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Documentation - minor error

in the README.md file, you have

tar -xzf PanGIA_20180915_taxonomy.tar.gz
tar -xzf PanGIA_20180915_NCBI_genomes_refseq89_BAV.fa.tar
tar -xzf PanGIA_20180915_NCBI_genomes_refseq89_adds.fa.tar
tar -xzf PanGIA_20180915_NCBI_genomes_refseq89_Human_GRCh38.p12.fa.tar

as the listed commands. However, as the tarballs are not gzipped, this does not work, and should be changed to

tar -xvf PanGIA_20180915_taxonomy.tar.gz
tar -xvf PanGIA_20180915_NCBI_genomes_refseq89_BAV.fa.tar
tar -xvf PanGIA_20180915_NCBI_genomes_refseq89_adds.fa.tar
tar -xvf PanGIA_20180915_NCBI_genomes_refseq89_Human_GRCh38.p12.fa.tar

Database downloads

Hello,
I am trying to download the PanGIA databases from https://edge-dl.lanl.gov/PanGIA/database/. The site is currently down for maintenance. Is there another download location? I did did find a ftp site but the databases appear to be older versions from 20180227 instead of 20180915.
Thanks,
Scott

PanGIA is broken: throws an internal `KeyError` when running test command

I installed PanGIA by cloning this repository and then downloading these two files:

$ curl -O https://edge-dl.lanl.gov/PanGIA/database/PanGIA_20190830_taxonomy.tar.gz
$ curl -O https://edge-dl.lanl.gov/PanGIA/database/PanGIA_20190830_NCBI_genomes_refseq89_BAV.fa.mmi.tar.gz

$ tar xzf PanGIA_20190830_taxonomy.tar.gz
$ tar xzf PanGIA_20190830_NCBI_genomes_refseq89_BAV.fa.mmi.tar.gz

Next, I ran the following command to test if PanGIA could classify a bunch of artificially generated reads:

(pangia) xapple@server ~ $ ~/programs/pangia/bin/pangia.py --threads 4 --database ~/databases/pangia/PanGIA/NCBI_genomes_refseq89_BAV.fa --mode report --outdir ~/runs/pangia_test/ --readmapper minimap2 --prefix sample --input ~/runs/pangia_test/reads_fwd.fastq.gz ~/runs/pangia_test/reads_rev.fastq.gz

But it throws a KeyError and seems to be non-functional.

