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dahak-metagenomics / dahak

benchmarking and containerization of tools for analysis of complex non-clinical metagenomes.
https://dahak-metagenomics.github.io/dahak
BSD 3-Clause "New" or "Revised" License
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UBUNTU read filtering: Error: trimmomatic: command not found #111

Open nalbright opened 6 years ago

nalbright commented 6 years ago

In Ubuntu os I ran the command from the Really Quick Copy and Paste Quick Start: snakemake -p --configfile=config/custom_readfilt_workflow.json read_filtering_posttrim_workflow

and received this error:

2 of 12 steps (17%) done

Job 7: --- Quality trimming read data.

trimmomatic PE /data/SRR606249_subset25_1_reads.fq.gz /data/SRR606249_subset25_2_reads.fq.gz /data/SRR606249_subset25_1.trim2.fq.gz /data/SRR606249_subset25_1.trim2_se /data/SRR606249_subset25_2.trim2.fq.gz /data/SRR606249_subset25_2.trim2_se ILLUMINACLIP:/data/TruSeq2-PE.fa:2:40:15 LEADING:2 TRAILING:2 SLIDINGWINDOW:4:2 MINLEN:25 /bin/bash: trimmomatic: command not found Error in rule quality_trimming: jobid: 7 output: data/SRR606249_subset25_1.trim2.fq.gz, data/SRR606249_subset25_1.trim2_se, data/SRR606249_subset25_2.trim2.fq.gz, data/SRR606249_subset25_2.trim2_se log: data/trimmomatic_pe_SRR606249_subset25_trim2.log

RuleException: CalledProcessError in line 405 of /home/user/dahak_2018/dahak/workflows/read_filtering/Snakefile: Command ' set -euo pipefail; trimmomatic PE /data/SRR606249_subset25_1_reads.fq.gz /data/SRR606249_subset25_2_reads.fq.gz /data/SRR606249_subset25_1.trim2.fq.gz /data/SRR606249_subset25_1.trim2_se /data/SRR606249_subset25_2.trim2.fq.gz /data/SRR606249_subset25_2.trim2_se ILLUMINACLIP:/data/TruSeq2-PE.fa:2:40:15 LEADING:2 TRAILING:2 SLIDINGWINDOW:4:2 MINLEN:25 ' returned non-zero exit status 127. File "/home/user/dahak_2018/dahak/workflows/read_filtering/Snakefile", line 405, in __rule_quality_trimming File "/home/user/miniconda3/lib/python3.6/concurrent/futures/thread.py", line 56, in run Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /home/user/dahak_2018/dahak/workflows/.snakemake/log/2018-07-16T143339.201450.snakemake.log

charlesreid1 commented 6 years ago

This issue is related to #110 and should be solved by adding the --with-singularity flag, which was missing from the quickstart docs.