419 I 354 M 2 D 1 I 1 M 7 D 10 I 9 M 1 D 16 I 13 M 2 D 22 I 17 M 6 D 161 I 166 M 3 D 39 I 35 M 1 D 242 I 220 M 9 D 203 I 195 M 1 D 44 I 42 M 2 D 2 I 2 M 4 D 72 I 81 M 9 D 163 I 155 M 9 D 142 I 138 M 6 D 187 I 156 M 2 D 98 I 99 M 1 D 93 I 76 M 4 D 50 I 43 M 4 D 201 I 180 M 1 D 30 I 25 M 2 D 9 I 10 M 7 D 228 I 228 M 2 D 106 I 92 M 5 D 92 I 87 M 2 D 1 I 1 M 1 D 6 I 5 M 2 D 81 I 72 M 5 D 11 I 9 M 2 D 17 I 20 M 4 D 7 I 6 M 4 D 622 I 628 M 5 D 1 I 1 M 1 D 1 I 1 M 3 D 437 I 412 M 4 D 5 I 5 M 5 D 278 I 264 M 3 D 7 I 5 M 1 D 112 I 123 M 6 D 262 I 280 M 2 D 46 I 52 M 1 D 88 I 87 M 1 D 17 I 18 M 6 D 568 I 541 M 4 D 93 I 69 M 1 D 79 I 74 M 7 D 107 I 98 M 2 D 6 I 5 M 4 D 4 I 3 M 1 D 250 I 249 M 2 D 41 I 38 M 7 D 259 I 258 M 11 D 4 I 7 M 4 D 36 I 30 M 3 D 8 I 7 M 10 D 53 I 60 M 2 D 83 I 94 M 2 D 8 I 6 M 1 D 346 I 341 M 5 D 86 I 76 M 4 D 13 I 14 M 2 D 541 I 592 M 3 D 74 I 69 M 5 D 79 I 68 M 7 D 103 I 107 M 3 D 55 I 53 M 3 D 5 I 3 M 1 D 95 I 98 M 4 D 14 I 17 M 1 D 119 I 136 M 1 D 150 I 137 M 1 D 1 I 1 M 3 D 148 I 161 M 2 D 4 I 6 M 3 D 6 I 6 M 2 D 162 I 172 M 4 D 172 I 173 M 8 D 291 I 298 M 4 D 214 I 229 M 2 D 38 I 29 M 5 D 189 I 166 M 2 D 279 I 276 M 1 D 218 I 213 M 7 D 42 I 40 M 3 D 359 I 327 M 18 D 77 I 79 M 1 D 13 I 10 M 3 D 4 I 4 M 1 D 173 I 173 M 2 D 19 I 23 M 5 D 617 I 634 M 3 D 4 I 5 M 2 D 18 I 22 M 1 D 303 I 295 M 7 D 73 I 91 M 10 D 400 I 421 M 2 D 152 I 152 M 2 D 306 I 295 M 2 D 8 I 7 M 3 D 396 I 391 M 3 D 9 I 8 M 1 D 50 I 48 M 2 D 16 I 12 M 1 D 17 I 22 M 5 D 373 I 363 M 7 D 250 I 283 M 1 D 331 I 353 M 6 D 134 I 126 M 5 D 28 I 28 M 4 D 47 I 43 M 4 D 22 I 22 M 1 D 2 I 2 M 2 D 149 I 149 M 2 D 163 I 169 M 7 D 6 I 5 M 12 D 9 I 13 M 6 D 140 I 130 M 2 D 18 I 15 M 2 D 367 I 384 M 3 D 2 I 3 M 4 D 104 I 118 M 8 D 128 I 123 M 2 D 115 I 98 M 3 D 84 I 88 M 2 D 344 I 342 M 4 D 6 I 4 M 2 D 149 I 150 M 1 D 98 I 97 M 1 D 18 I 14 M 7 D 139 I 155 M 2 D 4 I 4 M 4 D 8 I 8 M 2 D 115 I 128 M 1 D 24 I 19 M 4 D 48 I 43 M 2 D 268 I 281 M 3 D 167 I 161 M 2 D 3 I 2 M 12 D 179 I 177 M 9 D 36 I 31 M 6 D 149 I 153 M 5 D 184 I 176 M 1 D 267 I 284 M 5 D 31 I 33 M 3 D 1 I 1 M 4 D 481 I 491 M 3 D 7 I 6 M 3 D 64 I 63 M 5 D 5 I 4 M 1 D 79 I 72 M 2 D 7 I 5 M 4 D 366 I 362 M 7 D 444 I 445 M 1 D 8 I 6 M 3 D 226 I 211 M 1 D 210 I 199 M 3 D 53 I 45 M 3 D 23 I 25 M 5 D 97 I 91 M 3 D 61 I 57 M 1 D 1 I 1 M 1 D 1 I 1 M 1 D 6 I 5 M 2 D 3 I 3 M 2 D 200 I 180 M 1 D 233 I 250 M 3 D 208 I 232 M 1 D 99 I 94 M 9 D 24 I 27 M 8 D 87 I 87 M 2 D 205 I 192 M 8 D 40 I 38 M 1 D 14 I 18 M 3 D 