[00:00:00] Starting PanGIA 1.0.0-RC6.1
[00:00:00] Temporary directory '~/runs/pangia_test//sample_tmp' found. Deleting directory...
[00:04:53] Arguments and dependencies checked:
[00:04:53]     Input reads       : ['~/runs/pangia_test/reads_fwd.fastq.gz', '~/runs/pangia_test/reads_rev.fastq.gz']
[00:04:53]     Input SAM file    : ~/runs/pangia_test//sample.pangia.sam
[00:04:53]     Input background  : None
[00:04:53]     Save background   : None
[00:04:53]     Scoring method    : standalone
[00:04:53]     Scoring parameter : 0.5:0.99
[00:04:53]     Database          : ['~/databases/pangia/PanGIA/NCBI_genomes_refseq89_BAV.fa.mmi']
[00:04:53]     Abundance         : DEPTH_COV
[00:04:53]     Output path       : ~/runs/pangia_test/
[00:04:53]     Prefix            : sample
[00:04:53]     Mode              : report
[00:04:53]     Specific taxid    : None
[00:04:53]     Threads           : 4
[00:04:53]     First #refs in XA : 30
[00:04:53]     Extra NM in XA    : 1
[00:04:53]     Minimal score     : 0
[00:04:53]     Minimal RSNB      : 2.5
[00:04:53]     Minimal reads     : 10
[00:04:53]     Minimal linear len: 200
[00:04:53]     Minimal genome cov: 0.004
[00:04:53]     Minimal depth (DC): 0.01
[00:04:53]     Minimal RSDCnr    : 0.0009
[00:04:53]     Aligner option    : -A1 -B2 -k 40 -m 60 -x sr -p 1 -N 30
[00:04:53]     Aligner seed len  : 40
[00:04:53]     Aligner min score : 60
[00:04:53]     Aligner path      : ~/mambaforge/envs/pangia/bin/minimap2
[00:04:53]     Samtools path     : ~/mambaforge/envs/pangia/bin/samtools
[00:04:53] Loading taxonomy information...
[00:05:00] Done.
[00:05:00] Loading pathogen information...
[00:05:00] Done. 2817 pathogens loaded.
[00:05:00] Loading taxonomic uniqueness information...
[00:05:00] Done. 31177 taxonomic uniqueness loaded.
[00:05:00] Loading sizes of genomes...
[00:05:55] Done. 1061 target and 0 host genome(s) loaded.
[00:05:55] Running read-mapping...
[00:05:55] Mapping to ~/databases/pangia/PanGIA/NCBI_genomes_refseq89_BAV.fa.mmi...
[00:06:53] Done mapping reads to the database(s).
[00:06:53] Merging SAM files...
[00:06:55] Logfile saved to ~/runs/pangia_test//sample.pangia.log.
[00:06:55] Done. Mapped SAM file saved to ~/runs/pangia_test//sample.pangia.sam.
[00:06:55] Total number of input reads: 400013
[00:06:55] Total number of mapped reads: 186478
[00:06:55] Total number of host reads: 0 (0.00%)
[00:06:55] Total number of ignored reads (cross superkingdom): 349 (0.19%)
[00:06:55] Processing SAM file...
[00:06:55] Parsing SAM files with 4 subprocesses...
[00:06:59] Merging results...
[00:06:59] Done.
[00:06:59] Calculating linear length...
[00:07:02] Done processing SAM file, 184670 alignment(s).
[00:07:02] Rolling up taxonomies...
[00:07:02] 17 strain(s) mapped.
Traceback (most recent call last):
  File "~/programs/pangia/bin/pangia.py", line 2320, in <module>
    res_rollup = taxonomyRollUp(res, patho_meta, mapped_r_cnt, argvs.minRsnb, argvs.minReads, argvs.minLen, argvs.minCov, argvs.minDc)
  File "~/programs/pangia/bin/pangia.py", line 1199, in taxonomyRollUp
    genome_size[taxid]
KeyError: '1582156.1'

keyError and taxid not is genome_size

[00:00:00] Starting PanGIA 1.0.0-RC6.1
[00:00:00] Arguments and dependencies checked:
[00:00:00] Input reads : ['/data2/data/mNGS/test_data/SRR172902.fastq']
[00:00:00] Input SAM file : ../result//SRR172902.pangia.sam
[00:00:00] Input background : None
[00:00:00] Save background : None
[00:00:00] Scoring method : standalone
[00:00:00] Scoring parameter : 0.5:0.99
[00:00:00] Database : ['/home/kdws/workdir/database/PanGIA/PanGIA/NCBI_genomes_refseq89_BAV.fa.mmi']
[00:00:00] Abundance : DEPTH_COV
[00:00:00] Output path : ../result/
[00:00:00] Prefix : SRR172902
[00:00:00] Mode : report
[00:00:00] Specific taxid : None
[00:00:00] Threads : 12
[00:00:00] First #refs in XA : 30
[00:00:00] Extra NM in XA : 1
[00:00:00] Minimal score : 0
[00:00:00] Minimal RSNB : 2.5
[00:00:00] Minimal reads : 10
[00:00:00] Minimal linear len: 200
[00:00:00] Minimal genome cov: 0.004
[00:00:00] Minimal depth (DC): 0.01
[00:00:00] Minimal RSDCnr : 0.0009
[00:00:00] Aligner option : -A1 -B2 -k 40 -m 60 -x sr -p 1 -N 30
[00:00:00] Aligner seed len : 40
[00:00:00] Aligner min score : 60
[00:00:00] Aligner path : /home/kdws/miniconda3/envs/mNGS/bin/minimap2
[00:00:00] Samtools path : /home/kdws/miniconda3/envs/mNGS/bin/samtools
[00:00:00] Loading taxonomy information...
[00:00:04] Done.
[00:00:04] Loading pathogen information...
[00:00:04] Done. 2817 pathogens loaded.
[00:00:04] Loading taxonomic uniqueness information...
[00:00:04] Done. 31177 taxonomic uniqueness loaded.
[00:00:04] Loading sizes of genomes...
[00:01:05] Done. 1061 target and 0 host genome(s) loaded.
[00:01:05] Running read-mapping...
[00:01:05] Mapping to /home/kdws/workdir/database/PanGIA/PanGIA/NCBI_genomes_refseq89_BAV.fa.mmi...
[00:03:08] Done mapping reads to the database(s).
[00:03:08] Merging SAM files...
[00:03:52] Logfile saved to ../result//SRR172902.pangia.log.
[00:03:52] Done. Mapped SAM file saved to ../result//SRR172902.pangia.sam.
[00:03:52] Total number of input reads: 13124130
[00:03:52] Total number of mapped reads: 3361870
[00:03:52] Total number of host reads: 0 (0.00%)
[00:03:52] Total number of ignored reads (cross superkingdom): 1857 (0.06%)
[00:03:52] Processing SAM file...
[00:03:52] Parsing SAM files with 12 subprocesses...
[00:04:22] Merging results...
[00:04:22] Done.
[00:04:22] Calculating linear length...
[00:05:02] Done processing SAM file, 3360013 alignment(s).
[00:05:02] Rolling up taxonomies...
[00:05:02] 994 strain(s) mapped.
Traceback (most recent call last):
File "pangia.py", line 2320, in
res_rollup = taxonomyRollUp(res, patho_meta, mapped_r_cnt, argvs.minRsnb, argvs.minReads, argvs.minLen, argvs.minCov, argvs.minDc)
File "pangia.py", line 1199, in taxonomyRollUp
genome_size[taxid]
KeyError: '1133852'

