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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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