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Data set #126
Comments
If you don't explicitly specify output directory with |
out/ is generated, but it does not have all the files as listed on your main page. Could you please tell me what data have you used to generate all those files ? I am not quite sure whether the discrepancy is in the data set I am using or something is missing from the pipeline installation. Thank you |
Could you also please tell me which fastqs you have used as part of running the pipeline ? as the data set coming from the Many thanks |
I have tried running it with different fastqs from various sources, but that crashes down with |
Did you specify species (hg38, mm10, ...) by |
Thanks Jin, yes I have specified |
Please post a full log (including |
The command is e.g :
and the output is :
|
Please do the following for more info:
```
$ cat /homes/reham/ATAC-Seq/atac_dnase_pipelines/default.env
$ ls -l /homes/reham/ATAC-Seq/genomes/mm10
$ ls -l /homes/reham/ATAC-Seq/genomes
```
Jin
```
…On Mon, Jul 2, 2018 at 8:22 AM, rehamFatima ***@***.***> wrote:
The command is e.g :
bds atac.bds -species mm10 -se -gensz mm -fastq1 ../genomes/mm10_no_alt_analysis_set_ENCODE.fastq.gz
-chrsz ../genomes/mm10/mm10.chrom.sizes
and the output is :
Picked up _JAVA_OPTIONS: -Xms8G -Xmx8G -XX:ParallelGCThreads=1
== git info
Latest git commit : d0babc6 (Tue Jun 5 18:40:20 2018)
Reading parameters from section (default) in file(/homes/reham/ATAC-Seq/atac_dnase_pipelines/default.env)...
== configuration file info
Hostname : ebi5-164.ebi.ac.uk
Configuration file :
Environment file : /homes/reham/ATAC-Seq/atac_dnase_pipelines/default.env
== parallelization info
No parallel jobs : false
Maximum # threads : 8
== cluster/system info
Walltime (general) : 5h50m
Max. memory (general) : 7G
Force to use a system : local
Process priority (niceness) : 0
Retiral for failed tasks : 0
Submit tasks to a cluster queue :
Unlimited cluster mem./walltime : false
Use --acount instead of SLURM partition : false
Java temporary directory : ${TMPDIR}
== shell environment info
Conda env. : bds_atac
Conda env. for python3 : bds_atac_py3
Conda bin. directory :
Shell cmd. for init. : if [[ -f $(which conda) && $(conda env list | grep bds_atac | wc -l) != "0" ]]; then source activate bds_atac; sleep 5; fi; export PATH=/homes/reham/ATAC-Seq/atac_dnase_pipelines/.:/homes/reham/ATAC-Seq/atac_dnase_pipelines/modules:/homes/reham/ATAC-Seq/atac_dnase_pipelines/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)
Shell cmd. for init.(py3) : if [[ -f $(which conda) && $(conda env list | grep bds_atac_py3 | wc -l) != "0" ]]; then source activate bds_atac_py3; sleep 5; fi; export PATH=/homes/reham/ATAC-Seq/atac_dnase_pipelines/.:/homes/reham/ATAC-Seq/atac_dnase_pipelines/modules:/homes/reham/ATAC-Seq/atac_dnase_pipelines/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)
Shell cmd. for fin. : TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."; sleep 0
Cluster task min. len. : 60
Cluster task delay : 0
== output directory/title info
Output dir. : /homes/reham/ATAC-Seq/atac_dnase_pipelines/out
Title (prefix) : atac_dnase_pipelines
Reading parameters from section (default) in file(/homes/reham/ATAC-Seq/atac_dnase_pipelines/default.env)...
== species settings
Species : mm10
Species file :
Species name (WashU browser) : mm10
Ref. genome seq. fasta :
Chr. sizes file : ../genomes/mm10/mm10.chrom.sizes
Black list bed :
Ref. genome seq. dir. :
== ENCODE accession settings
ENCODE experiment accession :
ENCODE award RFA :
ENCODE assay category :
ENCODE assay title :
ENCODE award :
ENCODE lab :
ENCODE assembly genome :
ENCODE alias prefix : KLAB_PIPELINE
ENCODE alias suffix :
== report settings
URL root for output directory :
Genome coord. for browser tracks :
== align multimapping settings
# alignments reported for multimapping : 0
== align bowtie2 settings
Bowtie2 index :
Replacement --score-min for bowtie2 :
Walltime (bowtie2) : 47h
Max. memory (bowtie2) : 12G
Extra param. (bowtie2) :
Disable index on memory (bowtie2) : false
== adapter trimmer settings
Maximum allowed error rate for cutadapt : 0.10
Minimum trim. length for cutadapt -m : 5
Walltime (adapter trimming) : 23h
Max. memory (adapter trimming) : 12G
== postalign bam settings
MAPQ reads rm thresh. : 30
Rm. tag reads with str. : chrM
No dupe removal in filtering raw bam : false
Walltime (bam filter) : 23h
Max. memory (bam filter) : 12G
Dup marker : picard
Use sambamba markdup (instead of picard) : false
== postalign bed/tagalign settings
Max. memory for UNIX shuf : 12G
No --random-source for UNIX shuf : false
== postalign cross-corr. analysis settings
Max. memory for UNIX shuf : 12G
User-defined cross-corr. peak strandshift : -1
Extra parameters for cross-corr. analysis :
Max. memory for cross-corr. analysis : 15G
Stack size for cross-corr. analysis :
== callpeak macs2 settings
Genome size (hs,mm) : mm
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 ...
00:00:00.925 Error (modules/align_bowtie2.bds, line 44, pos 3): Bowtie2 index (-bwt2_idx) doesn't exists! (file: .1.bt2 or .1.bt2l)
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|
Thanks Jin,
should I send you the output for these ?
…On 2018-07-02 16:28, Jin Lee wrote:
Please do the following for more info:
```
$ cat /homes/reham/ATAC-Seq/atac_dnase_pipelines/default.env
$ ls -l /homes/reham/ATAC-Seq/genomes/mm10
$ ls -l /homes/reham/ATAC-Seq/genomes
```
Jin
```
On Mon, Jul 2, 2018 at 8:22 AM, rehamFatima ***@***.***>
wrote:
> The command is e.g :
>
> bds atac.bds -species mm10 -se -gensz mm -fastq1
../genomes/mm10_no_alt_analysis_set_ENCODE.fastq.gz
> -chrsz ../genomes/mm10/mm10.chrom.sizes
>
> and the output is :
>
> Picked up _JAVA_OPTIONS: -Xms8G -Xmx8G -XX:ParallelGCThreads=1
>
>
> == git info
> Latest git commit : d0babc6 (Tue
Jun 5 18:40:20 2018)
> Reading parameters from section (default) in
file(/homes/reham/ATAC-Seq/atac_dnase_pipelines/default.env)...
>
>
> == configuration file info
> Hostname : ebi5-164.ebi.ac.uk
> Configuration file :
> Environment file :
/homes/reham/ATAC-Seq/atac_dnase_pipelines/default.env
>
>
> == parallelization info
> No parallel jobs : false
> Maximum # threads : 8
>
>
> == cluster/system info
> Walltime (general) : 5h50m
> Max. memory (general) : 7G
> Force to use a system : local
> Process priority (niceness) : 0
> Retiral for failed tasks : 0
> Submit tasks to a cluster queue :
> Unlimited cluster mem./walltime : false
> Use --acount instead of SLURM partition : false
> Java temporary directory : ${TMPDIR}
>
>
> == shell environment info
> Conda env. : bds_atac
> Conda env. for python3 : bds_atac_py3
> Conda bin. directory :
>
> Shell cmd. for init. : if [[ -f $(which conda) && $(conda env list |
grep bds_atac | wc -l) != "0" ]]; then source activate bds_atac; sleep
5; fi; export
PATH=/homes/reham/ATAC-Seq/atac_dnase_pipelines/.:/homes/reham/ATAC-Seq/atac_dnase_pipelines/modules:/homes/reham/ATAC-Seq/atac_dnase_pipelines/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
set -o pipefail; STARTTIME=$(date +%s)
>
> Shell cmd. for init.(py3) : if [[ -f $(which conda) && $(conda env
list | grep bds_atac_py3 | wc -l) != "0" ]]; then source activate
bds_atac_py3; sleep 5; fi; export
PATH=/homes/reham/ATAC-Seq/atac_dnase_pipelines/.:/homes/reham/ATAC-Seq/atac_dnase_pipelines/modules:/homes/reham/ATAC-Seq/atac_dnase_pipelines/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
set -o pipefail; STARTTIME=$(date +%s)
>
> Shell cmd. for fin. : TASKTIME=$[$(date +%s)-${STARTTIME}]; echo
"Task has finished (${TASKTIME} seconds)."; sleep 0
>
> Cluster task min. len. : 60
>
> Cluster task delay : 0
>
>
> == output directory/title info
> Output dir. : /homes/reham/ATAC-Seq/atac_dnase_pipelines/out
> Title (prefix) : atac_dnase_pipelines
> Reading parameters from section (default) in
file(/homes/reham/ATAC-Seq/atac_dnase_pipelines/default.env)...
