yp ( Yuri Pirola )

I'm trying to create new reference vcf file for GISAID sequences of COVID19. But MALVIRUS failed every time for these sequences. I've 24,497 sequences. And I take these error message from log.json;

{"alias":"20200813-111040_3c253ebf-57bc-4783-95f1-d861b32e84af","description":"europe","filename":"/jobs/vcf/20200813-111040_3c253ebf-57bc-4783-95f1-d861b32e84af/europe_2020_07_20_19-2.fasta","gtf":"/jobs/vcf/20200813-111040_3c253ebf-57bc-4783-95f1-d861b32e84af/sars-cov-2.gff","id":"20200813-111040_3c253ebf-57bc-4783-95f1-d861b32e84af","log":{"last_time":"2020-08-13 11:11:18","status":"Failed","steps":{"mafft":{"command":"mafft --thread 4 --auto --keeplength --addfragments /jobs/vcf/20200813-111040_3c253ebf-57bc-4783-95f1-d861b32e84af/europe_2020_07_20_19-2.fasta /jobs/vcf/20200813-111040_3c253ebf-57bc-4783-95f1-d861b32e84af/reference.fasta > /jobs/vcf/20200813-111040_3c253ebf-57bc-4783-95f1-d861b32e84af/mafft/multi_alignment.unfilled.msa 2> /jobs/vcf/20200813-111040_3c253ebf-57bc-4783-95f1-d861b32e84af/mafft/mafft.log","config":{"cores":4,"gtf":"/jobs/vcf/20200813-111040_3c253ebf-57bc-4783-95f1-d861b32e84af/sars-cov-2.gff","multifa":"/jobs/vcf/20200813-111040_3c253ebf-57bc-4783-95f1-d861b32e84af/europe_2020_07_20_19-2.fasta","reference":"/jobs/vcf/20200813-111040_3c253ebf-57bc-4783-95f1-d861b32e84af/reference.fasta","workdir":"/jobs/vcf/20200813-111040_3c253ebf-57bc-4783-95f1-d861b32e84af"},"input":{"fa":"/jobs/vcf/20200813-111040_3c253ebf-57bc-4783-95f1-d861b32e84af/reference.fasta","mfa":"/jobs/vcf/20200813-111040_3c253ebf-57bc-4783-95f1-d861b32e84af/europe_2020_07_20_19-2.fasta"},"log":"/opt/conda/envs/malva-env/bin/mafft: line 2745: 897 Killed "$prefix/addsingle" -Q 100 $legacygapopt -W $tuplesize -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>> "$progressfile"\n","output":{"msa":"/jobs/vcf/20200813-111040_3c253ebf-57bc-4783-95f1-d861b32e84af/mafft/multi_alignment.unfilled.msa"},"params":{},"result":"Failed","return_code":1,"time":"2020-08-13 11:11:18"}}},"params":{"cores":"4"},"reference":"/jobs/vcf/20200813-111040_3c253ebf-57bc-4783-95f1-d861b32e84af/reference.fasta","snakemake":"Building DAG of jobs...\nUsing shell: /bin/bash\nProvided cores: 4\nRules claiming more threads will be scaled down.