39 I 43 M 2 D 250 I 285 M 2 D 14 I 14 M 2 D 343 I 350 M 4 D 364 I 368 M 1 D 427 I 419 M 4 D 189 I 176 M 5 D 313 I 286 M 1 D 7 I 5 M 4 D 71 I 86 M 11 D 6 I 4 M 4 D 85 I 81 M 4 D 132 I 141 M 3 D 1 I 1 M 2 D 159 I 180 M 7 D 13 I 13 M 1 D 62 I 61 M 5 D 3 I 3 M 2 D 36 I 39 M 1 D 166 I 154 M 3 D 211 I 185 M 7 D 407 I 440 M 2 D 9 I 13 M 11 D 172 I 170 M 2 D 74 I 67 M 1 D 8 I 8 M 8 D 175 I 179 M 13 D 239 I 243 M 2 D 7 I 6 M 9 D 184 I 176 M 3 D 79 I 82 M 1 D 523 I 485 M 3 D 53 I 50 M 2 D 178 I 168 M 1 D 6 I 8 M 4 D 56 I 46 M 10 D 77 I 74 M 2 D 1 I 1 M 3 D 9 I 6 M 1 D 47 I 35 M 4 D 1 I 1 M 1 D 64 I 49 M 3 D 303 I 300 M 1 D 10 I 11 M 3 D 197 I 190 M 4 D 227 I 250 M 1 D 84 I 75 M 2 D 556 I 566 M 3 D 49 I 43 M 5 D 120 I 127 M 5 D 52 I 45 M 2 D 102 I 111 M 3 D 16 I 12 M 2 D 328 I 307 M 2 D 5 I 6 M 7 D 127 I 120 M 4 D 324 I 299 M 4 D 60 I 50 M 1 D 378 I 389 M 6 D 67 I 58 M 3 D 64 I 45 M 6 D 187 I 203 M 4 D 17 I 13 M 1 D 123 I 118 M 3 D 263 I 286 M 2 D 53 I 62 M 3 D 89 I 101 M 5 D 26 I 23 M 7 D 45 I 51 M 3 D 613 I 567 M 5 D 2 I 2 M 2 D 34 I 39 M 4 D 51 I 54 M 12 D 136 I 159 M 4 D 79 I 95 M 3 D 96 I 92 M 5 D 1177 I 1127
Traceback (most recent call last):
File "/foo/bar/software/marginAlign/submodules/jobTree/src/jobTreeSlave.py", line 271, in main
defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth)
File "/foo/bar/software/marginAlign/submodules/jobTree/scriptTree/stack.py", line 153, in execute
self.target.run()
File "/foo/bar/software/marginAlign/submodules/jobTree/scriptTree/target.py", line 197, in run
func(*((self,) + tuple(self.args)), **self.kwargs)
File "/foo/bar/software/marginAlign/src/margin/marginCallerLib.py", line 57, in posteriorProbabilityCalculationTargetFn
tempPosteriorProbsFile, options.alignmentModel))
File "/foo/bar/software/marginAlign/submodules/sonLib/bioio.py", line 182, in system
sts = subprocess.call(command, shell=True, bufsize=-1, stdout=sys.stdout, stderr=sys.stderr)
File "/usr/lib/python2.7/subprocess.py", line 523, in call
return Popen(*popenargs, **kwargs).wait()
File "/usr/lib/python2.7/subprocess.py", line 711, in init
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1343, in _execute_child
raise child_exception
OSError: [Errno 7] Argument list too long
Exiting the slave because of a failed job on host thecomputername
Due to failure we are reducing the remaining retry count of job /foo/bar/data/jobTree/jobs/t0/t3/t3/t0/job to 0
We have set the default memory of the failed job to 12884901888 bytes