>
>
> == species settings
> Species : mm10
> Species file :
>
> Species name (WashU browser) : mm10
> Ref. genome seq. fasta :
> Chr. sizes file : ../genomes/mm10/mm10.chrom.sizes
> Black list bed :
> Ref. genome seq. dir. :
>
>
> == ENCODE accession settings
> ENCODE experiment accession :
> ENCODE award RFA :
> ENCODE assay category :
> ENCODE assay title :
> ENCODE award :
> ENCODE lab :
> ENCODE assembly genome :
> ENCODE alias prefix : KLAB_PIPELINE
> ENCODE alias suffix :
>
>
> == report settings
> URL root for output directory :
> Genome coord. for browser tracks :
>
>
> == align multimapping settings
> # alignments reported for multimapping : 0
>
>
> == align bowtie2 settings
> Bowtie2 index :
> Replacement --score-min for bowtie2 :
> Walltime (bowtie2) : 47h
> Max. memory (bowtie2) : 12G
> Extra param. (bowtie2) :
> Disable index on memory (bowtie2) : false
>
>
> == adapter trimmer settings
> Maximum allowed error rate for cutadapt : 0.10
> Minimum trim. length for cutadapt -m : 5
> Walltime (adapter trimming) : 23h
> Max. memory (adapter trimming) : 12G
>
>
> == postalign bam settings
> MAPQ reads rm thresh. : 30
> Rm. tag reads with str. : chrM
> No dupe removal in filtering raw bam : false
> Walltime (bam filter) : 23h
> Max. memory (bam filter) : 12G
> Dup marker : picard
> Use sambamba markdup (instead of picard) : false
>
>
> == postalign bed/tagalign settings
> Max. memory for UNIX shuf : 12G
> No --random-source for UNIX shuf : false
>
>
> == postalign cross-corr. analysis settings
> Max. memory for UNIX shuf : 12G
> User-defined cross-corr. peak strandshift : -1
> Extra parameters for cross-corr. analysis :
> Max. memory for cross-corr. analysis : 15G
> Stack size for cross-corr. analysis :
>
>
> == callpeak macs2 settings
> Genome size (hs,mm) : mm
> 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 ...
> 00:00:00.925 Error (modules/align_bowtie2.bds, line 44, pos 3):
Bowtie2 index (-bwt2_idx) doesn't exists! (file: .1.bt2 or .1.bt2l)
>
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub
>
<#126 (comment)>,
> or mute the thread
>
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> .
>
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thread [2].
Links:
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[1]
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|
Please just post them here
On Mon, Jul 2, 2018 at 9:04 AM, rehamFatima <[email protected]>
wrote:
… Thanks Jin,
should I send you the output for these ?
On 2018-07-02 16:28, Jin Lee wrote:
> Please do the following for more info:
> ```
> $ cat /homes/reham/ATAC-Seq/atac_dnase_pipelines/default.env
> $ ls -l /homes/reham/ATAC-Seq/genomes/mm10
> $ ls -l /homes/reham/ATAC-Seq/genomes
> ```
>
> Jin
> ```
>
> On Mon, Jul 2, 2018 at 8:22 AM, rehamFatima ***@***.***>
> wrote:
>
>> The command is e.g :
>>
>> bds atac.bds -species mm10 -se -gensz mm -fastq1
> ../genomes/mm10_no_alt_analysis_set_ENCODE.fastq.gz
>> -chrsz ../genomes/mm10/mm10.chrom.sizes
>>
>> and the output is :
>>
>> Picked up _JAVA_OPTIONS: -Xms8G -Xmx8G -XX:ParallelGCThreads=1
>>
>>
>> == git info
>> Latest git commit : d0babc6 (Tue
> Jun 5 18:40:20 2018)
>> Reading parameters from section (default) in
> file(/homes/reham/ATAC-Seq/atac_dnase_pipelines/default.env)...
