Program still running while error occurred

[Zhenlisme]

Hi,
I recieved this error message while running TEMP2 absence program:

samtools view: failed to open "Sample1.sort.bam.sorted.bam" for reading: No such file or directory

Is seems that samtools tried to open the file 'Sample1.sort.bam' which can be found in the working directory. But TEMP2 mis referred the file name as 'Sample1.sort.bam.sorted.bam'. The program is still running but I don't know if I should kill the task.

Belows are the script:

module load samtools/1.18
module load bwa/0.7.17
module load bedtools/2.30.0
TEMP2 absence -i Sample1.sort.bam -o TEMPab_s1 -r TE.rmsk.bed -t genome.fa.2bit -c 20 -f 500

Thank you for your time.
Best

[tianxiongbb]

TEMP2 absence only accepts full path of input bam files, so you need to sepcify “-i $pwd/Sample1.sort.bam” Best, Tianxiong

…

On May 30, 2024, at 6:15 AM, Li Zhen ***@***.***> wrote: Hi, I recieved this error message while running TEMP2 absence program: samtools view: failed to open "Sample1.sort.bam.sorted.bam" for reading: No such file or directory Is seems that samtools tried to open the file 'Sample1.sort.bam' which can be found in the working directory. But TEMP2 mis referred the file name as 'Sample1.sort.bam.sorted.bam'. The program is still running but I don't know if I should kill the task. Belows are the script: module load samtools/1.18 module load bwa/0.7.17 module load bedtools/2.30.0 TEMP2 absence -i Sample1.sort.bam -o TEMPab_s1 -r TE.rmsk.bed -t genome.fa.2bit -c 20 -f 500 Thank you for your time. Best — Reply to this email directly, view it on GitHub <#27>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFPDEDFIFMXEN3CZRO7ZXJLZE333RAVCNFSM6AAAAABIQT4FIWVHI2DSMVQWIX3LMV43ASLTON2WKOZSGMZDKMRYGY2DCNQ>. You are receiving this because you are subscribed to this thread.

[Zhenlisme]

Thank you for your quick reply.

I gave TEMP2 absence the absolute path. Should I change it to relative path?

[tianxiongbb]

Absolute path should work. If not, you might need to rename the bam files from “sort.bam” to “sorted.bam”. Best, Tianxiong

…

On May 30, 2024, at 9:07 AM, Li Zhen ***@***.***> wrote: Thank you for your quick reply. I gave TEMP2 absence the absolute path. Should I change it to relative path? — Reply to this email directly, view it on GitHub <#27 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFPDEDAPCN4FTJGWQSCFNSDZE4QABAVCNFSM6AAAAABIQT4FIWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMZZGUYTQMRSGQ>. You are receiving this because you commented.

[Zhenlisme]

Hi again,
I renamed the bam file as sortd.bam and that error disappeared. However, I got new error messages:

twoBitToFa: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory
Can't open left.fa since No such file or directory

Do you think if I need to reinstall the package twoBitToFa?

Thank you very much for your time.
Zhen