Comments (7)
Thanks for your help. it is working now.
from tigmint.
Hello,
Could you provide the list of files in your working directory (ls -lah
), and the log produced by tigmint? Were there any errors generated?
from tigmint.
Below are the list of files from working directory.There were no error messages generated.
myassembly.fa
myassembly.fa.amb
myassembly.fa.ann
myassembly.fa.bwt
myassembly.fa.fai
myassembly.fa.pac
myassembly.fa.sa
myassembly.myreads.as0.65.nm5.molecule.bed
myassembly.myreads.as0.65.nm5.molecule.size2000.bed
myassembly.myreads.as0.65.nm5.molecule.size2000.trim0.window1000.span20.breaktigs.fa
myassembly.myreads.as0.65.nm5.molecule.size2000.trim0.window1000.span20.breaktigs.fa.bed
myassembly.myreads.as0.65.nm5.molecule.tsv
myassembly.myreads.bam
myassembly.myreads.sam
myassembly.myreads.sortbx.bam
myassembly.tigmint.fa
myreads.fq.gz
nohup.out
old_nohup.sh
out.txt
run_bwa.sh
run_tigmint.sh
These are the tail part of log file.
/data/labs/genomics_lab/shared/shameem/apps/tigmint/bin/tigmint-molecule -b myassembly.myreads.sortbx.bam -o myassembly.myreads.as0.65.nm5.molecule.tsv -a 0.65 -n 5 -q 0 -d 50000
awk 'NR>1 { print $1"\t"$2-1"\t"$3-1"\tReads="$7",Size="$4",Mapq="$8",AS="$9",NM="$10",BX="$5",MI="$6"\t"$7 }' myassembly.myreads.as0.65.nm5.molecule.tsv
| sort -k1,1 -k2,2n -k3,3n >myassembly.myreads.as0.65.nm5.molecule.bed
awk '$3 - $2 >= 2000' myassembly.myreads.as0.65.nm5.molecule.bed >myassembly.myreads.as0.65.nm5.molecule.size2000.bed
samtools faidx myassembly.fa
/data/labs/genomics_lab/shared/shameem/apps/tigmint/bin/tigmint-cut -p16 -w1000 -n20 -t0 -o myassembly.myreads.as0.65.nm5.molecule.size2000.trim0.window1000.span20.breaktigs.fa myassembly.fa myassembly.myreads.as0.65.nm5.molecule.size2000.bed
Started at: 2018-05-17 16:12:50.703750
Reading contig lengths...
Finding breakpoints...
Cutting assembly at breakpoints...
DONE!
Ended at: 2018-05-17 16:12:57.061767
ln -sf myassembly.myreads.as0.65.nm5.molecule.size2000.trim0.window1000.span20.breaktigs.fa myassembly.tigmint.fa
from tigmint.
Ok thanks -- can you also provide a few lines of the myassembly.myreads.sortbx.bam file? (Just with samtools view
)
from tigmint.
K00154:45:HKCNYBBXX:8:2210:30076:13025_TCACGCTAGGACAGCT 99 1 33 27 13M3I61M = 652 716 TCATATCATATAATATTATATTAATAATATTCATTGTAATATATTATTATAGAAGATATCCACAATTTTACGGCAAT JFFF7FFFJJJ-FJAFJJA<JJJFJAAFFJJJFJJFJ<7F<-AJJJJFJF<FJF<<AFFFJ7AAJJJJJFJF7FJ<< NM:i:4 MD:Z:11C62 MC:Z:3S97M AS:i:62 XS:i:72 XA:Z:7263,-76685,77M,1;
K00154:45:HKCNYBBXX:4:2115:13220:48175_CTCTTTCAGAAGCCGT 99 1 53 0 77M = 357 390 ATAGTATTAATTGTAATATATTATTATAGAAGATATCCACAATTTTACGGCAATAATAATATTTGTGTTACTAAATA JFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJFJJ-FJJJJJJJJFJAJAF NM:i:2 MD:Z:3A4C68 MC:Z:86M14S
AS:i:68 XS:i:68 XA:Z:7263,-76662,77M,2;
K00154:45:HKCNYBBXX:8:2102:15899:2070_AAGGGTGGTGAACCTT 113 1 57 0 41M36S 7263 76920 0 TATTCATTGTAATATATTATTATAGAAGATATCCACAATTTGATATAGTGAAAATTATAGCGACATTCCTCCACTTT JJJJJJJJJJJJJJJJJFJFJJAFJJJJJJJJJJF<FJJJFJJJJJJJFJJJJJJFJJJJJJJJJFFJJFJJJJJJJ NM:i:0 MD:Z:41 MC:Z:75M25S AS:i:41 XS:i:41 SA:Z:7263,76772,-,38S39M,0,0; XA:Z:7263,+76694,36S41M,0;
K00154:45:HKCNYBBXX:8:1206:14336:23909_GATGAAAAGGTCAATA 99 1 72 40 68M1D9M = 228 253 ATTATTATAGAAGATATCCACAATTTTACGGCAATAATAATATTTGTGTTACTAAATATGTAGTACATATTATTTTG JJJFJJJJJJJFJJFJFJJJJJJJJJJJJJ7AJJJJJJJJJJFFJJF<FAJJJJJJJJJFJJJJJJJJJJJJJJJJJ NM:i:1 MD:Z:68^A9 MC:Z:27M1I3M1I20M1I47M AS:i:70 XS:i:72 XA:Z:7263,-76643,77M,1;
