BICF issueshttps://git.biohpc.swmed.edu/groups/BICF/-/issues2020-06-20T20:34:36-05:00https://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/atacseq_analysis/-/issues/36update version of nextflow2020-06-23T16:02:27-05:00Holly Ruessupdate version of nextflowupdate nextflow/0.31.0 to nextflow/19.09.0update nextflow/0.31.0 to nextflow/19.09.0Version 2.1.0Holly RuessHolly Ruesshttps://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/sra_pipeline/-/issues/13nullDataError2020-04-20T10:55:45-05:00Jonathan GesellnullDataErrorNeeds to throw an error when srapath returns null, example:
SRS070511Needs to throw an error when srapath returns null, example:
SRS070511Jonathan 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/Astrocyte/chipseq_analysis/-/issues/74Annotepeaks2020-06-23T15:49:23-05:00Venkat MalladiAnnotepeaksSeperate annotate peaks with different design file reading to chunk processing so it doesn't read it into memory.Seperate annotate peaks with different design file reading to chunk processing so it doesn't read it into memory.2.0.0https://git.biohpc.swmed.edu/BICF/KCE/kce_etl/-/issues/26Add tests surgery2020-02-07T09:26:16-06:00Venkat MalladiAdd tests surgeryhttps://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/35Change to 256 only if job fails2020-06-23T16:02:34-05:00Holly RuessChange to 256 only if job failsMay need to incorporate maxErrors and maxRetries into processesMay need to incorporate maxErrors and maxRetries into processesVersion 2.1.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/34Diff Peak analysis2020-06-23T16:02:40-05:00Holly RuessDiff Peak analysisVersion 2.1.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/33Motif search in peaks2020-06-23T16:02:46-05:00Holly RuessMotif search in peaksVersion 2.1.0Holly RuessHolly Ruesshttps://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 Ruess