BICF issueshttps://git.biohpc.swmed.edu/groups/BICF/-/issues2020-11-20T12:13:22-06:00https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/56Add 5GEXPE/SE as library options2020-11-20T12:13:22-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd 5GEXPE/SE as library optionsAuto 5GEX misidentify 5GEXSE as PE when sequencing strategy not customizedAuto 5GEX misidentify 5GEXSE as PE when sequencing strategy not customized3.0.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/51Version Zenodo2020-08-15T11:19:37-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduVersion ZenodoAdd Jon to author list
Keep pending until finishedAdd Jon to author list
Keep pending until finished2.2.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/50Generate Raw RDS file2020-08-14T14:01:39-05:00Venkat MalladiGenerate Raw RDS fileProvide Raw RDS file per sample (Seurat object)Provide Raw RDS file per sample (Seurat object)2.2.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/47Add Jon to author list2020-08-14T15:13:32-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd Jon to author list* [x] License
* [ ] Zenodo* [x] License
* [ ] Zenodo2.2.0https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/44Thread error on BioHPC2020-04-20T18:41:13-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduThread error on BioHPC# Summary
#40 not fixed for all cellranger processes
# Steps to reproduce
# Observed bug behavior
# Expected behavior
# Relevant logs and/or screenshots
# Potential fixes
/cc @ghenry# Summary
#40 not fixed for all cellranger processes
# Steps to reproduce
# Observed bug behavior
# Expected behavior
# Relevant logs and/or screenshots
# Potential fixes
/cc @ghenryv2.1.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/43Remove unnecessary files from output2020-04-14T10:01:25-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduRemove unnecessary files from outputv2.1.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/42Update params to current standards2020-04-15T10:04:24-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduUpdate params to current standardsnon-imputable params do not need to have "param." prefixnon-imputable params do not need to have "param." prefixv2.1.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/41Containerize2020-04-15T21:18:39-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduContainerizev2.1.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/38Add license2020-05-07T15:53:13-05:00Venkat MalladiAdd licenseVersion 2.0Venkat MalladiVenkat Malladihttps://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/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/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 Ruess