marginStats --mismatchesPerAlignedBase MarginAlign_em_bwa_pass2D_merged.sam pass_2d_merged.fastq ../RefSeq.fasta

Traceback (most recent call last): File "/Users/martinsmith/apps/marginAlign/src/margin/marginStats.py", line 97, in <module> main() File "/Users/martinsmith/apps/marginAlign/src/margin/marginStats.py", line 70, in main referenceFastaFile, globalAlignment=not options.localAlignment) File "/Users/martinsmith/apps/marginAlign/src/margin/utils.py", line 379, in getReadAlignmentStats refSequences[sam.getrname(aR.rname)], aR, globalAlignment), samIterator(sam)) File "/Users/martinsmith/apps/marginAlign/src/margin/utils.py", line 379, in <lambda> refSequences[sam.getrname(aR.rname)], aR, globalAlignment), samIterator(sam)) File "/Users/martinsmith/apps/marginAlign/src/margin/utils.py", line 308, in __init__ for aP in AlignedPair.iterator(alignedRead, self.refSeq, self.readSeq): File "/Users/martinsmith/apps/marginAlign/src/margin/utils.py", line 274, in iterator if aP.getReadBase().upper() != alignedSegment.query_alignment_sequence[readPos].upper(): IndexError: string index out of range

Hi,
Can we use .fasta as input read files?
Is it hard-coded to work only with only .fastaq files as input? If yes, where is the code for that?

The tests reads.fq file is too small to provide a thorough test. I propose we include around 20 reads in the file - this will provide a better sampling for testing purposes.

I followed the instructions and everything seems to be fine up to "make test". It was successful without using the virtualenv. And then when I tried to call marginAlign, I got "command not found". Not sure what I missed and I'd appreciate any help. Many thanks!

