dportik
commented
3 years ago Hello, Thank you for posting the error and the log file - this is very helpful for understanding the issue.
It seems that the -mdb flag isn't being recognized by MEGAN. The way MEGAN processes taxonomy information has changed over time, and the flags for using mapping files have also changed. Based on the log file, it appears that a very outdated version of MEGAN is being used (version 6.12.3, built 14 Aug 2018). It seems likely that this is the cause of the issue. Please download the newest release of MEGAN (and its tools), or ensure you have at least version 6.19.+. I'll make a note of the MEGAN version requirements in the documentation.
After you obtain an updated version of sam2rma, please let me know if your analysis finishes successfully.
kimnegrette3
Hi! I am trying to run the Taxonomic-Functional-Profiling-Protein pipeline, but there seems to be an error during the sam2rma step.
This is the command I am using: snakemake --snakefile Snakefile-taxprot --configfile configs/Sample-Config.yaml --use-conda --cores 32
This is the log: Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 32 Rules claiming more threads will be scaled down. Job counts: count jobs 1 MakeRMA 1 all 2
[Tue Oct 20 12:22:59 2020] rule MakeRMA: input: 3-merged/merged.ccs.merged.sam, inputs/merged.ccs.fasta output: 4-rma/merged.ccs.protein.readCount.rma log: logs/merged.ccs.MakeRMA.readCount.log jobid: 1 benchmark: benchmarks/merged.ccs.MakeRMA.readCount.tsv wildcards: sample=merged.ccs threads: 24
Activating conda environment: /hpcfs/home/je.gutierrez11/pb-metagenomics/pb-metagenomics-tools-master/Taxonomic-Functional-Profiling-Protein/.snakemake/conda/0ecc3683 [Tue Oct 20 12:23:04 2020] Error in rule MakeRMA: jobid: 1 output: 4-rma/merged.ccs.protein.readCount.rma log: logs/merged.ccs.MakeRMA.readCount.log (check log file(s) for error message) conda-env: /hpcfs/home/je.gutierrez11/pb-metagenomics/pb-metagenomics-tools-master/Taxonomic-Functional-Profiling-Protein/.snakemake/conda/0ecc3683 shell: /hpcfs/home/je.gutierrez11/.conda/envs/megan6/bin/sam2rma -i 3-merged/merged.ccs.merged.sam -r inputs/merged.ccs.fasta -o 4-rma/merged.ccs.protein.readCount.rma -lg -alg longReads -t 24 -mdb /hpcfs/home/je.gutierrez11/pb-metagenomics/megan-map-Jul2020-2.db -ram readCount -v 2> logs/merged.ccs.MakeRMA.readCount.log Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /hpcfs/home/je.gutierrez11/pb-metagenomics/pb-metagenomics-tools-master/Taxonomic-Functional-Profiling-Protein/.snakemake/log/2020-10-20T122250.697787.snakemake.log
And this is the merged.ccs.MakeRMA.readCount.log: SAM2RMA6 - Computes a MEGAN RMA (.rma) file from a SAM (.sam) file that was created by DIAMOND or MALT Options: Input --in: 3-merged/merged.ccs.merged.sam --reads: inputs/merged.ccs.fasta Output --out: 4-rma/merged.ccs.protein.readCount.rma --useCompression: true Reads --paired: false --pairedSuffixLength: 0 Parameters --longReads: true --maxMatchesPerRead: 100 --classify: true --minScore: 50.0 --maxExpected: 0.01 --topPercent: 10.0 --minSupportPercent: 0.05 --minSupport: 0 --minPercentReadCover: 0.0 --minPercentReferenceCover: 0.0 --lcaAlgorithm: longReads --lcaCoveragePercent: 100.0 --readAssignmentMode: readCount Classification support: --parseTaxonNames: true Other: --firstWordIsAccession: true --accessionTags: gb| ref| --verbose: true Version MEGAN Community Edition (version 6.12.3, built 14 Aug 2018) Copyright (C) 2018 Daniel H. Huson. This program comes with ABSOLUTELY NO WARRANTY. Caught: jloda.util.UsageException: Invalid, unknown or duplicate option: -t 24 -mdb /hpcfs/home/je.gutierrez11/pb-metagenomics/megan-map-Jul2020-2.db , use option '-h' for help at jloda.util.ArgsOptions.done(ArgsOptions.java:210) at megan.tools.SAM2RMA6.run(SAM2RMA6.java:151) at megan.tools.SAM2RMA6.main(SAM2RMA6.java:64)
the snakemake version I am using is 5.26.1
I would greatly appreciate any help or suggestion! Thanks in advance!