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nf-core / hic

Analysis of Chromosome Conformation Capture data (Hi-C)
https://nf-co.re/hic
MIT License
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markdown_to_html.py otuput.md -o results_description.html is failing #130

Closed laramieparatus closed 1 year ago

laramieparatus commented 2 years ago

Check Documentation

I have checked the following places for your error:

Description of the bug

markdown_to_html.py output.md -o results_description.html is failing

Steps to reproduce

Steps to reproduce the behaviour:

  1. Command line: nextflow run nf-core/hic -profile docker --input '/mnt/efs/fs1/Projects/Assembly/hic/*_R{1,2}.fastq.gz' --digestion 'arima' --fasta /mnt/efs/fs1/Projects/Assembly/hic/nfcore/asm.contigs.purged.fsa
  2. See error: N E X T F L O W ~ version 22.04.4 Launching [https://github.com/nf-core/hic](https://github.com/nf-core/hic%60) [modest_cori] DSL1 - revision: ac74763a91 [master]
                                    ,--./,-.
    ___     __   __   __   ___     /,-._.--~'

|\ | | / / \ |__) |__ } { | \| | \__, \__/ | \ |___ \-.,--, .,._,' nf-core/hic v1.3.0

WARN: The into operator should be used to connect two or more target channels -- consider to replace it with .set { fasta_for_index } Core Nextflow options revision : master runName : modest_cori containerEngine : docker container : nfcore/hic:1.3.0 launchDir : /mnt/efs/fs1/Projects/Assembly/hic/nfcore workDir : /mnt/efs/fs1/Projects/Assembly/hic/nfcore/work projectDir : /home/llindsey/.nextflow/assets/nf-core/hic userName : llindsey profile : docker configFiles : /home/llindsey/.nextflow/assets/nf-core/hic/nextflow.config

Input/output options input : /mnt/efs/fs1/Projects/Assembly/hic/*_R{1,2}.fastq.gz input_paths : false

Reference genome options fasta : /mnt/efs/fs1/Projects/Assembly/hic/nfcore/asm.contigs.purged.fsa

Digestion Hi-C digestion : arima restriction_site : ^GATC,G^ANT ligation_site : GATCGATC,GATCGANT,GANTGATC,GANTGANT

DNAse Hi-C min_cis_dist : 0

Alignments bwt2_opts_end2end : --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder bwt2_opts_trimmed : --very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder

Valid Pairs Detection max_insert_size : 0 min_insert_size : 0 max_restriction_fragment_size: 0 min_restriction_fragment_size: 0

Contact maps bin_size : 1000000 ice_filter_high_count_perc : 0

Downstream Analysis res_dist_decay : 250000 tads_caller : insulation res_tads : 40000

Generic options max_multiqc_email_size : 25 MB

Max job request options max_cpus : 8 max_memory : 24 GB max_time : 10d

Only displaying parameters that differ from defaults. executor > local (5) [79/ee1055] process > get_software_versions [ 0%] 0 of 1 [1a/2d517d] process > makeBowtie2Index (asm.contigs.purged) [ 0%] 0 of 1 [35/5b873c] process > makeChromSize (asm.contigs.purged.fsa) [ 0%] 0 of 1 [9e/d976a0] process > getRestrictionFragments (asm.contigs.purged.fsa ^GATC,G^ANT) [ 0%] 0 of 1 [- ] process > bowtie2_end_to_end - executor > local (5) [79/ee1055] process > get_software_versions [ 0%] 0 of 1 [1a/2d517d] process > makeBowtie2Index (asm.contigs.purged) [ 0%] 0 of 1 [35/5b873c] process > makeChromSize (asm.contigs.purged.fsa) [100%] 1 of 1, failed: 1 ✘ [9e/d976a0] process > getRestrictionFragments (asm.contigs.purged.fsa ^GATC,G^ANT) [ 0%] 0 of 1 [- ] process > bowtie2_end_to_end - [- ] process > trim_reads - executor > local (5) [79/ee1055] process > get_software_versions [100%] 1 of 1, failed: 1 ✘ [1a/2d517d] process > makeBowtie2Index (asm.contigs.purged) [100%] 1 of 1, failed: 1 ✘ [35/5b873c] process > makeChromSize (asm.contigs.purged.fsa) [100%] 1 of 1, failed: 1 ✘ [9e/d976a0] process > getRestrictionFragments (asm.contigs.purged.fsa ^GATC,G^ANT) [100%] 1 of 1, failed: 1 ✘ [- ] process > bowtie2_end_to_end - [- ] process > trim_reads - [- ] process > bowtie2_on_trimmed_reads - [- ] process > bowtie2_merge_mapping_steps - executor > local (5) [79/ee1055] process > get_software_versions [100%] 1 of 1, failed: 1 ✘ [1a/2d517d] process > makeBowtie2Index (asm.contigs.purged) [100%] 1 of 1, failed: 1 ✘ [35/5b873c] process > makeChromSize (asm.contigs.purged.fsa) [100%] 1 of 1, failed: 1 ✘ [9e/d976a0] process > getRestrictionFragments (asm.contigs.purged.fsa ^GATC,G^ANT) [100%] 1 of 1, failed: 1 ✘ [- ] process > bowtie2_end_to_end - [- ] process > trim_reads - [- ] process > bowtie2_on_trimmed_reads - [- ] process > bowtie2_merge_mapping_steps - [- ] process > combine_mates - [- ] process > get_valid_interaction - [- ] process > remove_duplicates - [- ] process > merge_stats - [- ] process > build_contact_maps - [- ] process > run_ice - [- ] process > convert_to_pairs - [- ] process > cooler_raw - [- ] process > cooler_balance - [- ] process > cooler_zoomify - [- ] process > dist_decay - [- ] process > compartment_calling - [- ] process > tads_hicexplorer - [- ] process > tads_insulation - [- ] process > multiqc - [4c/d884b8] process > output_documentation [100%] 1 of 1, failed: 1 ✘ Execution cancelled -- Finishing pending tasks before exit Error executing process > 'output_documentation'

Caused by: Process output_documentation terminated with an error exit status (1)

Command executed:

markdown_to_html.py output.md -o results_description.html

Command exit status: 1

Command output: (empty)

Command error: touch: cannot touch '.command.trace': Permission denied

Work dir: /mnt/efs/fs1/Projects/Assembly/hic/nfcore/work/4c/d884b8fcff6811f8652a06cafae5ad

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

Expected behaviour

Expected completion of nf-core/hic pipeline without failure

Log files

Have you provided the following extra information/files:

System

Nextflow Installation

Container engine

nservant commented 2 years ago

Hi, it seems that this is just a right issue. You cannot write in your work outputs