PanGIA/pangia.py

Line 1199 in 3f7fe3d

genome_size[taxid]

PanGIA basic installation is broken

I followed the instructions in the README to install PanGIA. This did not work. It seems like this software is left in a non-functional state.

The following command (from the QUICK INSTALLATION section):

$ curl -O https://edge-dl.lanl.gov/PanGIA/database/PanGIA_20180915_taxonomy.tar.gz

Results in the following file being downloaded:

<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
<html><head>
<title>404 Not Found</title>
</head><body>
<h1>Not Found</h1>
<p>The requested URL /PanGIA/database/PanGIA_20180915_taxonomy.tar.gz was not found on this server.</p>
</body></html>

Could you please fix PanGIA so that the bioinformatics community can actually install and use it? Thanks.

PanGIA-Docker error

Hello,
I installed the docker version of PanGIA. I ran some nanopore data using all 3 processes (pre-processing, PanGIA and supplementary classification). All finished running except PanGIA which had the following error in pangia.log:

[00:00:11] Running read-mapping...
[00:00:11] Mapping to /home/edge/edge_dev/scripts/microbial_profiling/../../database/PanGIA/NCBI_genomes_refseq89_BAV.fa...
[00:00:11] [ERROR] error occurred while running read mapping (code: 1, message: + minimap2 -aL -t 12 -x map-ont /home/edge/edge_dev/scripts/microbial_profiling/../../database/PanGIA/NCBI_genomes_refseq89_BAV.fa /home/edge/edge_dev/edge_ui/EDGE_output//9da940633105a9e2be60b7f0bf03add4/ReadsBasedAnalysis/Taxonomy/allReads.fastq

This is from process-current.log:
Tool (pangia) - PID: 17739, starting...
[RUN_TOOL] [pangia] COMMAND: uge-pangia.sh -i '/home/edge/edge_dev/edge_ui/EDGE_output//9da940633105a9e2be60b7f0bf03add4/ReadsBasedAnalysis/Taxonomy/allReads.fastq' -p allReads -o /home/edge/edge_dev/edge_ui/EDGE_output//9da940633105a9e2be60b7f0bf03add4/ReadsBasedAnalysis/Taxonomy/1_allReads/pangia -t 12 -d 'NCBI_genomes_refseq89_BAV.fa NCBI_genomes_refseq89_adds.fa' -x /home/edge/edge_dev/scripts/microbial_profiling/../../database/PanGIA -s n -b '' -r DEPTH_COV -T standalone -A 60 -W 24 -S 0 -R 10 -B 3 -L 200 -D 0.01 -G 0.005 -C 0.001 -a ' -se --nanopore'
[RUN_TOOL] [pangia] Logfile: /home/edge/edge_dev/edge_ui/EDGE_output//9da940633105a9e2be60b7f0bf03add4/ReadsBasedAnalysis/Taxonomy/log/allReads-pangia.log
[RUN_TOOL] [pangia] Error occured.
[RUN_TOOL] [pangia] Running time: 00:00:13

