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10XGenomics / bamtofastq

Convert 10x BAM files to the original FASTQs compatible with 10x pipelines
MIT License
59 stars 6 forks source link

Output directory doesn't exist error #26

Closed Diennguyen8290 closed 3 years ago

Diennguyen8290 commented 3 years ago

Hi, Thanks for developing the tool. I'm trying to convert 05 BAM files produced by cellranger (GSE115469) and got the error as follow: "bamtofastq v1.3.5 bamtofastqerror: error creating output directory: "/scratch/c.c1942783/Liver.scRNA/fastq/fastqs". Does it already exist? Please contact patrick@10xgenomics.com for assistance. Please re-run with --traceback and include stack trace with an error report see below for more details: error creating output directory: "/scratch/c.c1942783/Liver.scRNA/fastq/fastqs". Does it already exist?” Those BAM files are the original ones. My script is (here is for 01 of those files (https://sra-pub-src-1.s3.amazonaws.com/SRR7276478/P5TLH.bam.1)): bamtofastq P5TLH.bam.1 /scratch/c.c1942783/Liver.scRNA/fastq/fastqs The above directory has been created and does exist. Any help would be greatly appreciated. Kind regards, Dien

k3yavi commented 3 years ago

hey @Diennguyen8290 ,

It's complaining because the directory exist, try deleting the directory and running again.

Diennguyen8290 commented 3 years ago

hey @Diennguyen8290 ,

It's complaining because the directory exist, try deleting the directory and running again.

@k3yavi Many thanks for your quick response. Sorry, I still didn't get it. To my understanding, we need an output folder to save the results and that folder has just created for that purpose. Also, if I delete this directory, how can I specify the output directory in the command line? Many thanks, Dien

k3yavi commented 3 years ago

Sure, I understand the confusion. You'd have to provide the output directory to the tool but don't create the last directory manually, the tool would do it for you. Basically provide /scratch/c.c1942783/Liver.scRNA/fastq/fastqs this as output directory to the tool but don't create the last directory fastqs, if you have then delete it. I think that's the problem, I can be wrong.

Diennguyen8290 commented 3 years ago

Sure, I understand the confusion. You'd have to provide the output directory to the tool but don't create the last directory manually, the tool would do it for you. Basically provide /scratch/c.c1942783/Liver.scRNA/fastq/fastqs this as output directory to the tool but don't create the last directory fastqs, if you have then delete it. I think that's the problem, I can be wrong.

@k3yavi Thanks for your clarification. Unfortunately it's still there. Even I don't create any new directory and specify the output to the current directory, the error still comes out. I have also tried with older version or with other HPC account and still get the same error. Please could you advise me with the case. Many thanks.

Diennguyen8290 commented 3 years ago

Sure, I understand the confusion. You'd have to provide the output directory to the tool but don't create the last directory manually, the tool would do it for you. Basically provide /scratch/c.c1942783/Liver.scRNA/fastq/fastqs this as output directory to the tool but don't create the last directory fastqs, if you have then delete it. I think that's the problem, I can be wrong.

@k3yavi Thanks for your clarification. Unfortunately it's still there. Even I don't create any new directory and specify the output to the current directory, the error still comes out. I have also tried with older version or with other HPC account and still get the same error. Please could you advise me with the case. Many thanks.

@k3yavi I made an error. It's then solved with that way. Many thanks, Dien