\nJob counts:\n\tcount\tjobs\n\t1\tfill_msa\n\t1\tindex_reference\n\t1\tmulti_align\n\t1\trun\n\t1\tvcf_add_freqs\n\t1\tvcf_build\n\t1\tvcf_clean_header\n\t7\n\n[Thu Aug 13 11:10:42 2020]\nrule multi_align:\n input: /jobs/vcf/20200813-111040_3c253ebf-57bc-4783-95f1-d861b32e84af/reference.fasta, /jobs/vcf/20200813-111040_3c253ebf-57bc-4783-95f1-d861b32e84af/europe_2020_07_20_19-2.fasta\n output: /jobs/vcf/20200813-111040_3c253ebf-57bc-4783-95f1-d861b32e84af/mafft/multi_alignment.unfilled.msa\n log: /jobs/vcf/20200813-111040_3c253ebf-57bc-4783-95f1-d861b32e84af/mafft/mafft.log, /jobs/vcf/20200813-111040_3c253ebf-57bc-4783-95f1-d861b32e84af/mafft/mafft.json\n jobid: 6\n threads: 4\n\n\u001b[33mJob counts:\n\tcount\tjobs\n\t1\tmulti_align\n\t1\u001b[0m\n\u001b[32m[Thu Aug 13 11:11:18 2020]\u001b[0m\n\u001b[31mError in rule multi_align:\u001b[0m\n\u001b[31m jobid: 0\u001b[0m\n\u001b[31m output: /jobs/vcf/20200813-111040_3c253ebf-57bc-4783-95f1-d861b32e84af/mafft/multi_alignment.unfilled.msa\u001b[0m\n\u001b[31m log: /jobs/vcf/20200813-111040_3c253ebf-57bc-4783-95f1-d861b32e84af/mafft/mafft.log, /jobs/vcf/20200813-111040_3c253ebf-57bc-4783-95f1-d861b32e84af/mafft/mafft.json (check log file(s) for error message)\u001b[0m\n\u001b[31m\u001b[0m\n\u001b[31mRuleException:\nCalledProcessError in line 102 of /snakemake/Snakefile.vcf:\nCommand 'mafft --thread 4 --auto --keeplength --addfragments /jobs/vcf/20200813-111040_3c253ebf-57bc-4783-95f1-d861b32e84af/europe_2020_07_20_19-2.fasta /jobs/vcf/20200813-111040_3c253ebf-57bc-4783-95f1-d861b32e84af/reference.fasta > /jobs/vcf/20200813-111040_3c253ebf-57bc-4783-95f1-d861b32e84af/mafft/multi_alignment.unfilled.msa 2> /jobs/vcf/20200813-111040_3c253ebf-57bc-4783-95f1-d861b32e84af/mafft/mafft.log' returned non-zero exit status 1.\n File "/snakemake/Snakefile.vcf", line 112, in __rule_multi_align\n File "/snakemake/Snakefile.vcf", line 102, in __rule_multi_align\n File "/opt/conda/envs/malva-env/lib/python3.7/subprocess.py", line 411, in check_output\n File "/opt/conda/envs/malva-env/lib/python3.7/subprocess.py", line 512, in run\n File "/opt/conda/envs/malva-env/lib/python3.7/concurrent/futures/thread.py", line 57, in run\u001b[0m\n\u001b[31mExiting because a job execution failed. Look above for error message\u001b[0m\nShutting down, this might take some time.\nExiting because a job execution failed. Look above for error message\nComplete log: /jobs/vcf/20200813-111040_3c253ebf-57bc-4783-95f1-d861b32e84af/.snakemake/log/2020-08-13T111041.968450.snakemake.log\n","submission_time":1597317041}

