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Facing difficulties decompressing bam file #30

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sagnikbanerjee15 opened this issue Mar 20, 2021 · 0 comments
Open

Facing difficulties decompressing bam file #30

sagnikbanerjee15 opened this issue Mar 20, 2021 · 0 comments

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@sagnikbanerjee15
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sagnikbanerjee15 commented Mar 20, 2021

Hello,

I used the following command to compress a sam file and it completed without any error.

(/usr/bin/time --verbose  \
/90daydata/maizegdb/sagnik/softwares/quip-1.1.8/src/quip \
--input=bam \
-r /90daydata/maizegdb/sagnik/data/ARATH/genome/Arabidopsis_thaliana.TAIR10.dna_sm.toplevel.fa.quip \
/90daydata/maizegdb/sagnik/ABRIDGE/rough/SRR13711353_SE.bam \
-c \
) \
1> /90daydata/maizegdb/sagnik/ABRIDGE/rough/SRR13711353_SE.quip \
2> /90daydata/maizegdb/sagnik/ABRIDGE/rough/SRR13711353_SE.quip.compress.error 

I keep getting an error when I attempt to decompress the same file. I think I am not correctly interpreting the command line arguments

(/usr/bin/time --verbose  \
/90daydata/maizegdb/sagnik/softwares/quip-1.1.8/src/quip \
-d \
--input=quip \
-r /90daydata/maizegdb/sagnik/data/ARATH/genome/Arabidopsis_thaliana.TAIR10.dna_sm.toplevel.fa.quip \
/90daydata/maizegdb/sagnik/ABRIDGE/rough/SRR13711353_SE.quip \
-c \
) \
1> /90daydata/maizegdb/sagnik/ABRIDGE/rough/SRR13711353_SE.quip.decompressed.sam \
2> /90daydata/maizegdb/sagnik/ABRIDGE/rough/SRR13711353_SE.quip.decompress.error 

The error is

quip: /90daydata/maizegdb/sagnik/ABRIDGE/rough/SRR13711353_SE.quip: Unknown SAM field type: 

Could you please look into it?

Thank you.

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