This is from error.log:
convert: unable to open image /home/edge/edge_dev/edge_ui/EDGE_output//9da940633105a9e2be60b7f0bf03add4/QcReads/Log_LengthvsQualityScatterPlot_kde.pdf': No such file or directory @ error/blob.c/OpenBlob/2643. convert: no images defined /home/edge/edge_dev/edge_ui/EDGE_output//9da940633105a9e2be60b7f0bf03add4/HTML_Report/images/QC_length_quality.png' @ error/convert.c/ConvertImageCommand/3046.
Use of uninitialized value in division (/) at /home/edge/edge_dev/scripts/pangia_report/create_pangia_report_w_temp.pl line 24.

Do you have any suggestions on how to resolve this issue with PanGIA?
Thanks,
Scott

Key error and custom database error

Hello,
I am having a couple of problems when trying to classify nanopore reads with PanGIA.

  1. When trying to classify a mix of 15 isolates PanGIA exits with the following error:
    (pangia.py -i /home/Analyzed_data/ATCC_gDNAs_plasmid_mix/mix.ghac.fastq -db /home/data0/pangia_db/PanGIA/NCBI_genomes_refseq89_*.fa -t 70 --keepTemp -sb -se -np )

Parsing SAM files with 70 subprocesses...
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/mnt/data0/miniconda3/envs/pangia/lib/python3.7/multiprocessing/pool.py", line 121, in worker
result = (True, func(*args, **kwds))
File "/home/pangia/pangia.py", line 714, in worker
lcr_lvl, lcr_name, lcr_info = lineageLCR(taxids)
File "/home/pangia/pangia.py", line 378, in lineageLCR
lng = t.taxid2lineageDICT(tid, 1, 1)
File "/home/pangia/taxonomy.py", line 265, in taxid2lineageDICT
return _taxid2lineage( tid, print_all_rank, print_strain, replace_space2underscore, output_type )
File "/home/pangia/taxonomy.py", line 305, in _taxid2lineage
rank = _getTaxRank(taxID)
File "/home/pangia/taxonomy.py", line 372, in _getTaxRank
return taxRanks[taxID]
KeyError: '134962'
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/home/pangia/pangia.py", line 2316, in
(res, mapped_r_cnt) = processSAMfile( os.path.abspath(samfile), argvs.threads, lines_per_process)
File "/home/pangia/pangia.py", line 921, in processSAMfile
results.append( job.get() )
File "/mnt/data0/miniconda3/envs/pangia/lib/python3.7/multiprocessing/pool.py", line 657, in get
raise self._value
KeyError: '134962'

  1. When trying to classify a single isolate with a custom built database, PanGIA exits with the following error:
    [00:05:49] Saving bitmasks in JSON format...
    [00:05:49] Done.
    Traceback (most recent call last):
    File "/home/DRDC/pangia/pangia.py", line 2357, in
    outputResultsAsReport( res_rollup, out_fp, argvs.relAbu, argvs.taxonomy, argvs.reportFields, argvs.scoreMethod, argvs.minScore, argvs.minCov, argvs.minRsnb, argvs.minReads, argvs.minLen, argvs.minDc, argvs.minRsdcnr, argvs.displayAll )
    File "/home/DRDC/pangia/pangia.py", line 1677, in outputResultsAsReport
    s = "%.6f"%res_rollup[tid]["S_SA_CL"] if res_rollup[tid]["S_SA_CL"] != "none" else "none"
    TypeError: must be real number, not str

Any help would be appreciated.
Thanks,
Scott

Mapping Issue

Hi everytime I run pangia I get this error message when its trying to map my reads could you tell me why?

[ERROR] error occurred while running read mapping (code: 1, message: + bwa mem -k40 -T60 -h100 -B2 -t24 database/NCBI_genomes_refseq89_BAV.fa SRR172902.fastq

  • gawk '-F\t' '!/^@/ { print }'
  • gawk '-F\t' '!and($2,256) && !and($2,2048) { print } END { print NR > "./SRR172902_tmp/raw_sam/NCBI_genomes_refseq89_BAV.fa.sam.count" }'
  • gawk '-F\t' '!and($2,4) { print }'
    ).

