Update RNA_calling.ipynb

[gouwh29]

Fix #475 in correct folder

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[hsun3163]

Hi @Gou-29, thanks for adding more to the pipeline. I wonder, is there a reason u want to keep the STARtmp files? Based on the STAR author these are to be removed and also the STAR pipeline from TensorQTL remove them as well.

"    rm -r ${_output[0]:nnnn}._STARtmp\n",

[gouwh29]

Hi @hsun3163 : in my running on single-ended data, there does not have a _STARtmp file so I removed that line. I do not know whether in PE data there will be one

[hsun3163]

Hi @hsun3163 : in my running on single-ended data, there does not have a _STARtmp file so I removed that line. I do not know whether in PE data there will be one

Per my understanding this is to rm the cache file in case STAR fail to do so themselves, could u push a new commit without it being deleted?

[gouwh29]

Hi @hsun3163 : in my running on single-ended data, there does not have a _STARtmp file so I removed that line. I do not know whether in PE data there will be one

Per my understanding this is to rm the cache file in case STAR fail to do so themselves, could u push a new commit without it being deleted?

Actually in my running, if I do not remove that line the code will return an error.

[gouwh29]

@hsun3163: I just reproduced the error message:

in .log file:

rm: cannot remove 'xxx/20Pre._STARtmp': No such file or directory`

in console:

ERROR: STAR_align_1 (id=65bd420a35f37e23) returns an error.
ERROR: [STAR_align_1]: [0]: Executing script in docker returns an error (exitcode=1, stdout=xxx/20Pre.Aligned.sortedByCoord.out.stdout).
The script has been saved to xxx.sh. To reproduce the error please run:
``docker run --rm -xxxx
[STAR_output]: Exits with 4 pending steps (STAR_output, strand_detected_1, strand_detected_2, picard_qc)

[hsun3163]

@Gou-29

Hmmm it is strange, is the tmp file ever generated on your case?

[gouwh29]

@Gou-29

Hmmm it is strange, is the tmp file ever generated on your case?

Yes, when the pipeline is initially running, there will be three files end with _STARgenome, _STARpass1, _STARtmp. As my previous running exclude the line remove rm -r xxx_STARtmp, maybe this file have been remove by STAR itself.

[hsun3163]

@Gou-29 I have added various accommodations of the SE in my new PR, incorporating some changes you suggested. I will close this PR now. can you try to pull once my new pr is merged and see if that works? particularly the trim adaptor part

[gouwh29]

@hsun3163: Thanks a lot for your updated pipeline! I have tested most parts of it can still, but there are two 3 issues:

• In fastqc: I notice that there is an option that the input fastq can be compressed or uncompressed. If my input is xxx.fq.gz, the output will be xxx.fq_fastq.html, and the pipeline failed to capture this. This small bug will not trigger the end of pipeline and will just throw out an error.
• In trimmomatic_trim_adaptor: since the PE data and CE data have different java configurations, the first line of the actual code should be java -jar -Xmx${java_mem} ${trimmomatic_jar} ${"PE" if is_paired_end else "SE"} -threads ${numThreads} \
• In STAR part: still, I need to exclude this line rm -r xxx_STARtmp to circumvent the error message (which may lead to a direct stop of the pipeline)