pipelines issueshttps://gitlab.com/groups/cgps/ghru/pipelines/-/issues2021-12-02T07:32:19Zhttps://gitlab.com/cgps/ghru/pipelines/assembly/-/issues/15Error while running SPADES assembly2021-12-02T07:32:19ZSreeram Chandra Murthy PeelaError while running SPADES assemblyI was trying to run the assembly pipeline and faced error (exit status 1) while the other parts of the pipeline worked well. Below is the screenshot of the error log, and the params file for your reference.[params.txt](/uploads/b7b0c9293...I was trying to run the assembly pipeline and faced error (exit status 1) while the other parts of the pipeline worked well. Below is the screenshot of the error log, and the params file for your reference.[params.txt](/uploads/b7b0c92932defb7af7289640a83f732e/params.txt)
[spades.log](/uploads/121a0174218805e65b8b85335dfb87be/spades.log)![Screenshot__13_](/uploads/a74bf1a5579822db73c716cfa628502e/Screenshot__13_.png)https://gitlab.com/cgps/ghru/pipelines/assembly/-/issues/9error executing process genome_size_estimation2019-11-09T11:56:14ZPWSmiterror executing process genome_size_estimationPipeline gets frequently aborted at genome_size_estimation step. The test files and some fastq work fine suggesting installation is working.
Tried with SRA project: ERP023526 (44 genomes). Atleast 28 out of the 44 seemed to have failed ...Pipeline gets frequently aborted at genome_size_estimation step. The test files and some fastq work fine suggesting installation is working.
Tried with SRA project: ERP023526 (44 genomes). Atleast 28 out of the 44 seemed to have failed or caused Nextflow to stop. I downloaded the fastq files to run them locally. Doesn't seem to be solely due to this project fastqs, same issue with some other public datasets.
Message:
Error executing process > 'genome_size_estimation (ERR2008069)'
Caused by:
Process `genome_size_estimation (ERR2008069)` terminated with an error exit status (1)
Command executed:
kat hist --mer_len 21 --thread 1 --output_prefix ERR2008069 ERR2008069_1.fastq.gz > /dev/null 2>&1 && minima=`cat ERR2008069.dist_analysis.json | jq '.global_minima .freq' | tr -d '\n'`
mash sketch -o sketch_ERR2008069 -k 32 -m $minima -r ERR2008069_1.fastq.gz 2> mash_stats.out
Command exit status:
1
Command output:
(empty)
Running locally on Macbook Pro:
nextflow version 19.07.0.5106
Docker version 18.09.2, build 6247962
pipeline version 1.4.0 (downloaded 2 days ago from gitlab)
openjdk 10.0.2 2018-07-17
OpenJDK Runtime Environment Zulu10.3+5 (build 10.0.2+13)
OpenJDK 64-Bit Server VM Zulu10.3+5 (build 10.0.2+13, mixed mode)
command: nextflow run assembly.nf --input_dir input --output_dir output --fastq_pattern "*_{1,2}*.fastq.gz" --adapter_file adapters.fas --qc_conditions qc_conditions.yml -with-docker bioinformant/ghru-assembly:latest -resumehttps://gitlab.com/cgps/ghru/pipelines/snp_phylogeny/-/issues/1Change help2019-07-17T05:50:40ZAnthony UnderwoodChange help`--reference_sequence` should be `--reference`
In https://gitlab.com/cgps/ghru/pipelines/snp_phylogeny/blob/master/snp_phylogeny.nf#L24
and in README`--reference_sequence` should be `--reference`
In https://gitlab.com/cgps/ghru/pipelines/snp_phylogeny/blob/master/snp_phylogeny.nf#L24
and in README