You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
when the following command is run the test profile fails
nextflow run nf-core/methylseq
-profile test,singularity
--outdir /projects/team/bioinformatics/nextflow_testing
--em_seq
Command used and terminal output
nextflow run nf-core/methylseq \ -profile test,singularity \ --outdir /projects/team/bioinformatics/nextflow_testing \ --em_seqexecutor > slurm (18)[f2/75208c] process > NFCORE_METHYLSEQ:METHYLSEQ:PREPARE_GENOME:BISMARK_GENOMEPREPARATION (BismarkIndex/genome.fa) [100%] 1 of 1 ✔[4b/d327e9] process > NFCORE_METHYLSEQ:METHYLSEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_test.csv) [100%] 1 of 1 ✔[1d/0ff225] process > NFCORE_METHYLSEQ:METHYLSEQ:CAT_FASTQ (SRR389222_sub2) [100%] 1 of 1 ✔[42/8765e1] process > NFCORE_METHYLSEQ:METHYLSEQ:FASTQC (SRR389222_sub2) [100%] 3 of 3 ✔[02/e5d1b7] process > NFCORE_METHYLSEQ:METHYLSEQ:TRIMGALORE (SRR389222_sub2) [100%] 3 of 3 ✔[be/805c6f] process > NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:BISMARK_ALIGN (SRR389222_sub2) [100%] 3 of 3 ✔[b6/996758] process > NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:SAMTOOLS_SORT_ALIGNED (SRR389222_sub2) [100%] 3 of 3 ✔[da/c0e0ca] process > NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:BISMARK_DEDUPLICATE (SRR389222_sub2) [100%] 3 of 3, failed: 2 ✘[- ] process > NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:BISMARK_METHYLATIONEXTRACTOR -[- ] process > NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:BISMARK_REPORT -[- ] process > NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:BISMARK_SUMMARY -[- ] process > NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:SAMTOOLS_SORT_DEDUPLICATED -[- ] process > NFCORE_METHYLSEQ:METHYLSEQ:QUALIMAP_BAMQC -[- ] process > NFCORE_METHYLSEQ:METHYLSEQ:PRESEQ_LCEXTRAP -[- ] process > NFCORE_METHYLSEQ:METHYLSEQ:CUSTOM_DUMPSOFTWAREVERSIONS -[- ] process > NFCORE_METHYLSEQ:METHYLSEQ:MULTIQC -Execution cancelled -- Finishing pending tasks before exit-[nf-core/methylseq] Pipeline completed with errors-ERROR ~ Error executing process > 'NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:BISMARK_DEDUPLICATE (SRR389222_sub1)'Caused by: Process `NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:BISMARK_DEDUPLICATE (SRR389222_sub1)` terminated with an error exit status (255)Command executed: deduplicate_bismark \ \ -s \ --bam SRR389222_sub1_trimmed_bismark_bt2.bam cat <<-END_VERSIONS > versions.yml "NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:BISMARK_DEDUPLICATE": bismark: $(echo $(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*$//') END_VERSIONSCommand exit status: 255Command output: (empty)Command error: Processing single-end Bismark output file(s) (SAM format): SRR389222_sub1_trimmed_bismark_bt2.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>SRR389222_sub1_trimmed_bismark_bt2.bam<< for signs of file truncation... ### File appears to be empty, terminating deduplication process. Please make sure the input file has not been truncated. ###Work dir: /projects/team/bioinformatics/nextflow_testing/work/b9/16a4f7d01afeea098756cd8c70a175Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line -- Check '.nextflow.log' file for details
Relevant files
No response
System information
No response
The text was updated successfully, but these errors were encountered:
Description of the bug
when the following command is run the test profile fails
nextflow run nf-core/methylseq
-profile test,singularity
--outdir /projects/team/bioinformatics/nextflow_testing
--em_seq
Command used and terminal output
Relevant files
No response
System information
No response
The text was updated successfully, but these errors were encountered: