golobor
commented
4 years ago Hi!
(1) the command file mentioned by nextflow can be found in the work folder (i.e. a temporary folder created for execution of this specific task). In your case, it must be /home/biophymember/Projets/HiC_premiereanalyse/essai nextflow/work/25/b975c5500ab3a684c907871e216052 , as mentioned in the bug report.
(2) looks like you may not have working docker on your computer, is that right?
Anton.
On Fri, Feb 21, 2020, 16:46 gopel notifications@github.com wrote:
Hi,
Distiller is very interesting for my research, so thank you. However, I stumble upon a weird problem upon running it (cf title). Could someone help me please?
Here is the line I enter in my nextflow repository: $ nextflow run distiller.nf -params-file project.yml
And here is the full message: N E X T F L O W ~ version 20.01.0 Launching distiller.nf [gigantic_mercator] - revision: 4b2ff8d377 executor > local (3) [- ] process > download_truncate_chunk_fastqs - executor > local (3) [- ] process > download_truncate_chunk_fastqs - [- ] process > local_truncate_chunk_fastqs - [- ] process > fastqc - [25/b975c5] process > map_parse_sort_chunks [ 67%] 2 of 3, failed: 2, retries: 2 [- ] process > merge_dedup_splitbam - [- ] process > bin_zoom_library_pairs - [- ] process > merge_zoom_library_group_coolers - [- ] process > merge_stats_libraries_into_groups - [89/ab2821] NOTE: Process map_parse_sort_chunks (library:your_library_name_1 run:lane1 chunk:0) terminated with an error exit status (127) -- Execution is retried (1) [aa/2fc4a3] NOTE: Process map_parse_sort_chunks (library:your_library_name_1 run:lane1 chunk:0) terminated with an error exit status (127) -- Execution is retried (2) Error executing process > 'map_parse_sort_chunks (library:your_library_name_1 run:lane1 chunk:0)'
executor > local (3) [- ] process > download_truncate_chunk_fastqs - [- ] process > local_truncate_chunk_fastqs - [- ] process > fastqc - [25/b975c5] process > map_parse_sort_chunks [100%] 3 of 3, failed: 3, retries: 2 ✘ [- ] process > merge_dedup_splitbam - [- ] process > bin_zoom_library_pairs - [- ] process > merge_zoom_library_group_coolers - [- ] process > merge_stats_libraries_into_groups - [89/ab2821] NOTE: Process map_parse_sort_chunks (library:your_library_name_1 run:lane1 chunk:0) terminated with an error exit status (127) -- Execution is retried (1) [aa/2fc4a3] NOTE: Process map_parse_sort_chunks (library:your_library_name_1 run:lane1 chunk:0) terminated with an error exit status (127) -- Execution is retried (2) Error executing process > 'map_parse_sort_chunks (library:your_library_name_1 run:lane1 chunk:0)'
executor > local (3) [- ] process > download_truncate_chunk_fastqs - [- ] process > local_truncate_chunk_fastqs - [- ] process > fastqc - [25/b975c5] process > map_parse_sort_chunks [100%] 3 of 3, failed: 3, retries: 2 ✘ [- ] process > merge_dedup_splitbam - [- ] process > bin_zoom_library_pairs - [- ] process > merge_zoom_library_group_coolers - [- ] process > merge_stats_libraries_into_groups - [89/ab2821] NOTE: Process map_parse_sort_chunks (library:your_library_name_1 run:lane1 chunk:0) terminated with an error exit status (127) -- Execution is retried (1) [aa/2fc4a3] NOTE: Process map_parse_sort_chunks (library:your_library_name_1 run:lane1 chunk:0) terminated with an error exit status (127) -- Execution is retried (2) Error executing process > 'map_parse_sort_chunks (library:your_library_name_1 run:lane1 chunk:0)'
Caused by: Process map_parse_sort_chunks (library:your_library_name_1 run:lane1 chunk:0) terminated with an error exit status (127)
Command executed:
TASK_TMP_DIR=$(mktemp -d -p ./ distiller.tmp.XXXXXXXXXX) touch your_library_name_1.lane1.hg38.0.bam bwa mem -t 8 -SP hg38_reference.fasta SRR027958_1.fastq.gz SRR027958_2.fastq.gz | tee >(samtools view -bS > your_library_name_1.lane1.hg38.0.bam) | pairtools parse --drop-readid --add-columns mapq -c hg38_chrom_sizes.txt | pairtools sort --nproc 8 -o your_library_name_1.lane1.hg38.0.pairsam.gz --tmpdir $TASK_TMP_DIR | cat
rm -rf $TASK_TMP_DIR
Command exit status: 127
Command output: (empty)
Command error: .command.run: line 259: docker: command not found
Work dir:
/home/biophymember/Projets/HiC_premiere_analyse/essai_nextflow/work/25/b975c5500ab3a684c907871e216052
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh
I don't know where the file '.command.sh' is. Here is the content of my folder: (base)biophymember@rddm503nc:~/Projets/HiC_premiere_analyse/essai_nextflow$ ls bin configs docker LICENSE pipeline_info README.md test work CHANGES.md distiller.nf environment.yml nextflow.config project.yml sorted_chromsizes VERSION
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gopel
Hi,
Distiller is very interesting for my research, so thank you. However, I stumble upon a weird problem upon running it (cf title). Could someone help me please?
Here is the line I enter in my nextflow repository: $ nextflow run distiller.nf -params-file project.yml
And here is the full message: N E X T F L O W ~ version 20.01.0 Launching
distiller.nf[gigantic_mercator] - revision: 4b2ff8d377 executor > local (3) [- ] process > download_truncate_chunk_fastqs - executor > local (3) [- ] process > download_truncate_chunk_fastqs - [- ] process > local_truncate_chunk_fastqs - [- ] process > fastqc - [25/b975c5] process > map_parse_sort_chunks [ 67%] 2 of 3, failed: 2, retries: 2 [- ] process > merge_dedup_splitbam - [- ] process > bin_zoom_library_pairs - [- ] process > merge_zoom_library_group_coolers - [- ] process > merge_stats_libraries_into_groups - [89/ab2821] NOTE: Processmap_parse_sort_chunks (library:your_library_name_1 run:lane1 chunk:0)terminated with an error exit status (127) -- Execution is retried (1) [aa/2fc4a3] NOTE: Processmap_parse_sort_chunks (library:your_library_name_1 run:lane1 chunk:0)terminated with an error exit status (127) -- Execution is retried (2) Error executing process > 'map_parse_sort_chunks (library:your_library_name_1 run:lane1 chunk:0)'executor > local (3) [- ] process > download_truncate_chunk_fastqs - [- ] process > local_truncate_chunk_fastqs - [- ] process > fastqc - [25/b975c5] process > map_parse_sort_chunks [100%] 3 of 3, failed: 3, retries: 2 ✘ [- ] process > merge_dedup_splitbam - [- ] process > bin_zoom_library_pairs - [- ] process > merge_zoom_library_group_coolers - [- ] process > merge_stats_libraries_into_groups - [89/ab2821] NOTE: Process
map_parse_sort_chunks (library:your_library_name_1 run:lane1 chunk:0)terminated with an error exit status (127) -- Execution is retried (1) [aa/2fc4a3] NOTE: Processmap_parse_sort_chunks (library:your_library_name_1 run:lane1 chunk:0)terminated with an error exit status (127) -- Execution is retried (2) Error executing process > 'map_parse_sort_chunks (library:your_library_name_1 run:lane1 chunk:0)'executor > local (3) [- ] process > download_truncate_chunk_fastqs - [- ] process > local_truncate_chunk_fastqs - [- ] process > fastqc - [25/b975c5] process > map_parse_sort_chunks [100%] 3 of 3, failed: 3, retries: 2 ✘ [- ] process > merge_dedup_splitbam - [- ] process > bin_zoom_library_pairs - [- ] process > merge_zoom_library_group_coolers - [- ] process > merge_stats_libraries_into_groups - [89/ab2821] NOTE: Process
map_parse_sort_chunks (library:your_library_name_1 run:lane1 chunk:0)terminated with an error exit status (127) -- Execution is retried (1) [aa/2fc4a3] NOTE: Processmap_parse_sort_chunks (library:your_library_name_1 run:lane1 chunk:0)terminated with an error exit status (127) -- Execution is retried (2) Error executing process > 'map_parse_sort_chunks (library:your_library_name_1 run:lane1 chunk:0)'Caused by:
Process
map_parse_sort_chunks (library:your_library_name_1 run:lane1 chunk:0)terminated with an error exit status (127)Command executed:
TASK_TMP_DIR=$(mktemp -d -p ./ distiller.tmp.XXXXXXXXXX) touch your_library_name_1.lane1.hg38.0.bam bwa mem -t 8 -SP hg38_reference.fasta SRR027958_1.fastq.gz SRR027958_2.fastq.gz | tee >(samtools view -bS > your_library_name_1.lane1.hg38.0.bam) | pairtools parse --drop-readid --add-columns mapq -c hg38_chrom_sizes.txt | pairtools sort --nproc 8 -o your_library_name_1.lane1.hg38.0.pairsam.gz --tmpdir $TASK_TMP_DIR | cat
rm -rf $TASK_TMP_DIR
Command exit status: 127
Command output: (empty)
Command error: .command.run: line 259: docker: command not found
Work dir: /home/biophymember/Projets/HiC_premiere_analyse/essai_nextflow/work/25/b975c5500ab3a684c907871e216052
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named
.command.shI don't know where the file '.command.sh' is. Here is the content of my folder: (base)biophymember@rddm503nc:~/Projets/HiC_premiere_analyse/essai_nextflow$ ls bin
configs docker LICENSE pipeline_info README.md test work CHANGES.md distiller.nf environment.yml nextflow.config project.yml sorted_chromsizes VERSION