Snakemake-Prokaryotic-RNAseq-Pipeline issueshttps://gitlab.rc.uab.edu/CCTS-Informatics-Pipelines/Snakemake-Prokaryotic-RNAseq-Pipeline/-/issues2020-11-11T06:50:20-06:00https://gitlab.rc.uab.edu/CCTS-Informatics-Pipelines/Snakemake-Prokaryotic-RNAseq-Pipeline/-/issues/12Pass Exam With AZ-104 PDF Dumps 2020: Practice Material2020-11-11T06:50:20-06:00harrisonfieldingPass Exam With AZ-104 PDF Dumps 2020: Practice Material<p><strong>Updated Microsoft AZ-104&nbsp;PDF Dumps</strong><br />&nbsp;<br />As we are acquainted with this actuality the Microsoft Azure Administrator exam is noticed not merely given that the topmost IT certification exam which has bee...<p><strong>Updated Microsoft AZ-104 PDF Dumps</strong><br /> <br />As we are acquainted with this actuality the Microsoft Azure Administrator exam is noticed not merely given that the topmost IT certification exam which has been made available from Microsoft but also quite possibly the most regarded and warm exam round the globe. The Microsoft <a href="https://www.dumpsmaster.com/AZ-104-pdf-dumps">AZ-104 pdf dumps</a> are already recognized as one of the top trending examination planning for which related certification specialists are tending for. Microsoft Azure Administrator licensed on the resume can help you to keep up to date plus more likelihood of acquiring large paid out job in lieu of related certification pros not able to sustain.</p>
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<p>You can also avail our Microsoft Azure Administrator pdf dumps, indicate you'll be able to get ready for your AZ-104 question from anywhere you desire to. We have a agency believer in our Microsoft AZ-104 pdf questions dumps that is why we provide 100% passing guarantee with our AZ-104 dumps. Final although not the the very least you could also get the 24/7 buyer treatment company with our related certification AZ-104 braindumps pdf. Obviously these things make our Microsoft Azure Administrator study materials your sole companion for that preparation of Microsoft Azure Administrator AZ-104 dumps pdf questions.<br /> </p>https://gitlab.rc.uab.edu/CCTS-Informatics-Pipelines/Snakemake-Prokaryotic-RNAseq-Pipeline/-/issues/11move specification of reference genome from Snakefile to a config file.2019-10-10T10:54:01-05:00Curtis Hendricksoncurtish@uab.edumove specification of reference genome from Snakefile to a config file.Currently you need to un-comment lines or edit lines in the [Snakefile](Snakefile#L48)
```
# REFERENCE GENOME
REF_SPECIES="REF SPECIES"
REF_ACCESSION="ACCESSION"
REF_ANNO_FILE="GCX_#########.#_ASM###v#_genomic"
#REF: Mtb strain H37R
#RE...Currently you need to un-comment lines or edit lines in the [Snakefile](Snakefile#L48)
```
# REFERENCE GENOME
REF_SPECIES="REF SPECIES"
REF_ACCESSION="ACCESSION"
REF_ANNO_FILE="GCX_#########.#_ASM###v#_genomic"
#REF: Mtb strain H37R
#REF_SPECIES="Mycobacterium_tuberculosis_H37Rv_uid57777"
#REF_ACCESSION="NC_000962"
#REF_ANNO_FILE="GCF_000195955.2_ASM19595v2_genomic"
```Curtis Hendricksoncurtish@uab.eduCurtis Hendricksoncurtish@uab.eduhttps://gitlab.rc.uab.edu/CCTS-Informatics-Pipelines/Snakemake-Prokaryotic-RNAseq-Pipeline/-/issues/10Comments in Snakefile are from an earlier variant calling pipeline from which...2019-10-10T10:50:38-05:00Curtis Hendricksoncurtish@uab.eduComments in Snakefile are from an earlier variant calling pipeline from which the basic Snakefile was lifted, and need to be overhauled* [ ] remove incorrect comments in Snakefile
* [ ] have Snakefile refer to README.md - and remove redundancy.* [ ] remove incorrect comments in Snakefile
* [ ] have Snakefile refer to README.md - and remove redundancy.Curtis Hendricksoncurtish@uab.eduCurtis Hendricksoncurtish@uab.eduhttps://gitlab.rc.uab.edu/CCTS-Informatics-Pipelines/Snakemake-Prokaryotic-RNAseq-Pipeline/-/issues/9add public test data/configs with results2019-10-10T10:37:12-05:00Curtis Hendricksoncurtish@uab.eduadd public test data/configs with results* [ ] define directory structure for test data/ref/results
* [ ] will data be LFS committed, or run-time download?