[miten@ku margin]$ ./marginAlign tests/reads.fq tests/reference.fa tests/test.sam --jobTree ./jobTree
The job seems to have left a log file, indicating failure: /hive/users/miten/pipeline_full_runs/marginAlign/margin/jobTree/jobs/job
Reporting file: /hive/users/miten/pipeline_full_runs/marginAlign/margin/jobTree/jobs/log.txt
log.txt: ---JOBTREE SLAVE OUTPUT LOG---
log.txt: /bin/sh: line 1: 19327 Done echo cigar: RAT_1_read_1 0 38435 + HUMAN 0 57553 +
1 D 41310 I 23895 M 93 D 1 M 16 I 1 M 1 I 3 M 4 I 2 M 8 D 1 M 14 I 1 M 27 D 1 M 89 D 1 M 5 I 1 M 7
D 4 M 13 D 36 I 135 M 15 I 1 M 8 I 1 M 32 D 1 M 6 D 1 M 9 D 1 M 5 I 2 M 7 D 1 M 32 D 1 M 51 D 4 M
4 D 2 M 3 I 1 M 9 D 5 M 18 D 4 M 59 I 1 M 3 I 2 M 25 I 1 M 27 D 1 M 9 I 1 M 4 I 1 M 5 I 2 M 8 D 1
M 13 D 2 M 17 I 3 M 9 I 1 M 3 D 3 M 15 I 3 M 13 D 2 M 64 D 1 M 17 I 8 M 2 I 3 M 3 I 1 M 2 I 1 M 1
1 I 1 M 7 I 1 M 3 I 6 M 46 I 2 M 38 I 3 M 21 D 1 M 7 I 1 M 26 I 1 M 2 D 1 M 5 D 2 M 1 D 1 M 4 D 5
M 3 D 1 M 1 D 5 M 23 D 3 M 21 I 3 M 4 D 1 M 6 I 4 M 2 I 2 M 4 I 1 M 2 I 2 M 5 I 1 M 11 D 1 M 9 D 1
M 31 D 2 M 3 I 1 M 32 I 2 M 2 I 1 M 4 I 2 M 19 D 1 M 13 D 3 M 4 D 1 M 13 D 2 M 1 D 12 M 5 D 2 M 3
D 1 M 4 D 3 M 14 D 12 M 3 D 3 M 1 D 1 M 33 D 2 M 19 D 1 M 4 D 5 M 63 D 2 M 3 D 3 M 17 D 1 M 12 D
2 M 19 D 1 M 4 D 3 M 11 I 1 M 72 I 6 M 2 I 2 M 2 I 2 M 5 I 1 M 4 I 7 M 4 I 2 M 3 I 1 M 6 I 2 M 2 I
4 M 4 I 3 M 3 I 4 M 3 I 1 M 3 I 3 M 1 I 8 M 4 I 4 M 2 I 2 M 3 I 2 M 9 I 5 M 1 I 3 M 11 I 5 M 21 I
1 M 7 I 1 M 11 I 1 M 27 I 3 M 4 D 3 M 9 D 3 M 3 I 4 M 4 I 1 M 3 I 1 M 3 I 1 M 6 D 1 M 16 D 2 M 5
I 1 M 61 D 1 M 17 D 6 M 3 D 2 M 1 D 2 M 4 D 6 M 11 D 1 M 55 D 1 M 11 D 1 M 9 I 1 M 7 D 2 M 4 I 2 M
23 I 3 M 3 I 5 M 5 I 2 M 1 I 8 M 2 I 3 M 1 I 6 M 3 I 1 M 41 D 2 M 48 D 3 M 33 D 1 M 9 I 1 M 5 I 2
M 18 D 1 M 8 D 14027 I 12195
19328 Segmentation fault | cactus_realign /tmp/tmpiZzkHK/localTempDir/ref.fa /tmp/tmpiZz
kHK/localTempDir/read.fa --diagonalExpansion=10 --splitMatrixBiggerThanThis=3000 --loadHmm hmm.txt
--gapGamma=0.5 --matchGamma=0.0 >> /hive/users/miten/pipeline_full_runs/marginAlign/margin/jobTre
e/jobs/gTD1/tmp_BO6zheoVpY/tempOutput_1.txt
Traceback (most recent call last):
File "/hive/users/miten/pipeline_full_runs/marginAlign/margin/submodules/jobTree/src/jobTreeSlav
e.py", line 271, in main
defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth)
File "/hive/users/miten/pipeline_full_runs/marginAlign/margin/submodules/jobTree/scriptTree/stac
k.py", line 153, in execute
self.target.run()
