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Running TRUST4 with example files (checking if everything works well) #206

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silvia1234567890 opened this issue Jul 31, 2023 · 2 comments

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@silvia1234567890
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Hello,

I am testing TRUST4 with the example files. I share my command line to ask especially for the last line "Results do not match the pregenerated example results. Please check TRUST4's version or the example files are in the folder". What does it mean? the version of TRUST4 I have installed is: trust4 1.0.11 on conda. And the example files are in the corresponding TRUST4 folder.

Thank you for your help,
Kind regards,
Silvia

(base) Ana@iMac-de-EMITB643558 TRUST4 % /Users/Ana/TRUST4/run-trust4 -b example/example.bam -f hg38_bcrtcr.fa --ref human_IMGT+C.fa
[Mon Jul 31 14:38:01 2023] TRUST4 begins.
[Mon Jul 31 14:38:01 2023] SYSTEM CALL: /Users/Ana/TRUST4/bam-extractor -b example/example.bam -t 1 -f hg38_bcrtcr.fa -o TRUST_example_toassemble
[Mon Jul 31 14:38:01 2023] Start to extract candidate reads from bam file.
[Mon Jul 31 14:38:01 2023] Finish obtaining the candidate read ids.
[Mon Jul 31 14:38:01 2023] Finish extracting reads.
[Mon Jul 31 14:38:01 2023] SYSTEM CALL: /Users/Ana/TRUST4/trust4 -f hg38_bcrtcr.fa -o TRUST_example -1 TRUST_example_toassemble_1.fq -2 TRUST_example_toassemble_2.fq
[Mon Jul 31 14:38:01 2023] Found 394 reads.
[Mon Jul 31 14:38:01 2023] Finish sorting the reads.
[Mon Jul 31 14:38:01 2023] Finish rough annotations.
[Mon Jul 31 14:38:01 2023] Assembled 394 reads.
[Mon Jul 31 14:38:01 2023] Try to rescue 0 reads for assembly.
[Mon Jul 31 14:38:01 2023] Rescued 0 reads.
[Mon Jul 31 14:38:01 2023] Extend assemblies by mate pair information.
[Mon Jul 31 14:38:01 2023] Remove redundant assemblies.
[Mon Jul 31 14:38:01 2023] Finish assembly.
[Mon Jul 31 14:38:01 2023] SYSTEM CALL: /Users/Ana/TRUST4/annotator -f human_IMGT+C.fa -a TRUST_example_final.out -t 1 -o TRUST_example -r TRUST_example_assembled_reads.fa --airrAlignment > TRUST_example_annot.fa
[Mon Jul 31 14:38:01 2023] Start to annotate assemblies.
[Mon Jul 31 14:38:01 2023] Start to realign reads for CDR3 analysis.
[Mon Jul 31 14:38:01 2023] Compute CDR3 abundance.
[Mon Jul 31 14:38:01 2023] Finish annotation.
[Mon Jul 31 14:38:01 2023] SYSTEM CALL: perl /Users/Ana/TRUST4/trust-simplerep.pl TRUST_example_cdr3.out > TRUST_example_report.tsv
[Mon Jul 31 14:38:01 2023] SYSTEM CALL: perl /Users/Ana/TRUST4/trust-airr.pl TRUST_example_report.tsv TRUST_example_annot.fa --airr-align TRUST_example_airr_align.tsv > TRUST_example_airr.tsv
[Mon Jul 31 14:38:01 2023] TRUST4 finishes.
(base) Ana@iMac-de-EMITB643558 TRUST4 % sh trust-example-test.sh
[Mon Jul 31 14:40:08 2023] TRUST4 begins.
[Mon Jul 31 14:40:08 2023] SYSTEM CALL: /Users/Ana/TRUST4/bam-extractor -b example/example.bam -t 1 -f hg38_bcrtcr.fa -o example_test_toassemble
[Mon Jul 31 14:40:08 2023] Start to extract candidate reads from bam file.
[Mon Jul 31 14:40:08 2023] Finish obtaining the candidate read ids.
[Mon Jul 31 14:40:08 2023] Finish extracting reads.
[Mon Jul 31 14:40:08 2023] SYSTEM CALL: /Users/Ana/TRUST4/trust4 -f hg38_bcrtcr.fa -o example_test -1 example_test_toassemble_1.fq -2 example_test_toassemble_2.fq
[Mon Jul 31 14:40:08 2023] Found 394 reads.
[Mon Jul 31 14:40:08 2023] Finish sorting the reads.
[Mon Jul 31 14:40:08 2023] Finish rough annotations.
[Mon Jul 31 14:40:08 2023] Assembled 394 reads.
[Mon Jul 31 14:40:08 2023] Try to rescue 0 reads for assembly.
[Mon Jul 31 14:40:08 2023] Rescued 0 reads.
[Mon Jul 31 14:40:08 2023] Extend assemblies by mate pair information.
[Mon Jul 31 14:40:08 2023] Remove redundant assemblies.
[Mon Jul 31 14:40:08 2023] Finish assembly.
[Mon Jul 31 14:40:08 2023] SYSTEM CALL: /Users/Ana/TRUST4/annotator -f human_IMGT+C.fa -a example_test_final.out -t 1 -o example_test -r example_test_assembled_reads.fa --airrAlignment > example_test_annot.fa
[Mon Jul 31 14:40:08 2023] Start to annotate assemblies.
[Mon Jul 31 14:40:09 2023] Start to realign reads for CDR3 analysis.
[Mon Jul 31 14:40:09 2023] Compute CDR3 abundance.
[Mon Jul 31 14:40:09 2023] Finish annotation.
[Mon Jul 31 14:40:09 2023] SYSTEM CALL: perl /Users/Ana/TRUST4/trust-simplerep.pl example_test_cdr3.out > example_test_report.tsv
[Mon Jul 31 14:40:09 2023] SYSTEM CALL: perl /Users/Ana/TRUST4/trust-airr.pl example_test_report.tsv example_test_annot.fa --airr-align example_test_airr_align.tsv > example_test_airr.tsv
[Mon Jul 31 14:40:09 2023] TRUST4 finishes.
Results do not match the pregenerated example results. Please check TRUST4's version or the example files are in the folder.

@mourisl
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mourisl commented Jul 31, 2023

Did you download the example file results from the github repo? Could you please try the github version to see whether you can obtain consistent results? Thank you.

@mourisl
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mourisl commented Aug 1, 2023

I just tested the conda version. I think this might due to the sort in the perl script. Could you please check whether the example_test_report.tsv file is the same as the example/TRUST_example_report.tsv after sorting them with bash "sort"?

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