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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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issue on bowtie index2 is missing #100

Closed hongchaoguo closed 6 years ago

hongchaoguo commented 6 years ago

Hi ,

I used the command below to run the script in SCG cluster according the link you sent to me. It still tells me the bowtie index2 is missing. Could you have a look? bds_scr atac.bds.BDS . atac.bds -q batch --account=joewu -species hg19 -nth 2 -fastq1_1 SRR4011961_1.fastq -fastq1_2 SRR4011961_2.fastq [SCR_NAME] : atac.bds.BDS.BDS [HOST] : dper730xd-srcf-d16-01.scg.stanford.edu [LOG_FILE_NAME] : . [BDS_PARAM] : atac.bds -q batch --account=joewu -species hg19 -nth 2 -fastq1_1 SRR4011961_1.fastq -fastq1_2 SRR4011961_2.fastq Then I opened the “atac.bds.BDS.BDS.log” created and it wrote like this: Walltime (macs2) : 23h Max. memory (macs2) : 15G Cap number of peaks (macs2) : 300K Extra parameters for macs2 callpeak : == callpeak naiver overlap settings Bedtools intersect -nonamecheck : false == IDR settings Append IDR threshold to IDR out_dir : false == ATAQC settings

TSS enrichment bed :

DNase bed for ataqc :

Promoter bed for ataqc :

Enhancer bed for ataqc :

Reg2map for ataqc :

Reg2map_bed for ataqc :

Roadmap metadata for ataqc :

Max. memory for ATAQC : 20G

Walltime for ATAQC : 47h

===atac pipeline settings

Type of pipeline : atac-seq

Align only : false

reads to subsample replicates (0 if no subsampling) : 0

reads to subsample for cross-corr. analysis : 25000000

No pseudo replicates : false

No ATAQC (advanced QC report) : false

No Cross-corr. analysis : false

Use CSEM for alignment : false

Smoothing window for MACS2 : 150

DNase Seq : false

IDR threshold : 0.1

Force to use ENCODE3 parameter set : false

Force to use ENCODE parameter set : false

Disable genome browser tracks : false

p-val thresh. for overlapped peaks : 0.01

MACS2 p-val thresh. for peaks : 0.01

MACS2 p-val thresh. for BIGWIGs : 0.01

Enable IDR on called peaks : false

Automatically find/trim adapters : false

== checking atac parameters ...

00:00:00.796 Error (modules/align_bowtie2.bds, line 44, pos 3): Bowtie2 index (-bwt2_idx) doesn't exists! (file: .1.bt2 or .1.bt2l)

leepc12 commented 6 years ago

Pipeline supports new SCG now. Replace -q batch --account=joewu with -q joewu and try again.

===================== There has been some important updates about SLURM support on Kundaje lab's genomic pipelines (ChIP-Seq and ATAC-Seq) for the new SCG cluster.

0) You don't need to re-install Conda and dependencies

1) Update BigDataScript (IMPORTANT) cd $HOME rm -rf .bds/ wget https://github.com/leepc12/BigDataScript/blob/master/distro/bds_Linux.tgz?raw=true -O bds_Linux.tgz tar zxvf bds_Linux.tgz

2) Update pipeline code Do git pull on the pipeline git directory.

3) Usage Add -q YOUR_PI_ACCOUNT_ON_SCG to the pipeline run command line. The parameter -q is used for sbatch --account on SCG and -p on Sherlock.

-ATAC-Seq: bds atac.bds ... -q YOUR_PI_ACCOUNT_ON_SCG -ChIP-Seq: bds chipseq.bds ... -q YOUR_PI_ACCOUNT_ON_SCG

Thanks,

Jin

leepc12 commented 6 years ago

closing this due to long inactivity.

hongchaoguo commented 6 years ago

Ok. Can I contact you at 4:30pm? Hongchao

2018-04-26 15:59 GMT-07:00 Jin Lee notifications@github.com:

Closed #100 https://github.com/kundajelab/atac_dnase_pipelines/issues/100.

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