pigx-rnaseq error in trim_qc_reads_pe

[Karam Ibrahim]

dear maintainer of pigx-RNAseq pipeline

I'm a PhD student at AG_Ohler and I tried to run the pigxRNA-seq pipeline and got this error.

Error in rule trim_qc_reads_pe:

    jobid: 15

    output: /fast/AG_Ohler/karam/RNA_seq/output/trimmed_reads/4Db.trimmed.R1.fq.gz, /fast/AG_Ohler/karam/RNA_seq/output/trimmed_reads/4Db.trimmed.R2.fq.gz, /fast/AG_Ohler/karam/RNA_seq/output/QC/4Db.pe.fastp.html, /fast/AG_Ohler/karam/RNA_seq/output/QC/4Db.pe.fastp.json

    log: /fast/AG_Ohler/karam/RNA_seq/output/logs/trim_reads.4Db.log (check log file(s) for error message)

    shell:

        /gnu/store/67d5kv8kl44g8imh74wxji146407ijsr-fastp-0.23.2/bin/fastp --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --in1 /fast/AG_Ohler/karam/RNA_seq/data/reads/P1784_2_4Db_S10_L002_R1_001.fastq --in2 /fast/AG_Ohler/karam/RNA_seq/data/reads/P1784_2_4Db_S10_L002_R2_001.fastq --out1 /fast/AG_Ohler/karam/RNA_seq/output/trimmed_reads/4Db.trimmed.R1.fq.gz --out2 /fast/AG_Ohler/karam/RNA_seq/output/trimmed_reads/4Db.trimmed.R2.fq.gz -h /fast/AG_Ohler/karam/RNA_seq/output/QC/4Db.pe.fastp.html -j /fast/AG_Ohler/karam/RNA_seq/output/QC/4Db.pe.fastp.json >> /fast/AG_Ohler/karam/RNA_seq/output/logs/trim_reads.4Db.log 2>&1

        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

    cluster_jobid: Your job 6117087 ("snakejob.trim_qc_reads_pe.15.sh") has been submitted

Error executing rule trim_qc_reads_pe on cluster (jobid: 15, external: Your job 6117087 ("snakejob.trim_qc_reads_pe.15.sh") has been submitted, jobscript: /fast/AG_Ohler/karam/RNA_seq/output/.snakemake/tmp.59bz1jki/snakejob.trim_qc_reads_pe.15.sh). For error details see the cluster log and the log files of the involved rule(s).

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However

the log file that the error refers to " log: /fast/AG_Ohler/karam/RNA_seq/output/logs/trim_reads.4Db.log" is empty and so I couldn't debug it.

Thank you in advance for your help

best

Karam