I'm new this area and I'm trying to understand. Can anybody help me about this error message?

Thanks

closed time in a month

busrasevimm

issue commentAlgoLab/MALVIRUS

Help! Cannot create new reference vcf file?

Closing since the issue seems resolved.

busrasevimm

comment created time in a month

delete branch AlgoLab/MALVIRUS

delete branch : use_snpEff

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push eventAlgoLab/MALVIRUS

Marco Previtali

commit sha b51f254e4d364244a109bb5ffcd6551ef3c5847f

Add snpEff to MALVIRUS pipeline - Add snpEff to conda environment - Add snpEff step to the snakemake pipeline - Add a step to "clean" the vcf output by malva (i.e., remove unused ALTs entries that will break snpEff) - Update GenotypeTable.jsx to report the effect of SNPs

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Yuri Pirola

commit sha 15e7e6e3becee9457bb73a076e7a381a1260eb84

SNAKEFILE: remove threads from snpEff command line (it says that multithreading not supported in this version)

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Yuri Pirola

commit sha a7bbbf71aff327cebaf248ef31087e44b15b0cf3

FE: report all the effects in the genotype table

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Yuri Pirola

commit sha f405fcf86b90cf7e9475eb1fdb59cb1d3fbfaa5b

Merge branch 'master' into use_snpEff

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Yuri Pirola

commit sha ec5e788e3187e868995e4c23d1f8f2f8003f385f

BE: security check on path joining

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Yuri Pirola

commit sha 495b35aebae5525992dc4f3d349fc7ce7553f114

BE: add the list of references

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Yuri Pirola

commit sha 03e4ebfdac38f13ad779391d05e3043de5df6619

BE: allow to use MALVIRUS-provided genomic sequences

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Yuri Pirola

commit sha 706a87a0edb455bc4f7218cb99d4053d54b021e5

FE: allow to use MALVIRUS-provided genomic sequences

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Yuri Pirola

commit sha 153aca2fb4eaae2f01579fcba49c9688190b33b5

SNAKEFILE: run snpEff if and only if refname is given

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Yuri Pirola

commit sha e93be17c501ce0a679e13b9d8760bb7e0b8a3aaa

FE: upgrade dep (and related minor changes)

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Yuri Pirola

commit sha ba065e81ed6613be325ac9e0ffba51b8230948e8

HELP: update docs

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Yuri Pirola

commit sha 2271e64134a6ee2db549c1adb5887def97a67e68

HELP: small fix

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commit sha 6fac35f5ec0c06147853bd92cd3cbe539a607556

Merge pull request #18 from AlgoLab/use_snpEff Add SnpEff to MALVIRUS pipeline

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PR merged AlgoLab/MALVIRUS

Reviewers

Add snpEff to MALVIRUS pipeline enhancement

Add snpEff to conda environment
Add snpEff step to the snakemake pipeline
Add a step to "clean" the vcf output by malva (i.e., remove unused ALTs entries that will break snpEff)
Update GenotypeTable.jsx to report the effect of SNPs

+1054 -696

12 commit in AlgoLab/MALVIRUS/tree/use_snpEff AlgoLab/MALVIRUS/tree/master

8 comments

31 changed files

mpre

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Yuri Pirola

commit sha 2271e64134a6ee2db549c1adb5887def97a67e68

HELP: small fix

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pull request commentAlgoLab/MALVIRUS

Add snpEff to MALVIRUS pipeline

I've just modified the documentation including SnpEff. Unless someone spots an error, I will merge to master and I will prepare a new release.

mpre

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Yuri Pirola

commit sha e93be17c501ce0a679e13b9d8760bb7e0b8a3aaa

FE: upgrade dep (and related minor changes)

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Yuri Pirola

commit sha ba065e81ed6613be325ac9e0ffba51b8230948e8

HELP: update docs

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issue commentAlgoLab/MALVIRUS

Help! Cannot create new reference vcf file?

Thanks for reporting the issue. Could you please attach the file http://localhost:56733/jobs/vcf/20200813-111040_3c253ebf-57bc-4783-95f1-d861b32e84af/mafft/mafft.log ?

busrasevimm

comment created time in 3 months

pull request commentAlgoLab/MALVIRUS

Add snpEff to MALVIRUS pipeline

I added the directory refs in commit Algolab/MALVIRUS-data@7b85357af29f60e37cb0ea23a532bd2d9ab97aaf with the genomic references already known to MALVIRUS (only SARS-CoV2-2, now). If the user uploads or creates a new catalog based on one of those references, then snpEff is also executed, otherwise that step is skipped. @AlgoLab/malvirus what do you think about that? Could you perform some tests, please?

mpre

comment created time in 3 months

PR closed AlgoLab/MALVIRUS

Reviewers

Bump elliptic from 6.5.2 to 6.5.3 in /frontend dependencies

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Bumps elliptic from 6.5.2 to 6.5.3. <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/indutny/elliptic/commit/8647803dc3d90506aa03021737f7b061ba959ae1"><code>8647803</code></a> 6.5.3</li> <li><a href="https://github.com/indutny/elliptic/commit/856fe4d99fe7b6200556e6400b3bf585b1721bec"><code>856fe4d</code></a> signature: prevent malleability and overflows</li> <li>See full diff in <a href="https://github.com/indutny/elliptic/compare/v6.5.2...v6.5.3">compare view</a></li> </ul> </details> <br />

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