No taxid in taxRanks

I've run into this issue using PanGIA command line. Logs are attached:

[00:00:00] Starting PanGIA 1.0.0-RC6.1
[00:00:00] Arguments and dependencies checked:
[00:00:00]     Input reads       : ['/srv/test_fastq/strawman_pathogen-miseq_95gg9031_05vv10245.fastq']
[00:00:00]     Input SAM file    : /srv/strawman_pathogen-miseq_95gg9031_05vv10245.pangia.sam
[00:00:00]     Input background  : None
[00:00:00]     Save background   : None
[00:00:00]     Scoring method    : standalone
[00:00:00]     Scoring parameter : 0.5:0.99
[00:00:00]     Database          : ['database/NCBI_genomes_refseq89_BAV.fa.mmi']
[00:00:00]     Abundance         : DEPTH_COV
[00:00:00]     Output path       : /srv
[00:00:00]     Prefix            : strawman_pathogen-miseq_95gg9031_05vv10245
[00:00:00]     Mode              : report
[00:00:00]     Specific taxid    : None
[00:00:00]     Threads           : 8
[00:00:00]     First #refs in XA : 30
[00:00:00]     Extra NM in XA    : 1
[00:00:00]     Minimal score     : 0
[00:00:00]     Minimal RSNB      : 1
[00:00:00]     Minimal reads     : 3
[00:00:00]     Minimal linear len: 50
[00:00:00]     Minimal genome cov: 0.004
[00:00:00]     Minimal depth (DC): 0.01
[00:00:00]     Minimal RSDCnr    : 0.0009
[00:00:00]     Aligner option    : -x map-ont
[00:00:00]     Aligner seed len  : 40
[00:00:00]     Aligner min score : 60
[00:00:00]     Aligner path      : /opt/conda/envs/pangia/bin/minimap2
[00:00:00]     Samtools path     : /opt/conda/envs/pangia/bin/samtools
[00:00:00] Loading taxonomy information...
[00:00:08] Done.
[00:00:08] Loading pathogen information...
[00:00:08] Done. 2817 pathogens loaded.
[00:00:08] Loading taxonomic uniqueness information...
[00:00:08] Done. 31177 taxonomic uniqueness loaded.
[00:00:08] Loading sizes of genomes...
[00:00:08] Done. 9634 target and 0 host genome(s) loaded.
[00:00:08] Running read-mapping...
[00:00:08] Mapping to database/NCBI_genomes_refseq89_BAV.fa.mmi...
[WARNING]�[1;31m For a multi-part index, no @SQ lines will be outputted. Please use --split-prefix.�[0m
[M::main::12.096*1.00] loaded/built the index for 2010 target sequence(s)
[M::mm_mapopt_update::15.182*1.00] mid_occ = 236
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 2010
[M::mm_idx_stat::17.103*1.00] distinct minimizers: 154437548 (33.40% are singletons); average occurrences: 4.873; average spacing: 5.353
[M::worker_pipeline::31.420*2.60] mapped 799768 sequences
[M::main::42.605*2.18] loaded/built the index for 11332 target sequence(s)
[M::mm_mapopt_update::42.605*2.18] mid_occ = 236
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 11332
[M::mm_idx_stat::45.388*2.11] distinct minimizers: 139932295 (37.69% are singletons); average occurrences: 3.883; average spacing: 5.353
[M::worker_pipeline::58.889*2.95] mapped 799768 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -aL -t 8 -x map-ont database/NCBI_genomes_refseq89_BAV.fa.mmi /srv/test_fastq/strawman_pathogen-miseq_95gg9031_05vv10245.fastq
[M::main] Real time: 59.028 sec; CPU: 173.916 sec; Peak RSS: 11.823 GB
[00:01:08] Done mapping reads to the database(s).
[00:01:08] Merging SAM files...
[00:01:09] Logfile saved to /srv/strawman_pathogen-miseq_95gg9031_05vv10245.pangia.log.
[00:01:09] Done. Mapped SAM file saved to /srv/strawman_pathogen-miseq_95gg9031_05vv10245.pangia.sam.
[00:01:09] Total number of input reads: 1713173
[00:01:09] Total number of mapped reads: 41953
[00:01:09] Total number of host reads: 0 (0.00%)
[00:01:09] Total number of ignored reads (cross superkingdom): 29 (0.07%)
[00:01:09] Processing SAM file... 
[00:01:09] Parsing SAM files with 8 subprocesses...
