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tf2 / CNest

Copy Number Methods for Detection and Genome Wide Association Tests
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ERROR: no lines available in input #13

Open akshayware94 opened 2 years ago

akshayware94 commented 2 years ago

Dear Tomas,

I am facing an error in Step2:

The command I ran:

sudo docker run -v "/home/tools/CNest:/input" -v "/home/tools/CNest:/output" -w "/output" -it --rm \
>     tomas81/cnest:dev step2 \
>     --project test \
>     --sample 'test1' \
>     --input 'input/test.bam'

The error I got:

10/27/2022 11:59:34 | INFO: Start step2 for sample test1
10/27/2022 11:59:34 | INFO: bam-to-rd done.
10/27/2022 11:59:34 | INFO: rd-dump done.
10/27/2022 11:59:35 | ERROR: processtobin failed with exit code 1.
b'Loading required package: ViteRbi\nLoading required package: mixtools\nmixtools package, version 1.2.0, Released 2020-02-05\nThis package is based upon work supported by the National Science Foundation under Grant No. SES-0518772.\n\nError in read.table(inputfile, sep = "\\t", skip = 1) : \n  no lines available in input\nCalls: processtobin -> read.table\nExecution halted\n'
10/27/2022 11:59:35 | INFO: Step2 done!

Please kindly help! Thanks in Advance.