File "/hive/users/miten/pipeline_full_runs/marginAlign/margin/submodules/jobTree/scriptTree/targ
et.py", line 197, in run
func(_((self,) + tuple(self.args)), *_self.kwargs)
File "/hive/users/miten/pipeline_full_runs/marginAlign/margin/src/margin/marginAlignLib.py", lin
e 319, in realignCigarTargetFn
options.gapGamma, options.matchGamma, outputCigarFile))
File "/hive/users/miten/pipeline_full_runs/marginAlign/margin/submodules/sonLib/bioio.py", line
184, in system
raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts))
RuntimeError: Command: echo cigar: RAT_1_read_1 0 38435 + HUMAN 0 57553 + 1 D 41310 I 23895 M 93 D
1 M 16 I 1 M 1 I 3 M 4 I 2 M 8 D 1 M 14 I 1 M 27 D 1 M 89 D 1 M 5 I 1 M 7 D 4 M 13 D 36 I 135 M 1
5 I 1 M 8 I 1 M 32 D 1 M 6 D 1 M 9 D 1 M 5 I 2 M 7 D 1 M 32 D 1 M 51 D 4 M 4 D 2 M 3 I 1 M 9 D 5 M
18 D 4 M 59 I 1 M 3 I 2 M 25 I 1 M 27 D 1 M 9 I 1 M 4 I 1 M 5 I 2 M 8 D 1 M 13 D 2 M 17 I 3 M 9 I
1 M 3 D 3 M 15 I 3 M 13 D 2 M 64 D 1 M 17 I 8 M 2 I 3 M 3 I 1 M 2 I 1 M 11 I 1 M 7 I 1 M 3 I 6 M
46 I 2 M 38 I 3 M 21 D 1 M 7 I 1 M 26 I 1 M 2 D 1 M 5 D 2 M 1 D 1 M 4 D 5 M 3 D 1 M 1 D 5 M 23 D 3
M 21 I 3 M 4 D 1 M 6 I 4 M 2 I 2 M 4 I 1 M 2 I 2 M 5 I 1 M 11 D 1 M 9 D 1 M 31 D 2 M 3 I 1 M 32 I
2 M 2 I 1 M 4 I 2 M 19 D 1 M 13 D 3 M 4 D 1 M 13 D 2 M 1 D 12 M 5 D 2 M 3 D 1 M 4 D 3 M 14 D 12 M
3 D 3 M 1 D 1 M 33 D 2 M 19 D 1 M 4 D 5 M 63 D 2 M 3 D 3 M 17 D 1 M 12 D 2 M 19 D 1 M 4 D 3 M 11
I 1 M 72 I 6 M 2 I 2 M 2 I 2 M 5 I 1 M 4 I 7 M 4 I 2 M 3 I 1 M 6 I 2 M 2 I 4 M 4 I 3 M 3 I 4 M 3 I
1 M 3 I 3 M 1 I 8 M 4 I 4 M 2 I 2 M 3 I 2 M 9 I 5 M 1 I 3 M 11 I 5 M 21 I 1 M 7 I 1 M 11 I 1 M 27
I 3 M 4 D 3 M 9 D 3 M 3 I 4 M 4 I 1 M 3 I 1 M 3 I 1 M 6 D 1 M 16 D 2 M 5 I 1 M 61 D 1 M 17 D 6 M
3 D 2 M 1 D 2 M 4 D 6 M 11 D 1 M 55 D 1 M 11 D 1 M 9 I 1 M 7 D 2 M 4 I 2 M 23 I 3 M 3 I 5 M 5 I 2
M 1 I 8 M 2 I 3 M 1 I 6 M 3 I 1 M 41 D 2 M 48 D 3 M 33 D 1 M 9 I 1 M 5 I 2 M 18 D 1 M 8 D 14027 I
12195 | cactus_realign /tmp/tmpiZzkHK/localTempDir/ref.fa /tmp/tmpiZzkHK/localTempDir/read.fa --di
agonalExpansion=10 --splitMatrixBiggerThanThis=3000 --loadHmm hmm.txt --gapGamma=0.5 --mat
chGamma=0.0 >> /hive/users/miten/pipeline_full_runs/marginAlign/margin/jobTree/jobs/gTD1/tmp_BO6zh
eoVpY/tempOutput_1.txt exited with non-zero status 139
Exiting the slave because of a failed job on host ku.sdsc.edu
Due to failure we are reducing the remaining retry count of job /hive/users/miten/pipeline_full_ru
ns/marginAlign/margin/jobTree/jobs/job to 0
We have set the default memory of the failed job to 2147483648 bytes

