kevinjacobs-progenity
commented
4 years ago The problem is that you are passing the tabix index of your SAM file to index your BAM file. i.e. you're using the wrong index. You need to index your BAM file and if you do it conventionally, there will be no need to manually pass in the index file.
jaredjurss
Hello, I am just starting with psyam. I get an error running this code:
import pysam samfile = pysam.AlignmentFile("scenedesmus_sorted.bam", "rb", index_filename="scenedesmus_sorted.sam.gz.tbi") reads = [] for read in samfile.fetch("unitig_855"): reads.append(read) print(len(reads))
The error is: [E::bgzf_read] Read block operation failed with error 2 after 0 of 4 bytes Traceback (most recent call last): File "/Users/jjurss/PycharmProjects/Bam_filter/test.py", line 7, in
for read in samfile.fetch("unitig_855"):
File "pysam/libcalignmentfile.pyx", line 2092, in pysam.libcalignmentfile.IteratorRowRegion.next
OSError: truncated file
I made my sam file using BWA and sorted it with samtools. I then used tabix to make the index file. I also used samtools to make the bam file.
I have checked the sam and bam file using samtools quickcheck, gatk ValidateSamFile and also pysam's check_truncation() function. All of which say the files have no issues.
Thanks, Jared