Running st pipeline unrecognized arguments

[ajyaca]

Hello

Thank you very much for your work. I'm trying to run the pipeline using the following code : st_pipeline_run.py --output-folder $OUTPUT --ids $ID --ref-map $MAP --ref-annotation $ANN --expName $EXP --htseq-no-ambiguous --verbose --log-file $OUTPUT/${EXP}_log.txt --allowed-kmer 5 --mapping-threads 20 --temp-folder $TMP --no-clean-up --umi-start-position 16 --umi-end-position 26 --overhang 0 --min-length-qual-trimming 10 $FW $RV

I get this error message : st_pipeline_run.py: error: unrecognized arguments: --allowed-kmer 5 --mapping-threads 20 --overhang 0

Do you know how I could fix the problem ?

Thank you very much for your help!!

A

[jfnavarro]

Hi and thanks for your message!

I believe you need to update some of the parameters since the names were updated recently to be more comprehensive. You can use st_pipeline_run.py --help to see the full list of parameters. Also, note that this repository will be deprecated so I would advice to use the original one

https://github.com/jfnavarro/st_pipeline

Best, Jose

[ajyaca]

Hi Jose Thank you so much.I changed the argument and it worked.Sorry for bothering you again but when I try to run the pipeline , I got this error message. ST Pipeline, logger created

Error running the pipeline

Error parsing parameters.

Invalid input files /gpfs/loomis/pi/kaminski/public/Backup/Aurelien/FastQc/Sample_319-42/2.rawdata/319-42_S27_L004_R2_001.fastq.gz /gpfs/loomis/pi/kaminski/public/Backup/Aurelien/FastQc/Sample_319-42/R1/319-42_S27_L004_R1_001.fastqc.gz

This is what I can find in the log.txt file:ERROR:STPipeline:Error while starting the decompression of GZIP/BZIP2 input files /gpfs/loomis/pi/kaminski/public/Backup/Aurelien/FastQc/Sample_319-42/319-42_S27_L004_R2_001_processed.fastq.gz /gpfs/loomis/pi/kaminski/public/Backup/Aurelien/FastQc/Sample_319-42/R1/319-42_S27_L004_R1_001.fastq.gz I tried to decompress the files, it worked well.Any clue to solve the problem ? Thanks again for your help Aurelien

Le lundi 30 août 2021, 04:19:10 UTC−4, José Fernández Navarro ***@***.***> a écrit :  

Hi and thanks for your message!

I believe you need to update some of the parameters since the names were updated recently to be more comprehensive. You can use st_pipeline_run.py --help to see the full list of parameters. Also, note that this repository will be deprecated so I would advice to use the original one

https://github.com/jfnavarro/st_pipeline

Best, Jose

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[jfnavarro]

Hi Aurelien,

Mmmm, this sounds weird. How did you compress/decompress the files? Are those paths correct and reachable by your user?

[ajyaca]

Hi Jose  Thanks for taking the time for answering.I used gzip. I'm working on a cluster and the path are reachable, I checked.Here are the format of the files 319-42_S27_L008_R1_001.fastq.gz.My samples have been sequenced on 3 differents lanes, should I merged first the Fastq files and then run the pipeline ?Sorry again for bothering you  Aurelien Le mardi 31 août 2021, 03:26:55 UTC−4, José Fernández Navarro @.***> a écrit :

Hi Aurelien,

Mmmm, this sounds weird. How did you compress/decompress the files? Are those paths correct and reachable by your user?

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[jfnavarro]

You should merge the 3 different lanes indeed but also make sure that the files are correct FASTQ files, perhaps run FASTQC on them.