>>
>>
>> == configuration file info
>> Hostname : ebi5-164.ebi.ac.uk
>> Configuration file :
>> Environment file :
> /homes/reham/ATAC-Seq/atac_dnase_pipelines/default.env
>>
>>
>> == parallelization info
>> No parallel jobs : false
>> Maximum # threads : 8
>>
>>
>> == cluster/system info
>> Walltime (general) : 5h50m
>> Max. memory (general) : 7G
>> Force to use a system : local
>> Process priority (niceness) : 0
>> Retiral for failed tasks : 0
>> Submit tasks to a cluster queue :
>> Unlimited cluster mem./walltime : false
>> Use --acount instead of SLURM partition : false
>> Java temporary directory : ${TMPDIR}
>>
>>
>> == shell environment info
>> Conda env. : bds_atac
>> Conda env. for python3 : bds_atac_py3
>> Conda bin. directory :
>>
>> Shell cmd. for init. : if [[ -f $(which conda) && $(conda env list |
> grep bds_atac | wc -l) != "0" ]]; then source activate bds_atac; sleep
> 5; fi; export
> PATH=/homes/reham/ATAC-Seq/atac_dnase_pipelines/.:/homes/
reham/ATAC-Seq/atac_dnase_pipelines/modules:/homes/
reham/ATAC-Seq/atac_dnase_pipelines/utils:${PATH}:/bin:/
usr/bin:/usr/local/bin:${HOME}/.bds;
> set -o pipefail; STARTTIME=$(date +%s)
>>
>> Shell cmd. for init.(py3) : if [[ -f $(which conda) && $(conda env
> list | grep bds_atac_py3 | wc -l) != "0" ]]; then source activate
> bds_atac_py3; sleep 5; fi; export
> PATH=/homes/reham/ATAC-Seq/atac_dnase_pipelines/.:/homes/
reham/ATAC-Seq/atac_dnase_pipelines/modules:/homes/
reham/ATAC-Seq/atac_dnase_pipelines/utils:${PATH}:/bin:/
usr/bin:/usr/local/bin:${HOME}/.bds;
> set -o pipefail; STARTTIME=$(date +%s)
>>
>> Shell cmd. for fin. : TASKTIME=$[$(date +%s)-${STARTTIME}]; echo
> "Task has finished (${TASKTIME} seconds)."; sleep 0
>>
>> Cluster task min. len. : 60
>>
>> Cluster task delay : 0
>>
>>
>> == output directory/title info
>> Output dir. : /homes/reham/ATAC-Seq/atac_dnase_pipelines/out
>> Title (prefix) : atac_dnase_pipelines
>> Reading parameters from section (default) in
> file(/homes/reham/ATAC-Seq/atac_dnase_pipelines/default.env)...
>>
>>
>> == species settings
>> Species : mm10
>> Species file :
>>
>> Species name (WashU browser) : mm10
>> Ref. genome seq. fasta :
>> Chr. sizes file : ../genomes/mm10/mm10.chrom.sizes
>> Black list bed :
>> Ref. genome seq. dir. :
>>
>>
>> == ENCODE accession settings
>> ENCODE experiment accession :
>> ENCODE award RFA :
>> ENCODE assay category :
>> ENCODE assay title :
>> ENCODE award :
>> ENCODE lab :
>> ENCODE assembly genome :
>> ENCODE alias prefix : KLAB_PIPELINE
>> ENCODE alias suffix :
>>
>>
>> == report settings
>> URL root for output directory :
>> Genome coord. for browser tracks :
>>
>>
>> == align multimapping settings
>> # alignments reported for multimapping : 0
>>
>>
>> == align bowtie2 settings
>> Bowtie2 index :
>> Replacement --score-min for bowtie2 :
>> Walltime (bowtie2) : 47h
>> Max. memory (bowtie2) : 12G
>> Extra param. (bowtie2) :
>> Disable index on memory (bowtie2) : false
>>
>>
>> == adapter trimmer settings
>> Maximum allowed error rate for cutadapt : 0.10
>> Minimum trim. length for cutadapt -m : 5
>> Walltime (adapter trimming) : 23h
>> Max. memory (adapter trimming) : 12G
>>
>>
>> == postalign bam settings
>> MAPQ reads rm thresh. : 30
>> Rm. tag reads with str. : chrM
>> No dupe removal in filtering raw bam : false
>> Walltime (bam filter) : 23h
>> Max. memory (bam filter) : 12G
>> Dup marker : picard
>> Use sambamba markdup (instead of picard) : false
>>
>>
>> == postalign bed/tagalign settings
>> Max. memory for UNIX shuf : 12G
>> No --random-source for UNIX shuf : false
>>
>>
>> == postalign cross-corr. analysis settings
>> Max. memory for UNIX shuf : 12G
>> User-defined cross-corr. peak strandshift : -1
>> Extra parameters for cross-corr. analysis :
>> Max. memory for cross-corr. analysis : 15G
>> Stack size for cross-corr. analysis :
>>
>>
>> == callpeak macs2 settings
>> Genome size (hs,mm) : mm
>> 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 ...