* proposed data set
* [ ] strep
* Hey Curtis here is an SRA link to some fastqs from a paper looking at doing RNA-s...* [ ] define directory structure for test data/ref/results
* [ ] will data be LFS committed, or run-time download?
* proposed data set
* [ ] strep
* Hey Curtis here is an SRA link to some fastqs from a paper looking at doing RNA-seq on strep: https://www.ncbi.nlm.nih.gov/sra?LinkName=pubmed_sra&from_uid=31409659 and here’s a link to the paper: https://www.ncbi.nlm.nih.gov/pubmed/31409659 -Liam
* [ ] mtb
* [ ] CI integration with gitlabCurtis Hendricksoncurtish@uab.eduCurtis Hendricksoncurtish@uab.eduhttps://gitlab.rc.uab.edu/CCTS-Informatics-Pipelines/Snakemake-Prokaryotic-RNAseq-Pipeline/-/issues/8EDGE_pro 1.3.1: crashes when resolving overlapping protein genes on the same ...2019-09-13T12:09:37-05:00Curtis Hendricksoncurtish@uab.eduEDGE_pro 1.3.1: crashes when resolving overlapping protein genes on the same strandSubmitted bug report:
TO: edge.comments@gmail.com
SUBJECT: bugfix: edge-pro 1.3.1: crashes when resolving overlapping protein genes on the same strand
Folks
Running EDGE-pro 1.3.1 on NZ_CP010555.1, the edge.pl script crashed on line...Submitted bug report:
TO: edge.comments@gmail.com
SUBJECT: bugfix: edge-pro 1.3.1: crashes when resolving overlapping protein genes on the same strand
Folks
Running EDGE-pro 1.3.1 on NZ_CP010555.1, the edge.pl script crashed on line 455:
```
PREPROCESSING:
Getting sizes
Combining ptt and rnt files
Can't use string ("-") as an ARRAY ref while "strict refs" in use at /home/curtish/.conda/envs/edge-pro/bin/edge.pl line 455.
```
The problem is triggered by overlapping CDS on the same strang, and triggers code where it looks like a code re-write that switched from indexing into @combined to using @arr1 and @arr2 accidently left an [$j] index on @arr2. The fix is
```
455c459,460
< elsif(($arr2[5] eq "tRNA") || ($arr2[$j][5] eq "rRNA")){ #the second gene is tRNA/rRNA, so ignore the first gene
---
> elsif(($arr2[5] eq "tRNA") || ($arr2[5] eq "rRNA")){ #the second gene is tRNA/rRNA, so ignore the first gene
```
I would provide a pull request, but I don’t see EDGE-Pro code hosted on github or the like.
Regards,Van Der Pol WilliamVan Der Pol Williamhttps://gitlab.rc.uab.edu/CCTS-Informatics-Pipelines/Snakemake-Prokaryotic-RNAseq-Pipeline/-/issues/6Add support for pulling ref genome annotation from NCBI and converting to rnt...2019-02-11T14:02:32-06:00Curtis Hendricksoncurtish@uab.eduAdd support for pulling ref genome annotation from NCBI and converting to rnt/pttrnt/ptt annotation is an older format NCBI dropped, but is required by EDGE-PRO.
Some people wget gbk file, then convert to rnt/ntt:
* https://www.biostars.org/p/161066/
or the like… other google hits:
* http://seqanswers.com/fo...rnt/ptt annotation is an older format NCBI dropped, but is required by EDGE-PRO.
Some people wget gbk file, then convert to rnt/ntt:
* https://www.biostars.org/p/161066/
or the like… other google hits:
* http://seqanswers.com/forums/showthread.php?p=190839
Genome2D servers still provides .rnt/.ptt files, so we've been using that.
