is it SAM/BAM format? Consider opening with check_sq=False

[nbutyrate]

HI i am trying to run IGGsearch, following is the workflow and error

run_iggsearch.py search --m1 test.fastq.gz --outdir test --test

Warning: this is a quick test run; results should not be interpreted

Initializing database

total species: 4558
total genes: 100000
module: 0.9 seconds, program: 0.9 seconds, peak RAM: 0.08 GB

Aligning reads

running: bowtie2 --no-unal -q -x /data/ubuntu/ALL_FASTQ_FASTAs/IGGsearch/iggdb_v1.0.0_gut/iggdb_v1.0.0_gut -u 1000 --threads 1 -U test.fastq.gz | samtools view -b - --threads 1 | samtools sort - --threads 1 -O BAM > test/mapped_reads.bam
module: 11.68 seconds, program: 12.58 seconds, peak RAM: 1.78 GB

Counting mapped reads

Traceback (most recent call last):
File "/data/ubuntu/ALL_FASTQ_FASTAs/IGGsearch/run_iggsearch.py", line 28, in
search.main()
File "/data/ubuntu/ALL_FASTQ_FASTAs/IGGsearch/iggsearch/search.py", line 382, in main
count_reads_bt2(args, db)
File "/data/ubuntu/ALL_FASTQ_FASTAs/IGGsearch/iggsearch/search.py", line 269, in count_reads_bt2
bamfile = pysam.AlignmentFile(bam_path, "r")
File "pysam/libcalignmentfile.pyx", line 736, in pysam.libcalignmentfile.AlignmentFile.cinit
File "pysam/libcalignmentfile.pyx", line 985, in pysam.libcalignmentfile.AlignmentFile._open
ValueError: file has no sequences defined (mode='r') - is it SAM/BAM format? Consider opening with check_sq=False

[nbutyrate]

please avoid, i have sorted it out

[JiaZhong28]

hi, I've gotten the same error and i wonder how you sovle the problems, thx.

[Sunny Songss]

hi, I've gotten the same error and I also wonder how you solve the problems, thx.

[Sunny Songss]

please avoid, i have sorted it out

Hi, may I ask how you sorted it out?