BICF issueshttps://git.biohpc.swmed.edu/groups/BICF/-/issues2020-06-01T13:28:23-05:00https://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/15Convert SOLID sequencing to basecall2020-06-01T13:28:23-05:00Venkat MalladiConvert SOLID sequencing to basecallSolid seqencing comes back as csqual and csfasta by default.
Use the -B option to convert to base call output to run in our pipelinesSolid seqencing comes back as csqual and csfasta by default.
Use the -B option to convert to base call output to run in our pipelinesJeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/78Paired-end Diffbind peaks gives different answer2020-04-20T09:01:39-05:00Venkat MalladiPaired-end Diffbind peaks gives different answerJob [#79740](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/jobs/79740) failed for e09a8b62fdf02774214dee75f6096b94c7b5f8fe:Job [#79740](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/jobs/79740) failed for e09a8b62fdf02774214dee75f6096b94c7b5f8fe:1.1.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/onboarding/-/issues/16Authorship guidelines2020-03-31T12:02:51-05:00Venkat MalladiAuthorship guidelinesVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/39Add base mask2020-06-20T20:34:36-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd base mask`-use-bases-mask=Y28n*,I8n*,n*,Y*``-use-bases-mask=Y28n*,I8n*,n*,Y*`v2.1.5Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/38Ignore dual index2020-06-20T20:34:36-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduIgnore dual indexadd `--ignore-dual-index` to cellranger mkfastq commandadd `--ignore-dual-index` to cellranger mkfastq commandv2.1.5Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/77Update to Astrocyte 0.2.02020-03-21T11:16:24-05:00Venkat MalladiUpdate to Astrocyte 0.2.0astrocyte/0.2.0astrocyte/0.2.01.1.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/37Add ulimit to cellranger process2020-06-20T20:34:35-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd ulimit to cellranger processsee: BICF/Astrocyte/cellranger_count#40see: BICF/Astrocyte/cellranger_count#40v2.1.5Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/40BUG: thread error on Astrocyte2020-04-20T18:31:32-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduBUG: thread error on AstrocyteDetected by Lavanya (Gupta Lab)...
Exceeding thread limit on Astrocyte intermittently
Appears to be localized to 256v1 nodes (see below, 1574863-1590532)
```
1049334 nf-count3+ FAILED Nucleus024 128GB
1363646 nf-count3+ FAILED Nucleus1...Detected by Lavanya (Gupta Lab)...
Exceeding thread limit on Astrocyte intermittently
Appears to be localized to 256v1 nodes (see below, 1574863-1590532)
```
1049334 nf-count3+ FAILED Nucleus024 128GB
1363646 nf-count3+ FAILED Nucleus156 256GBv1
1432212 nf-count3+ FAILED Nucleus010 128GB
1492005 nf-count3+ NODE_FAIL Nucleus025 128GB
1503055 nf-count3+ FAILED Nucleus059 256GB
1503183 nf-count3+ FAILED Nucleus059 256GB
1574863 nf-count3+ FAILED Nucleus142 256GBv1
1581543 nf-count3+ FAILED Nucleus132 256GBv1
1581544 nf-count3+ FAILED Nucleus193 256GBv1
1581550 nf-count3+ FAILED Nucleus132 256GBv1
1582398 nf-count3+ FAILED Nucleus152 256GBv1
1585588 nf-count3+ FAILED Nucleus140 256GBv1
1590532 nf-count3+ FAILED Nucleus140 256GBv1
```
Where ulimit -u is being reduced for an unknown reason
```
Nucleus140
core file size (blocks, -c) 0
data seg size (kbytes, -d) unlimited
scheduling priority (-e) 0
file size (blocks, -f) unlimited
pending signals (-i) 1031252
max locked memory (kbytes, -l) 64
max memory size (kbytes, -m) unlimited
open files (-n) 4096
pipe size (512 bytes, -p) 8
POSIX message queues (bytes, -q) 819200
real-time priority (-r) 0
stack size (kbytes, -s) 8192
cpu time (seconds, -t) unlimited
max user processes (-u) 4096
virtual memory (kbytes, -v) unlimited
file locks (-x) unlimited
```
**FIX**
Add this code to the cellranger process start:
`ulimit -u 16384`v2.1.1https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/76Update version of multiqc2020-03-15T12:55:45-05:00Holly RuessUpdate version of multiqcuse image /project/shared/bicf_workflow_ref/singularity_images/bicf-multiqc-2.0.0.imguse image /project/shared/bicf_workflow_ref/singularity_images/bicf-multiqc-2.0.0.img1.1.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/14updateUnitTests2020-06-17T05:53:20-05:00Jonathan GesellupdateUnitTestsThe tests need to be updated to the following style:
Unit Tests: Test the individual commands in the pipeline for logic and functionality
Integration Tests: Runs the pipeline end-to-end and verifies that it runs without issue
Consistency...The tests need to be updated to the following style:
Unit Tests: Test the individual commands in the pipeline for logic and functionality
Integration Tests: Runs the pipeline end-to-end and verifies that it runs without issue
Consistency Tests: Tests the pipeline outputs to ensure that they are consistent from version to version.Singularity 2.0.0 CompatabilityJonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/75Rename Plot profile to be consistent with naming2020-04-21T08:52:40-05:00Venkat MalladiRename Plot profile to be consistent with naming1.1.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/onboarding/-/issues/15Make a link in redmine.md2020-01-24T11:00:54-06:00Venkat MalladiMake a link in redmine.mdVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/12Update to Singularity Image 2.0.0 compatability.2020-02-05T14:52:20-06:00Jonathan GesellUpdate to Singularity Image 2.0.0 compatability.Singularity 2.0.0 CompatabilityJonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/32Annotate peaks2020-06-11T16:18:58-05:00Holly RuessAnnotate peaksVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/31Blacklist of regions2020-06-09T14:55:50-05:00Holly RuessBlacklist of regionsAdd a blacklist of regions to ignore for each genomeAdd a blacklist of regions to ignore for each genomeVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/30TSS enrichment score2020-05-28T20:56:04-05:00Holly RuessTSS enrichment scoreSee ATAqc for code in python for this.See ATAqc for code in python for this.Version 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/29Add FRiP score2020-05-13T09:30:50-05:00Holly RuessAdd FRiP score# total reads
total_reads=$(samtools view -c ${sample}.bam)
# reads in peaks
reads_in_peaks=$(bedtools sort -i ${sample}_peaks.narrowPeak \
| bedtools merge -i stdin | bedtools intersect -u -nonamecheck \
-a ${sample}.bam -b stdin -...# total reads
total_reads=$(samtools view -c ${sample}.bam)
# reads in peaks
reads_in_peaks=$(bedtools sort -i ${sample}_peaks.narrowPeak \
| bedtools merge -i stdin | bedtools intersect -u -nonamecheck \
-a ${sample}.bam -b stdin -ubam | samtools view -c)
# FRiP score
FRiP=$(awk "BEGIN {print "${reads_in_peaks}"/"${total_reads}"}")
Do this step after calling peaks; add in multiQC report
Colored cutoff:
The fraction of reads in called peak regions (FRiP score) should be >0.3, though values greater than 0.2 are acceptable. For EN-TEx tissues (ENCODE GTEx tissue sample), FRiP scores will not be enforced as QC metric. TSS enrichment remains in place as a key signal to noise measure.Version 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/28Add percent of reads - mitochondria2020-03-24T14:23:39-05:00Holly RuessAdd percent of reads - mitochondriaDo this at the filter bam file step; may need to divide the filter into multiple parts to include this step. Add into multiQC report but don't set a cutoffDo this at the filter bam file step; may need to divide the filter into multiple parts to include this step. Add into multiQC report but don't set a cutoffVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/27Add fragment size distribution2020-06-09T09:15:49-05:00Holly RuessAdd fragment size distributionMake a graphic of fragment size distributionMake a graphic of fragment size distributionVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/73Single Rep Pool and Pseudo2020-03-24T11:46:18-05:00Venkat MalladiSingle Rep Pool and PseudoCheck if for a single rep pool and pseudo replicate works based on new refactored code.Check if for a single rep pool and pseudo replicate works based on new refactored code.1.1.1Venkat MalladiVenkat Malladi