lpantano
commented
2 years ago Hi,
that version of the pipeline doesn't use the input file, it needs the path where all the fastq files are. And we have seen issues when using the genome and bowtie index as inputs. It is better to leave the pipeline to create the indexes. As well, I will recommend to use the devel branch of the pipeline.
We are in an effort to migrate to the new nextflow DSL 2.0 version. There is a PR to devel that will be the latest version soon. That one uses the input file: #104. Hopefully it will available soon.
Thanks
rakeshponnala
klkeys
Hello, I'm trying to run multiple microRNA samples and the pipeline start to die at the trimming step : Any suggestions
nextflow run nf-core/smrnaseq -r 1.1.0 --input sample.sheet.csv -profile singularity --protocol qiaseq --fasta genome.fa --mirtrace_species cfa --mirna_gtf cfa.gff3 --bt_index /pathtogenomebowtie/ --hairpin hairpin.fa --mature mature.fa --mirtrace_protocol qiaseq --max_cpus 90 --max_memory 1000GB &&
eg: sample.sheet.csv is below:
sample, fastq_1 01-C04,01-C04_S15_R1_001.fastq.gz 01-C04, 01-C04_S3_R1_001.fastq.gz 01-C07, 01-C07S5_R1_001.fastq.gz 01-C08, 01-C08S9_R1_001.fastq.gz 01-C10, 01-C10S8_R1_001.fastq.gz 01-D01,01-D01S4_R1_001.fastq.gz 01-D02,01-D02S1_R1_001.fastq.gz 01-D02,01-D02S2_R1_001.fastq.gz 01-D03, 01-D03__S2_R1_001.fastq.gz
Error executing process > 'trim_galore (sample.sheet.csv)'
Caused by: Process
trim_galore (sample.sheet.csv)terminated with an error exit status (25)Command executed:
trim_galore --adapter AACTGTAGGCACCATCAAT --length 17 --max_length 40 --gzip sample.sheet.csv --fastqc
Command exit status: 25
Command output: (empty)
Command error: Multicore support not enabled. Proceeding with single-core trimming. Path to Cutadapt set as: 'cutadapt' (default) Cutadapt seems to be working fine (tested command 'cutadapt --version') Cutadapt version: 3.4 single-core operation. No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default)
Maximum length cutoff set to >> 40 bp <<; sequences longer than this threshold will be removed (only advised for smallRNA-trimming!)
File seems to be in SOLiD colorspace format which is not supported by Trim Galore (sequence is: '01-C04,01-C04_S15_R1_001.fastq.gz ')! Please use Cutadapt on colorspace files separately and check its documentation!