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kundajelab / atac_dnase_pipelines

ATAC-seq and DNase-seq processing pipeline
BSD 3-Clause "New" or "Revised" License
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BDS reporting wrong line #76

Closed amirshams84 closed 6 years ago

amirshams84 commented 6 years ago

It seems with recent update bds keep reporting one line before the actual command running (RUNNING) | bowtie2_PE rep1 | | if [[ -f $(which conda) && $(conda env list | grep bds_atac | wc -l) != "0" ]]; then source activate bds_atac; sleep 5; fi; export PATH=/usr/local/at

running (RUNNING) | markdup_bam_picard rep1 | | if [[ -f $(which conda) && $(conda env list | grep bds_atac | wc -l) != "0" ]]; then source activate bds_atac; sleep 5; fi; export PATH=/usr/local/a

running (RUNNING) | dedup_bam_PE_2 rep1 | | if [[ -f $(which conda) && $(conda env list | grep bds_atac | wc -l) != "0" ]]; then source activate bds_atac; sleep 5; fi; export PATH=/usr/local/at

leepc12 commented 6 years ago

Our pipeline does not correctly work with the latest BDS release. Please use a forked one on my repo (https://github.com/leepc12/BigDataScript).

Can you modify $HOME/.bds/bds.config and try again?

Replace

filterOutTaskHint = export

with

filterOutTaskHint = conda

Thanks,

Jin

On Mon, Oct 23, 2017 at 10:31 AM, amirshams notifications@github.com wrote:

It seems with recent update bds keep reporting one line before the actual command running (RUNNING) | bowtie2_PE rep1 | | if [[ -f $(which conda) && $(conda env list | grep bds_atac | wc -l) != "0" ]]; then source activate bds_atac; sleep 5; fi; export PATH=/usr/local/at

running (RUNNING) | markdup_bam_picard rep1 | | if [[ -f $(which conda) && $(conda env list | grep bds_atac | wc -l) != "0" ]]; then source activate bds_atac; sleep 5; fi; export PATH=/usr/local/a

running (RUNNING) | dedup_bam_PE_2 rep1 | | if [[ -f $(which conda) && $(conda env list | grep bds_atac | wc -l) != "0" ]]; then source activate bds_atac; sleep 5; fi; export PATH=/usr/local/at

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amirshams84 commented 6 years ago

I am using the bds version on your repo https://github.com/leepc12/BigDataScript/blob/master/distro/bds_Linux.tgz Updating the bds.config did not fix the issue

leepc12 commented 6 years ago

It's weird. It works fine on my cluster.

            | ----- | ----------------- | --------------- |

------------ |

| | 47346 | running (RUNNING) | bowtie2_PE rep1 | | bowtie2 -k 4 -X2000 --mm --local --threads 1 -x /mnt/data/bds_pipeline_genome_data/mm10_ENCODE/bowtie2_index/mm10_no_alt_analysis_set_ENCODE.fasta; -1 /srv/scratch/shared/wotan/leepc12/run/ENCODE3_NEW2/ENCSR983JWA/out/align/rep1/ENCFF847BCI.trim.fastq.gz -2 /srv/scratch/shared/wotan/leepc12/run/ENCO |

Did you have bds.config on the right location ($HOME/.bds/bds.config)?

You can simply ignore it. It's just for showing a task hint, doesn't affect outputs.

Thanks,

Jin

On Mon, Oct 23, 2017 at 12:16 PM, amirshams notifications@github.com wrote:

I am using the bds version on your repo https://github.com/leepc12/BigDataScript/blob/master/distro/bds_Linux.tgz Updating the bds.config did not fix the issue

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