K00154:45:HKCNYBBXX:8:2210:24058:17860_TGTTCGCTCTCATGTT 163 1 132 33 11S8M1D81M = 372 317 CGCTCTCATGTTAGTACATATTATTTTGAAAATAATATTTTATAATATATTATTGATAAAGGATATTAGAATATTCTCCGTGTATTAGGGATTGGACATG AAFFFFJJJJJJJJJJJJJJJJJJJJAJJJJJJJJJJJJJJJJJJJJJJJJJJJAFFJJJJFFJJJJJJJJJJAFJFFFFFJFJJFJJ<7AFAFJFJJ<J NM:i:1 MD:Z:8^A81 MC:Z:77M AS:i:82 XS:i:76 XA:Z:7263,-76569,30M2D59M11S,3;
K00154:45:HKCNYBBXX:8:2107:18213:6290_CTACCTGAGTCATGCT 163 1 143 60 100M = 412 346 TATTTTGAAAATAATATTTTATAATATATTATTGATAAAGGATATTAGAATATTCTCCGTGTATTAGGGATTGGACATGTTTTTGAATCCATTTTTCGCT AAAFFJJJJJJJJJJJJJJJJJJJJJFFFJJJJJFJJJFJJJJJJJJJJJJJJJJJJFJJJJJJJJJAAJJFJ-AJ<JFFJFJJFJJF-AFJF-AFJ<F< NM:i:0 MD:Z:100 MC:Z:77M AS:i:100 XS:i:89 XA:Z:7263,-76551,3S48M2D49M,2;
K00154:45:HKCNYBBXX:8:2107:18254:6290_CTACCTGAGTCATGCT 163 1 143 60 100M = 412 346 TATTTTGAAAATAATATTTTATAATATATTATTGATAAAGGATATTAGAATATTCTCCGTGTATTAGGGATTGGACATGTTTTTGAATCCATTTTTCGCT AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJAFJJJFAJJJJFFAFFJAJAJAFFFFAAJJFJ< NM:i:0 MD:Z:100 MC:Z:77M AS:i:100 XS:i:89 XA:Z:7263,-76551,3S48M2D49M,2;
from tigmint.
By mistake I closed the ticket.Please can you open it.
from tigmint.
It looks like you don't have the barcode in the BX tag in those alignments. Tigmint expects the chromium barcode to be in the BX:Z
tag of the alignments, and will sort the alignment file by this tag. Make sure your chromium reads have the "BX:Z" tag in the comment of the read header:
Ex:
@E00316:145:HMVG3CCXX:5:1214:6786:3014 BX:Z:AAACACCAGACAATAC-1
TCTGTCTCTCTGTCCATCTCTGTCTTTCTATGTCTGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCCTGTGCCTCTCCCCCCCCCCCCCCCCTCGTCCTTCCCCTCTCCGCCTTCCCCC
+
FAAFAKKKFKKKKFFAAF<AFKF,FFA<FKKAKFKK<AFKFKKKK77F,F7FFFKF<<AF,A,AFAFKKKAFFF,,,,,,,7,7,,7,<<FA,(AAA(,AA(((,,,,,,,,,,(,,,7(((,,,7,7
@E00316:145:HMVG3CCXX:5:1214:6786:3014 BX:Z:AAACACCAGACAATAC-1
AAATGGACAGAGAGAGAAACAGACAGACAGGGAGGGAGGGAGGGGGGCGAGACGGGGGGGGGGAGGGAGGGGGGGAGGGAGGGAGGGGGAGAGACAGAAATAGAGAGAGAGAGAGGGAGAGAGAGAGAGAGAGAAGGGTGGTGGGTGGTGT
+
AAFFFKKKKKKKKKKKKKKKKKKKKKFKKKKKKKKKAFKKF<AF,(,(((<,,,,(((,(,(((,(,,,(,(,,<(,<A,7(,,7(,((,,,,,,7,,7F,,,,,<,7,,A,,,,,,,,<FF<,,,,,<FF<F7,,,,7,,,,,,,,7,7,
This is the format produced by longranger basic.
from tigmint.
Related Issues (20)
- About samtools invalid option in tigmint-make arcs mode HOT 4
- pre-alignment HOT 2
- Forward+reverse + long reads HOT 4
- yet another "make: *** No rule to make target" issue HOT 5
- Feature has length = 0, Skipping - followed by empty output from tigmint-long HOT 9
- Understanding tigmint-long outputs HOT 3
- tigmint compilation issue HOT 2
- _sqlite3.cpython-310-x86_64-linux-gnu.so: undefined symbol: sqlite3_trace_v2
- Error : no progress of scaffolding running HOT 5
- tigmint-long error HOT 1
- Respect $TMPDIR as anticipated by sort tool HOT 1
- samtools sort may be replaced by bamsort which scales better HOT 2
- pigz may be better replaced by bgzip HOT 2
- tigmint-make ignores $PATH and is supposed to be run from unpacked source tree instead HOT 3
- README does not list all dependencies HOT 2
- Does bin/tigmint_estimate_dist.py really work with FASTA files as well? HOT 5
- src/long-to-linked-pe v1.0: Using more than 6 threads does not scale, reverting to 6. HOT 5
- tigmint_molecule_paf.py: TypeError: expected string or bytes-like object HOT 11
- Cannot compile the bundled while modified copy of make: make-4.1/glob/glob.c:1342: undefined reference to `__alloca' HOT 6
- tigmint-make: minimap2 is being called with -y argument HOT 3
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from tigmint.