How to run the pipeline in local machine with read data

[ld9866]

Ask away!

Hello developer We have been interested in pore-c recently. We can deploy and execute test files on our server smoothly, but we find that we have encountered many problems in using real data and can not understand the operation method of the pipeline error. We download the https://www.nature.com/articles/s41587-022-01289-z#Sec13 data "PRJNA627432" and the human reference, we want to use the "LNCaP_vehicle.fastq.gz" to try the pipeline, but we do not know how to write the propore code, can you help us?

Code: nextflow run /home/test/HIC/wf-pore-c-1.1.0 \

--fastq /home/test/HIC/PoreC/LNCaP_vehicle.fastq.gz \ --ref GCF_000001405.40_GRCh38.p14_genomic.fna \ --cutter NlaIII \ --bed \ --threads 64 \ --paired_end_minimum_distance 100 --paired_end_maximum_distance 200 --hi_c --mcool --paired_end

---

This is epi2me-labs/wf-pore-c v1.1.0.

Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files. executor > local (5) [3d/97faf1] process > POREC:fastcat (1) [ 0%] 0 of 1 [- ] process > POREC:index_bam - [be/26ebf9] process > POREC:prepare_genome:index_ref_fai (1) [100%] 1 of 1 ✔ [f2/bf376a] process > POREC:prepare_genome:index_ref_mmi (1) [ 0%] 0 of 1 [- ] process > POREC:digest_align_annotate - [- ] process > POREC:haplotag_alignments - [- ] process > POREC:merge_coordsorted_bams - [- ] process > POREC:merge_namesorted_bams - [- ] process > POREC:create_restriction_bed - [- ] process > POREC:to_pairs_file - [- ] process > POREC:pairsToCooler - [- ] process > POREC:merge_mcools - executor > local (5) [3d/97faf1] process > POREC:fastcat (1) [100%] 1 of 1, failed: 1 ✘ [- ] process > POREC:index_bam - [be/26ebf9] process > POREC:prepare_genome:index_ref_fai (1) [100%] 1 of 1 ✔ [f2/bf376a] process > POREC:prepare_genome:index_ref_mmi (1) [ 0%] 0 of 1 [- ] process > POREC:digest_align_annotate - [- ] process > POREC:haplotag_alignments - [- ] process > POREC:merge_coordsorted_bams - [- ] process > POREC:merge_namesorted_bams - [- ] process > POREC:create_restriction_bed - [- ] process > POREC:to_pairs_file - [- ] process > POREC:pairsToCooler - [- ] process > POREC:merge_mcools - executor > local (5) [3d/97faf1] process > POREC:fastcat (1) [100%] 1 of 1, failed: 1 ✘ [- ] process > POREC:index_bam - [be/26ebf9] process > POREC:prepare_genome:index_ref_fai (1) [100%] 1 of 1 ✔ [f2/bf376a] process > POREC:prepare_genome:index_ref_mmi (1) [ 0%] 0 of 1 [- ] process > POREC:digest_align_annotate - [- ] process > POREC:haplotag_alignments -[- ] process > POREC:merge_coordsorted_bams - [- ] process > POREC:merge_namesorted_bams - [- ] process > POREC:create_restriction_bed - [- ] process > POREC:to_pairs_file - [- ] process > POREC:pairsToCooler - [- ] process > POREC:merge_mcools - [- ] process > POREC:merge_pairs - [- ] process > POREC:merge_pairs_stats - [- ] process > POREC:pair_stats_report - [- ] process > POREC:merge_paired_end_bams - [7b/2f5194] process > POREC:getVersions [100%] 1 of 1 ✔ [0a/edeb72] process > POREC:getParams [100%] 1 of 1 ✔ [- ] process > POREC:makeReport [ 0%] 0 of 1[- ] process > POREC:prepare_hic - [- ] process > POREC:createBed - [- ] process > POREC:get_filtered_out_bam - [- ] process > output - ERROR ~ Error executing process > 'POREC:fastcat (1)'

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

Command executed:

mkdir fastcat_stats fastcat -s LNCaP_vehicle -r >(bgzip -c > fastcat_stats/per-read-stats.tsv.gz) -f fastcat_stats/per-file-stats.tsv --histograms histograms input | bgzip > seqs.fastq.gz

mv histograms/* fastcat_stats

extract the run IDs from the per-read stats

csvtk cut -tf runid fastcat_stats/per-read-stats.tsv.gz | csvtk del-header | sort | uniq > fastcat_stats/run_ids

Command exit status: 1

Command output: (empty)

Command error: Truncated quality string found for record in file 'input'. Completed processing with errors. Outputs may be incomplete.

Work dir: /home/test/HIC/PoreC/work/3d/97faf1d8e114f90d1ed856b6c6d761

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

-- Check '.nextflow.log' file for details

[sarahjeeeze]

Hi, thanks for trying out the pipeline - Looks like there is something wrong with that fastq file quality scores, does the repo include a BAM file? If so you could try that with the workflow. I don't have access to that fastq file to try to recreate the error but have requested access so will take another look if i manage to get the file.

[sarahjeeeze]

Closing through lack of response

[Blosers]

您好，请问您是如何下载并安装该软件到本地的？可以给我一个具体的流程吗？实在是抱歉，对于生信这方面我是一个小白，不是很明白，所以希望您可以在有空的时候给我一些建议和方法，非常感谢您，谢谢。