>> 00:00:00.925 Error (modules/align_bowtie2.bds, line 44, pos 3):
> Bowtie2 index (-bwt2_idx) doesn't exists! (file: .1.bt2 or .1.bt2l)
>>
>>
>> —
>> You are receiving this because you commented.
>> Reply to this email directly, view it on GitHub
>>
> <#126#
issuecomment-401841414>,
>> or mute the thread
>>
> <https://github.com/notifications/unsubscribe-auth/AIOd_
GZ5SjTMj8HWBqaLWCUd0eu31tovks5uCjq6gaJpZM4U3hfe>
>> .
>>
> --
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub [1], or mute the
> thread [2].
>
> Links:
> ------
> [1]
> https://github.com/kundajelab/atac_dnase_pipelines/issues/
126#issuecomment-401843182
> [2]
> https://github.com/notifications/unsubscribe-auth/Aas3Z7KbU-
6dm79PMiLj4ZZhu-P7kzifks5uCjwhgaJpZM4U3hfe
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<#126 (comment)>,
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.
|
|
( I have had to reinstall the genome data to another location ) |
and
I hope these will help. |
Please add |
Command :
Output :
|
Can you share your BAM files for debugging? original: Is your input BAM file filtered/deduped? any quality problem with the input BAM file? |
PFA I just used the bed files within the mm10 genome installed and generated the bam file using bedtools bedtobam. Could you tell how or what should I be looking for in terms of quality problem with the bam file? |
That BED file in the mm10 genome data is not for testing purpose. If you just wanted to test our pipeline. I recommend to use a new pipeline https://github.com/ENCODE-DCC/atac-seq-pipeline. |
Thanks Jin, if you could please tell me what data set you used to generate the files on your main page. As I have tried even ATAC seq data sets from ENA. |
We recommend to use our new pipeline at https://github.com/ENCODE-DCC/atac-seq-pipeline/. This new pipeline supports docker, DNANexus and Google Cloud platform so that you will avoid any dependency problems. Please read through documentation and then find an example at |
Thank you Jin. May I ask how the atac-seq uses phantompeakqualtools ? as it is seemingly tripping there. |
@rehamFatima: Sure, What kind of error did you get? |
@rehamFatima I actually don't understand why you want to test our pipeline with a BED file (or its BAM conversion) which is not designed to be used as a valid input to the pipeline. The error you got in the issue #128 is input data quality problem. Please try with some samples on the ENCODE portal. Instead of using this old pipeline, can you work with our new pipeline? A very detailed tutorial with sample data is available at https://github.com/ENCODE-DCC/atac-seq-pipeline/blob/hotfix_PIP-357/docs/tutorial_google.md You may need to sign up for Google Cloud Platform. |
Hi,
I have been trying to run your pipeline on the mm10 data set (as setup by running install_genome_data.sh ). As there were no fast files, I made a bam file from the bed files and am running the pipeline using the following command :
$ bds atac.bds -species mm10 -gensz mm -bam1 ../genomes/mm10_enh_dhs.bam -chrsz ../genomes/mm10/mm10.chrom.sizes
I am not getting the output repository structure as mentioned on your main page, nor a Report.html file. If you could help with this, I would highly appreciate it.
Many thanks.
Kind Regards,
Reham
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