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harvardinformatics / snpArcher

Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.
MIT License
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Error in rule fastp #183

Closed spilornis-ng closed 1 month ago

spilornis-ng commented 2 months ago

Hi! Thanks for fixing the previous issue! However, when I am running the code now I get the following error. The log files generated are also empty.

Error in rule fastp: jobid: 29 input: /mnt/hdd/Naman/Naman_wgs_trial/2_clean/Turdus_simillimus_bourdilloni_B0937_R1_paired.fq.gz, /mnt/hdd/Naman/Naman_wgs_trial/2_clean/Turdus_simillimus_bourdilloni_B0937_R2_paired.fq.gz output: results/GCA_013186435.1_ASM1318643v1_genomic/filtered_fastqs/Turdus_simillimus_bourdilloni_B0937/1_1.fastq.gz, results/GCA_013186435.1_ASM1318643v1_genomic/filtered_fastqs/Turdus_simillimus_bourdilloni_B0937/1_2.fastq.gz, results/GCA_013186435.1_ASM1318643v1_genomic/summary_stats/Turdus_simillimus_bourdilloni_B0937/1.fastp.out log: logs/GCA_013186435.1_ASM1318643v1_genomic/fastp/Turdus_simillimus_bourdilloni_B0937/1.txt (check log file(s) for error details) conda-env: /mnt/hdd/Naman/Naman_wgs_trial/snparcher_trial/trialproject/.snakemake/conda/f949ce1fdb59cb745f9cb17349cd25d7 shell: fastp --in1 /mnt/hdd/Naman/Naman_wgs_trial/2_clean/Turdus_simillimus_bourdilloni_B0937_R1_paired.fq.gz --in2 /mnt/hdd/Naman/Naman_wgs_trial/2_clean/Turdus_simillimus_bourdilloni_B0937_R2_paired.fq.gz --out1 results/GCA_013186435.1_ASM1318643v1_genomic/filtered_fastqs/Turdus_simillimus_bourdilloni_B0937/1_1.fastq.gz --out2 results/GCA_013186435.1_ASM1318643v1_genomic/filtered_fastqs/Turdus_simillimus_bourdilloni_B0937/1_2.fastq.gz --thread 1 --detect_adapter_for_pe -j /dev/null -h /dev/null 2> results/GCA_013186435.1_ASM1318643v1_genomic/summary_stats/Turdus_simillimus_bourdilloni_B0937/1.fastp.out > logs/GCA_013186435.1_ASM1318643v1_genomic/fastp/Turdus_simillimus_bourdilloni_B0937/1.txt (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[Fri Apr 19 02:18:12 2024] Removing output files of failed job fastp since they might be corrupted: results/GCA_013186435.1_ASM1318643v1_genomic/summary_stats/Turdus_simillimus_bourdilloni_B0937/1.fastp.out

cademirch commented 2 months ago

Hmm sorry about that. From what you've pasted in I can't quite figure out what's going on. You can try pulling the PR I've linked which should make sure any errors from fastp make it to the logfile.

spilornis-ng commented 1 month ago

Hi! I was able to resolve this. Closing this issue! The issue was with fastp command not being found.