• http://genome2d.molgenrug.nl/RefSeq/Mycobacterium_tuberculosis_H37Rv/
However, Liam has a project that requires "Pseudomonas aeruginosa",[ASM82988v1](https://www.ncbi.nlm.nih.gov/genome/187?genome_assembly_id=218367), which is not hosted on the genome2d site.Van Der Pol WilliamVan Der Pol Williamhttps://gitlab.rc.uab.edu/CCTS-Informatics-Pipelines/Snakemake-Prokaryotic-RNAseq-Pipeline/-/issues/5snakemake[slurm] --use-conda doesn't successfully override Liam's QIIME conda...2019-02-07T15:20:22-06:00Curtis Hendricksoncurtish@uab.edusnakemake[slurm] --use-conda doesn't successfully override Liam's QIIME conda environment on cheahaIf runs
```
snakemakeslurm --use-conda
```
from @liamvdp account, we see that the deseq rule first loads the snakemake-local conda environment, but still pulls it's R exe from the QIIME environment, and thus fails, as the "rjson" packa...If runs
```
snakemakeslurm --use-conda
```
from @liamvdp account, we see that the deseq rule first loads the snakemake-local conda environment, but still pulls it's R exe from the QIIME environment, and thus fails, as the "rjson" package is not available in that R.
However, if we activate the local conda env on the command-line (with QIIME conda environment already active, then run vanilla snakemake, it works.
```
conda activate ./.snakemake/conda/...
which R # validate we're getting the local version
snakemake # works
```
We think when running ```snakemakeslurm --use-conda``` the conda load should have over-ridden his account settings.
Help? @jelaiw
### Notes
* https://github.com/rusalkaguy/snakemake-slurm-moduleJelai WangJelai Wanghttps://gitlab.rc.uab.edu/CCTS-Informatics-Pipelines/Snakemake-Prokaryotic-RNAseq-Pipeline/-/issues/4if samples names start with digits, then R will prepend them with X when load...2019-02-01T16:24:17-06:00Curtis Hendricksoncurtish@uab.eduif samples names start with digits, then R will prepend them with X when loading deseqFile.labeled.txtError will show up in the rule deseq2_diff_exp_analysis_step1 which runs file de_deseq2/deseq2_step1.R
```
Error: sample NAMES mismatch:
samples_meta.txt:4218_3_Fe 4218_3_Hm 4220_3_Fe 4220_3_Hm 4218_3_Hb 4218_3_No 4220_3_Hb 4220_3_No
de...Error will show up in the rule deseq2_diff_exp_analysis_step1 which runs file de_deseq2/deseq2_step1.R
```
Error: sample NAMES mismatch:
samples_meta.txt:4218_3_Fe 4218_3_Hm 4220_3_Fe 4220_3_Hm 4218_3_Hb 4218_3_No 4220_3_Hb 4220_3_No
deseqFile.labeled.txt:X4218_3_Fe X4218_3_Hb X4218_3_Hm X4218_3_No X4220_3_Fe X4220_3_Hb X4220_3_Hm X4220_3_No
Execution halted
```
but if you look at deseqFile.labeled.txt, there are NO X's!Curtis Hendricksoncurtish@uab.eduCurtis Hendricksoncurtish@uab.eduhttps://gitlab.rc.uab.edu/CCTS-Informatics-Pipelines/Snakemake-Prokaryotic-RNAseq-Pipeline/-/issues/3create conda environments for all dependences2019-09-19T15:47:59-05:00Curtis Hendricksoncurtish@uab.educreate conda environments for all dependencesfrom [Snakefile](Snakefile)
```
# Modules
MOD_FQC="FastQC/0.11.5-Java-1.8.0_74 "
MOD_BWA="BWA/0.7.13-intel-2016a"
LOAD_MULTIQC="module purge && module load shared rc-base && module load MultiQC/0.9-foss-2016b-Python-2.7.12"
MOD_SAMTOOLS...from [Snakefile](Snakefile)
```
# Modules
MOD_FQC="FastQC/0.11.5-Java-1.8.0_74 "
MOD_BWA="BWA/0.7.13-intel-2016a"
LOAD_MULTIQC="module purge && module load shared rc-base && module load MultiQC/0.9-foss-2016b-Python-2.7.12"
MOD_SAMTOOLS="SAMtools/1.6-intel-2017a"
MOD_GATK="GATK/3.7-Java-1.8.0_112"
MOD_PICARD="picard/2.10.0-Java-1.8.0_74"
LOAD_EDGEPRO="module purge && module load shared rc-base && module load EDGE_pro/1.3.1"
```Curtis Hendricksoncurtish@uab.eduCurtis Hendricksoncurtish@uab.edu