BICF issueshttps://git.biohpc.swmed.edu/groups/BICF/-/issues2020-06-01T13:28:23-05:00https://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/16BUG: Cannot handle multiple runs2020-06-01T13:28:23-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduBUG: Cannot handle multiple runs# Pipeline cannot handle experiments (samples) with multiple runs... for example:
| sample_id | sra_number |
| ------ | ------ |
| Sample1 | SRX172938 |
fails because SRX172938 has 4 runs:
| Run | # of Spots | # of Bases | Size ...# Pipeline cannot handle experiments (samples) with multiple runs... for example:
| sample_id | sra_number |
| ------ | ------ |
| Sample1 | SRX172938 |
fails because SRX172938 has 4 runs:
| Run | # of Spots | # of Bases | Size | Published |
|-----------|------------|------------|---------|------------|
| SRR531404 | 5,261,058 | 189.4M | 93.6Mb | 2012-09-11 |
| SRR531405 | 6,870,169 | 247.3M | 204.4Mb | 2012-09-11 |
| SRR531406 | 7,941,818 | 285.9M | 236.8Mb | 2012-09-11 |
| SRR531407 | 31,599,710 | 1G | 605.1Mb | 2012-09-11 |
## Advice
one or a combination of the following:
* make a note in instructions pointing out that the pipeline fails with samples with multiple sequencing runs and that users need to split those SRX's into separate SRR downloads
* don't accept any SRX's
* in check design, make sure that samples don't contain multiple runs and error if it does
* in check design, make sure that samples don't contain multiple runs and automatically split them
* if split then, consider concatenating SRR's after if submitted as 1 SRX
@venkat.malladi @s181706 @s189701 @s181385Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/onboarding/-/issues/18Software Development2020-04-08T09:17:45-05:00Venkat MalladiSoftware DevelopmentVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/37Fix runners and sigbus error2020-05-08T10:01:55-05:00Venkat MalladiFix runners and sigbus errorVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/82Disk quota exceeded2020-04-13T13:50:12-05:00Venkat MalladiDisk quota exceededVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/onboarding/-/issues/17CI and Nextflow configuration2020-04-13T15:31:27-05:00Venkat MalladiCI and Nextflow configurationVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/81Config Lock git2020-04-16T22:21:45-05:00Venkat MalladiConfig Lock gitcan't initiate new run due to config lock
error: failed to write new configuration file /project/BICF/shared/astrocyte_test_ci/011b97be/chipseq_analysis/6415/1/80885/.tmp/git-template/config.lock
Could be some disquota issuecan't initiate new run due to config lock
error: failed to write new configuration file /project/BICF/shared/astrocyte_test_ci/011b97be/chipseq_analysis/6415/1/80885/.tmp/git-template/config.lock
Could be some disquota issueVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/80Gitlab CI overridding concurrent pipelines2020-04-16T03:01:51-05:00Venkat MalladiGitlab CI overridding concurrent pipelinesVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/79Fix sigbus error2020-04-16T03:01:51-05:00Venkat MalladiFix sigbus errorFixing sigbus error for nextflowFixing sigbus error for nextflowVenkat MalladiVenkat Malladihttps://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/onboarding/-/issues/16Authorship guidelines2020-03-31T12:02:51-05:00Venkat MalladiAuthorship guidelinesVenkat MalladiVenkat Malladihttps://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/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/chipseq_analysis/-/issues/72Update multiqc with new singularity images2020-02-12T00:49:35-06:00Venkat MalladiUpdate multiqc with new singularity imageshttps://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/19Update Astrocyte instructions2020-01-07T11:33:51-06:00Venkat MalladiUpdate Astrocyte instructions`One or more input paired-end FASTQ files from a RNASeq experiment and a design file with the link between the same name and the sample group``One or more input paired-end FASTQ files from a RNASeq experiment and a design file with the link between the same name and the sample group`Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/onboarding/-/issues/14Docker Documentaion2021-04-06T08:26:21-05:00Venkat MalladiDocker DocumentaionJonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/onboarding/-/issues/13Update Hourly Help Desk for Subtask2020-02-26T16:14:33-06:00Venkat MalladiUpdate Hourly Help Desk for SubtaskHolly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/onboarding/-/issues/12TOC - Fee Structure2019-12-24T22:34:44-06:00Venkat MalladiTOC - Fee StructureVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/21Fix concurrent runners2020-05-28T13:59:21-05:00Venkat MalladiFix concurrent runnersVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/KCE/kce_etl/-/issues/25Add tests radiation2019-12-12T08:30:37-06:00Venkat MalladiAdd tests radiation