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pls2fasta not generating output

pls2fasta appears to be installed and functional, but I get no output when I run the tool against bax.h5 data...

jpummil ~-->ls -lh m16*
-rw-r--r-- 1 jpummil jpummil 6.3G May 10 10:17 m160926_204330_42238_c101113852550000001823244005011790_s1_p0.1.bax.h5
-rw-r--r-- 1 jpummil jpummil 8.6K May 10 11:17 m160926_204330_42238_c101113852550000001823244005011790_s1_p0.1.xfer.xml
-rw-r--r-- 1 jpummil jpummil 1.4G May 10 11:44 m160926_204330_42238_c101113852550000001823244005011790_s1_p0.2.bax.h5
-rw-r--r-- 1 jpummil jpummil 5.1K May 10 11:17 m160926_204330_42238_c101113852550000001823244005011790_s1_p0.2.xfer.xml
-rw-r--r-- 1 jpummil jpummil 6.2G May 10 10:22 m160926_204330_42238_c101113852550000001823244005011790_s1_p0.3.bax.h5
-rw-r--r-- 1 jpummil jpummil 5.1K May 10 11:17 m160926_204330_42238_c101113852550000001823244005011790_s1_p0.3.xfer.xml
-rw-r--r-- 1 jpummil jpummil 4.0K May 10 11:17 m160926_204330_42238_c101113852550000001823244005011790_s1_p0.metadata.xml

Run as follows:

jpummil ~-->pls2fasta *bax.h5 out.fastq -trimByRegion -fastq

No output generated...

Anything obvious I'm doing wrong???

software error
• 1,435 views • link
updated by GenoMax 16K • | written by jpummil 0

Have you tried using one bax.h5 file at one time?

Edit: I think you may need to create a file list (file of file names, *.fofn) to do multiple files at one time.

    $ ls *.bax.h5 > input.fofn
    $ cat input.fofn
    m160926_204330_42238_c101113852550000001823244005011790_s1_p0.1.bax.h5
    m160926_204330_42238_c101113852550000001823244005011790_s1_p0.2.bax.h5
    m160926_204330_42238_c101113852550000001823244005011790_s1_p0.3.bax.h5
    $ pls2fasta input.fofn out.fastq -trimByRegion -fastq
• 1 views • link
written by GenoMax 16K

Hey genomax! Thanks for the tip. It returns a different error...

jpummil ~-->pls2fasta input.fofn out.fastq -trimByRegion -fastq
[INFO] 2018-05-10T12:25:36 [pls2fasta] started.
ERROR, could not get the minimum and maximum hole numbers from ZMW HoleNumbers.
• 1 views • link
updated by GenoMax 16K • | written by jpummil 0

No idea about that one. Perhaps someone else will know.

• 1 views • link
written by GenoMax 16K

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