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Yuri Pirola yp @AlgoLab, Università degli Studi di Milano-Bicocca Bergamo, Italy https://algolab.eu/pirola Algorithms, programs, and Bioinformatics

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release AlgoLab/MALVIRUS

v1.1.0

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A fast and accurate tool for genotyping haploid individuals (such as SARS-CoV-2)

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issue closedAlgoLab/MALVIRUS

Help! Cannot create new reference vcf file?

Hello,

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

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busrasevimm

issue commentAlgoLab/MALVIRUS

Help! Cannot create new reference vcf file?

Closing since the issue seems resolved.

busrasevimm

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delete branch AlgoLab/MALVIRUS

delete branch : use_snpEff

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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

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FE: report all the effects in the genotype table

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Merge branch 'master' into use_snpEff

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BE: security check on path joining

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BE: add the list of references

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Yuri Pirola

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BE: allow to use MALVIRUS-provided genomic sequences

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Yuri Pirola

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FE: allow to use MALVIRUS-provided genomic sequences

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SNAKEFILE: run snpEff if and only if refname is given

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Yuri Pirola

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FE: upgrade dep (and related minor changes)

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HELP: update docs

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HELP: small fix

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

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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

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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.

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FE: upgrade dep (and related minor changes)

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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

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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

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PR closed AlgoLab/MALVIRUS

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Bump elliptic from 6.5.2 to 6.5.3 in /frontend dependencies

⚠️ Dependabot is rebasing this PR ⚠️

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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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pull request commentAlgoLab/MALVIRUS

Bump elliptic from 6.5.2 to 6.5.3 in /frontend

Superseded

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FE: upgrade dep

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Merge branch 'master' into use_snpEff

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BE: security check on path joining

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Yuri Pirola

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BE: allow to use MALVIRUS-provided genomic sequences

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Yuri Pirola

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FE: allow to use MALVIRUS-provided genomic sequences

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SNAKEFILE: run snpEff if and only if refname is given

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FE: upgrade dep

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Add common reference genomic sequences

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