[BUG?] Unable to recognize fq.gz file as a gzip file #8
Description
Hi there,
I confirmed the completeness and format of my input files:
zuoxiaotian@a203fast-PowerEdge-T640:~$ file /mnt/16T_2/metatranscriptome/MbPL202401629/2_cleandata/L2_se_clean_R2.fq.gz
/mnt/16T_2/metatranscriptome/MbPL202401629/2_cleandata/L2_se_clean_R2.fq.gz: gzip compressed data, original size modulo 2^32 627952
zuoxiaotian@a203fast-PowerEdge-T640:~$ head -c 10 /mnt/16T_2/metatranscriptome/MbPL202401629/2_cleandata/L2_se_clean_R1.fq.gz | xxd
00000000: 1f8b 0800 0000 0000 00ff
When I test the command:
bbmap.sh \
ref=/mnt/16T_1/zuo/bbmap_mapping/plasmid/plasmid_representatives.fna \
in=/mnt/16T_2/metatranscriptome/MbPL202401629/2_cleandata/L2_se_clean_R1.fq.gz \
in2=/mnt/16T_2/metatranscriptome/MbPL202401629/2_cleandata/L2_se_clean_R2.fq.gz \
out=/mnt/16T_1/zuo/bbmap_mapping/metaG/L2_se_filtered.sam \
pairedonly=t idfilter=1 threads=40 -Xmx40g
Error emerged as:
Exception in thread "BGZF-InputProducer" java.lang.AssertionError: Not a gzip file: 0, 0
at stream.bam.BgzfInputStreamMT2.readNextBlock(BgzfInputStreamMT2.java:215)
at stream.bam.BgzfInputStreamMT2.producerLoop(BgzfInputStreamMT2.java:135)
at stream.bam.BgzfInputStreamMT2.access$0(BgzfInputStreamMT2.java:127)
at stream.bam.BgzfInputStreamMT2$1.run(BgzfInputStreamMT2.java:109)
at java.base/java.lang.Thread.run(Thread.java:840)
I tried to flag unpigz=t but did not address it. Need for some help, thanks in advance.
-------↓ The latest update ↓-------
That's so strange. When I test threads=1 it seems to work. Maybe, the problem is only associated with using multiple threads to build sam file.