search

dcjones / quip

Compressing next-generation sequencing data with extreme prejudice.
http://www.cs.washington.edu/homes/dcjones/quip/
BSD 3-Clause "New" or "Revised" License
78 stars 10 forks source link

Facing difficulties decompressing bam file #30

Open sagnikbanerjee15 opened 3 years ago

sagnikbanerjee15 commented 3 years ago

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.