ERROR: Calculation of read length statistics failed!

[sneupane01]

bash SequelQC.sh -u subreads.txt -n 16 -o Sequelresult1010 -v -k -p a

Running in NO_SCRAPS mode
Extracting data from .bam files
Data extraction was sucessful
Beginning calculation of read length statistics
Traceback (most recent call last):
File "generateReadLenStats_noScraps_py2.py", line 93, in
start = int(coord.split("")[0]); stop = int(coord.split("")[1])
ValueError: invalid literal for int() with base 10: 'ccs'
ERROR: Calculation of read length statistics failed!

[DavidEHufnagel]

Hey thanks for trying out SequelQC! This error could be caused if the names of the reads in SAM format are unconventional. If you could send me a couple lines in SAM format of one of your subreads files I could look into whether that could be the issue. If you sent it in BAM format I could convert it to SAM, but probably your BAM files are very large and would not be easy to provide here.

[sneupane01]

@hd VN:1.5 SO:unknown pb:3.0.1
@rg ID:e1866f86 PL:PACBIO DS:READTYPE=CCS;BINDINGKIT=101-500-400;SEQUENCINGKIT=101-427-800;BASECALLERVERSION=5.0.0;FRAMERATEHZ=100.000000;BarcodeFile=/gpfs/shared/apps_local/SMRTLink/7.0.1/smrtlink/userdata/jobs_root/000/000134/pacbio-barcodes/barcodes/barcodeset.xml;BarcodeHash=537410622c99133c77417499d4bd566f;BarcodeCount=6;BarcodeMode=Symmetric;BarcodeQuality=Score PU:m54115_190802_131940 PM:SEQUEL
@pg ID:ccs-3.4.1 PN:ccs VN:3.4.1 DS:Generate circular consensus sequences (ccs) from subreads. CL:ccs
@pg ID:pbmerge-0.23.0 PN:pbmerge VN:0.23.0
m54115_190802_131940/4194396/ccs 4 * 0 255 * * 0 0

[DavidEHufnagel]

I should have specified that I would like to see the first few lines after the header, so after the lines that start with "@" Thanks!

[sneupane01]

These files are from circular consensus sequences (CCS). SequelQC worked perfectly for RAW .bam files. I was trying with the .bam files from CCS. Those are the headers I got after I converted .bam CCS file to sam file.

[DavidEHufnagel]

Oh, I see. SequelQC was never designed to be used on CCS sequences, so I'm not really sure how it would behave. I've never generated CCS sequences myself so I'm not sure what the format looks like. I imagine changing the names in the CCS files so that they match what would be expected with raw data would solve this error. I can't be certain whether or not you'll get other errors downstream. You are certainly welcome to modify SequelQC for your purposes!