[00:00:00] Starting PanGIA 1.0.0-RC6.1
[00:00:00] Temporary directory '/srv/strawman_pathogen-miseq_95gg9031_05vv10245_tmp' found. Deleting directory...
[00:00:00] Arguments and dependencies checked:
[00:00:00]     Input reads       : ['/srv/test_fastq/strawman_pathogen-miseq_95gg9031_05vv10245.fastq']
[00:00:00]     Input SAM file    : /srv/strawman_pathogen-miseq_95gg9031_05vv10245.pangia.sam
[00:00:00]     Input background  : None
[00:00:00]     Save background   : None
[00:00:00]     Scoring method    : standalone
[00:00:00]     Scoring parameter : 0.5:0.99
[00:00:00]     Database          : ['database/NCBI_genomes_refseq89_BAV.fa.mmi']
[00:00:00]     Abundance         : DEPTH_COV
[00:00:00]     Output path       : /srv
[00:00:00]     Prefix            : strawman_pathogen-miseq_95gg9031_05vv10245
[00:00:00]     Mode              : report
[00:00:00]     Specific taxid    : None
[00:00:00]     Threads           : 8
[00:00:00]     First #refs in XA : 30
[00:00:00]     Extra NM in XA    : 1
[00:00:00]     Minimal score     : 0
[00:00:00]     Minimal RSNB      : 1
[00:00:00]     Minimal reads     : 3
[00:00:00]     Minimal linear len: 50
[00:00:00]     Minimal genome cov: 0.004
[00:00:00]     Minimal depth (DC): 0.01
[00:00:00]     Minimal RSDCnr    : 0.0009
[00:00:00]     Aligner option    : -x map-ont
[00:00:00]     Aligner seed len  : 40
[00:00:00]     Aligner min score : 60
[00:00:00]     Aligner path      : /opt/conda/envs/pangia/bin/minimap2
[00:00:00]     Samtools path     : /opt/conda/envs/pangia/bin/samtools
[00:00:00] Loading taxonomy information...
[00:00:08] Done.
[00:00:08] Loading pathogen information...
[00:00:08] Done. 2817 pathogens loaded.
[00:00:08] Loading taxonomic uniqueness information...
[00:00:08] Done. 31177 taxonomic uniqueness loaded.
[00:00:08] Loading sizes of genomes...
[00:00:08] Done. 9634 target and 0 host genome(s) loaded.
[00:00:08] Running read-mapping...
[00:00:08] Mapping to database/NCBI_genomes_refseq89_BAV.fa.mmi...
[WARNING]�[1;31m For a multi-part index, no @SQ lines will be outputted. Please use --split-prefix.�[0m
[M::main::12.154*1.00] loaded/built the index for 2010 target sequence(s)
[M::mm_mapopt_update::15.333*1.00] mid_occ = 236
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 2010
[M::mm_idx_stat::17.257*1.00] distinct minimizers: 154437548 (33.40% are singletons); average occurrences: 4.873; average spacing: 5.353
[M::worker_pipeline::29.478*2.96] mapped 799768 sequences
[M::main::40.952*2.41] loaded/built the index for 11332 target sequence(s)
[M::mm_mapopt_update::40.952*2.41] mid_occ = 236
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 11332
[M::mm_idx_stat::42.893*2.35] distinct minimizers: 139932295 (37.69% are singletons); average occurrences: 3.883; average spacing: 5.353
[M::worker_pipeline::57.041*3.15] mapped 799768 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -aL -t 8 -x map-ont database/NCBI_genomes_refseq89_BAV.fa.mmi /srv/test_fastq/strawman_pathogen-miseq_95gg9031_05vv10245.fastq
[M::main] Real time: 57.196 sec; CPU: 179.640 sec; Peak RSS: 11.823 GB
[00:01:06] Done mapping reads to the database(s).
[00:01:06] Merging SAM files...
[00:01:08] Logfile saved to /srv/strawman_pathogen-miseq_95gg9031_05vv10245.pangia.log.
[00:01:08] Done. Mapped SAM file saved to /srv/strawman_pathogen-miseq_95gg9031_05vv10245.pangia.sam.
[00:01:08] Total number of input reads: 1713173
[00:01:08] Total number of mapped reads: 41953
[00:01:08] Total number of host reads: 0 (0.00%)
[00:01:08] Total number of ignored reads (cross superkingdom): 29 (0.07%)
[00:01:08] Processing SAM file... 
[00:01:08] Parsing SAM files with 8 subprocesses...

multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
  File "/opt/conda/envs/pangia/lib/python3.6/multiprocessing/pool.py", line 119, in worker
    result = (True, func(*args, **kwds))
  File "/home/pangia/pangia/pangia.py", line 714, in worker
    lcr_lvl, lcr_name, lcr_info = lineageLCR(taxids)
  File "/home/pangia/pangia/pangia.py", line 378, in lineageLCR
    lng = t.taxid2lineageDICT(tid, 1, 1)
  File "/home/pangia/pangia/taxonomy.py", line 265, in taxid2lineageDICT
    return _taxid2lineage( tid, print_all_rank, print_strain, replace_space2underscore, output_typ e )
  File "/home/pangia/pangia/taxonomy.py", line 305, in _taxid2lineage
    rank = _getTaxRank(taxID)
  File "/home/pangia/pangia/taxonomy.py", line 372, in _getTaxRank
    return taxRanks[taxID]
KeyError: '134962'
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/pangia/pangia/pangia.py", line 2319, in <module>
    (res, mapped_r_cnt) = processSAMfile( os.path.abspath(samfile), argvs.threads, lines_per_proce
ss)
  File "/home/pangia/pangia/pangia.py", line 921, in processSAMfile
    results.append( job.get() )
  File "/opt/conda/envs/pangia/lib/python3.6/multiprocessing/pool.py", line 644, in get
    raise self._value
KeyError: '134962'

pangia-vis fails

Hello,
I am trying to run PanGIA. pangia.py finished running but pangia-vis.pl fails to display anything in my browser. The following messages are printed in the terminal:

Opening PanGIA-VIS application on http://localhost:5006/pangia-vis
2020-08-18 17:14:19,627 Starting Bokeh server version 2.1.1 (running on Tornado 6.0.4)
2020-08-18 17:14:19,628 User authentication hooks NOT provided (default user enabled)
2020-08-18 17:14:19,630 Bokeh app running at: http://localhost:5006/pangia-vis
2020-08-18 17:14:19,630 Starting Bokeh server with process id: 5420
BokehDeprecationWarning: 'legend' keyword is deprecated, use explicit 'legend_label', 'legend_field', or 'legend_group' keywords instead
BokehDeprecationWarning: 'legend' keyword is deprecated, use explicit 'legend_label', 'legend_field', or 'legend_group' keywords instead
BokehDeprecationWarning: 'legend' keyword is deprecated, use explicit 'legend_label', 'legend_field', or 'legend_group' keywords instead
BokehDeprecationWarning: 'WidgetBox' is deprecated and will be removed in Bokeh 3.0, use 'bokeh.models.Column' instead
2020-08-18 17:14:19,965 Error running application handler <bokeh.application.handlers.directory.DirectoryHandler object at 0x7fa60f4c6550>: unexpected attribute 'callback' to Button, similar attributes are js_event_callbacks
File "has_props.py", line 282, in setattr:
(name, self.class.name, text, nice_join(matches))) Traceback (most recent call last):
File "/mnt/data0/miniconda3/envs/pangia2/lib/python3.6/site-packages/bokeh/application/handlers/code_runner.py", line 197, in run
exec(self._code, module.dict)
File "/home/DRDC/pangia/pangia-vis/main.py", line 1081, in
dl_btn.callback = CustomJS(args=dict(source=dp_source), code=open(join(dirname(file), "download.js")).read())
File "/mnt/data0/miniconda3/envs/pangia2/lib/python3.6/site-packages/bokeh/core/has_props.py", line 282, in setattr
(name, self.class.name, text, nice_join(matches)))
AttributeError: unexpected attribute 'callback' to Button, similar attributes are js_event_callbacks

Any help would be appreciated.
Thanks,
Scott

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