FAIL: testMarginCaller1Ref (main.TestCase)

Traceback (most recent call last):
File "tests/tests.py", line 64, in testMarginCaller1Ref
self.validateSam("./tests/input1Ref.sam")
File "tests/tests.py", line 26, in validateSam
self.assertTrue(os.path.isfile(samFile))
AssertionError: False is not true

FAIL: testMarginCallerNoMarginalize1Ref (main.TestCase)

Traceback (most recent call last):
File "tests/tests.py", line 71, in testMarginCallerNoMarginalize1Ref
self.validateSam("./tests/input1Ref.sam")
File "tests/tests.py", line 26, in validateSam
self.assertTrue(os.path.isfile(samFile))
AssertionError: False is not true

It seems all the tests for alignment failed with a similar error:

======================================================================
ERROR: testMarginAlignBwa (__main__.TestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "./tests/tests.py", line 129, in testMarginAlignBwa
    self.runMarginAlign(self.readFastqFile1, self.referenceFastaFile1, "--bwa")
  File "./tests/tests.py", line 88, in runMarginAlign
    readAlignmentStats = self.validateSam(self.outputSamFile, readFastqFile, referenceFastaFile)
  File "./tests/tests.py", line 60, in validateSam
    referenceFastaFile, globalAlignment=True)
  File "/genomicslab/datasets/volume2/shomron_home_p2/artemd/tools/marginAlign/src/margin/utils.py", line 379, in getReadAlignmentStats
    refSequences[sam.getrname(aR.rname)], aR, globalAlignment), samIterator(sam))
  File "/genomicslab/datasets/volume2/shomron_home_p2/artemd/tools/marginAlign/src/margin/utils.py", line 379, in <lambda>
    refSequences[sam.getrname(aR.rname)], aR, globalAlignment), samIterator(sam))
  File "/genomicslab/datasets/volume2/shomron_home_p2/artemd/tools/marginAlign/src/margin/utils.py", line 308, in __init__
    for aP in AlignedPair.iterator(alignedRead, self.refSeq, self.readSeq):
  File "/genomicslab/datasets/volume2/shomron_home_p2/artemd/tools/marginAlign/src/margin/utils.py", line 274, in iterator
    if aP.getReadBase().upper() != alignedSegment.query_alignment_sequence[readPos].upper():
IndexError: string index out of range

I have no idea what might cause the error.

Information about the system:
Version of bwa "0.7.15-r1142-dirty"
Version of lastal "lastal 801"
List of python packages installed:
['atlas==0.27.0', 'avro==1.8.1', 'biopython==1.64', 'bx-python==0.7.3', 'certifi==2016.2.28', 'cffi==1.7.0', 'click==6.6', 'cmd2==0.6.8', 'cnvkit==0.7.11', 'conversion==0.0.3', 'crossmap==0.2.3', 'cryptography==1.4', 'cycler==0.10.0', 'cython==0.21.1', 'docopt==0.6.2', 'ecdsa==0.13', 'enum34==1.1.6', 'fabric==1.12.0', 'flask==0.10.1', 'functools32==3.2.3.post2', 'future==0.15.2', 'gdc-client==1.0.1', 'h5py==2.6.0', 'htseq==0.6.1', 'idna==2.1', 'intervaltree==2.0.4', 'ipaddress==1.0.16', 'iso8601==0.1.11', 'itsdangerous==0.24', 'jinja2==2.8', 'jsonschema==2.5.1', 'lifelines==0.9.2', 'lxml==3.5.0b1', 'macs2==2.0.10.20131216', 'markupsafe==0.23', 'matplotlib==1.5.1', 'misopy==0.5.3', 'mpi4py==2.0.0', 'multiqc==0.8', 'myriad==0.1.3', 'mysql-python==1.2.5', 'nanonet==2.0.0', 'nanoraw==0.2', 'ndg-httpsclient==0.4.2', 'numpy==1.11.2', 'pandas==0.18.1', 'paramiko==1.17.2', 'parcel==0.1.13', 'pathoscope==2.0.6', 'pbalign==0.3.0', 'pbcommand==0.3.29', 'pbcore==1.2.10', 'pillow==3.2.0', 'pip==9.0.1', 'plotly==1.12.5', 'poreseq==0.1', 'poretools==0.6.0', 'progressbar==2.3', 'pyasn1==0.1.9', 'pycparser==2.14', 'pycrypto==2.6.1', 'pyfaidx==0.4.7.1', 'pyinstaller==3.2', 'pyopenssl==16.0.0', 'pyparsing==2.1.5', 'pysam==0.9.1.4', 'pysqlite==2.6.3', 'python-dateutil==2.5.3', 'pytz==2016.6.1', 'pyvcf==0.6.8', 'pyyaml==3.11', 'reportlab==3.3.0', 'requests==2.5.1', 'rpy2==2.8.3', 'rseqc==2.6.4', 'scipy==0.18.1', 'seaborn==0.7.1', 'setuptools==19.2', 'simplejson==3.10.0', 'singledispatch==3.4.0.3', 'six==1.10.0', 'sortedcontainers==1.5.3', 'tabulate==0.7.5', 'termcolor==1.1.0', 'theano==0.8.2', 'threadpool==1.2.7', 'tqdm==4.8.4', 'urllib3==1.16', 'virtualenv==15.0.2', 'werkzeug==0.11.10', 'xmlbuilder==1.0']