TypeError: unsupported operand type(s) for -: 'int' and 'NoneType'

[morispi]

Hello,

I'm trying to run NAIBR on a LongRanger generated BAM file (available here: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG002_NA24385_son/10XGenomics/).

However, NAIBR reports the following error:

Traceback (most recent call last):
  File "/home/genouest/genscale/pmorisse/NAIBR/NAIBR.py", line 7, in <module>
    from get_reads import *
  File "/home/genouest/genscale/pmorisse/NAIBR/src/get_reads.py", line 5, in <module>
    from utils import *
  File "/home/genouest/genscale/pmorisse/NAIBR/src/utils.py", line 3, in <module>
    from global_vars import *
  File "/home/genouest/genscale/pmorisse/NAIBR/src/global_vars.py", line 102, in <module>
    lmin,lmax = estimate_lmin_lmax()
  File "/home/genouest/genscale/pmorisse/NAIBR/src/global_vars.py", line 85, in estimate_lmin_lmax
    dist = read.reference_start-mate_pairs[read.query_name][1]
TypeError: unsupported operand type(s) for -: 'int' and 'NoneType'

My config file is as follows:

# minimum mapping quality (default=40)
min_mapq=40

# input bam file
bam_file=/home/genouest/genscale/pmorisse/Data/NA24385_phased_possorted_bam.bam

# output directory (default=.)
outdir=ResultsRefCallset

# list of intervals not to be intcluded in analysis (default=None)
blacklist=

# list in BEDPE format of novel adjacencies to be scored by NAIBR (default=None)
candidates=

# maximum distance between read-pairs in a linked-read (default=10000)
d=10000

# minimum size of structural variant (default=lmax)
min_sv=1000

# number of threads (default=1)
threads=16

# minimum number of barcode overlaps supporting a candidate NA (default = 3)
k=3

I found another issue reporting a similar error (#4), where you asked to check whether the reads where phased or not using samtools view [.bam file] | grep 'HP'. I did so, and reads do appear to be phased, as the file name suggests. First few lines of the output are as follows:

HISEQ-002:393:C7A29ANXX:4:1215:2691:54104 147 chr1 843446 60 98M = 843331 -213 ATAACTACCTACAAGTTTTCTGATTTATTCATTAGTGGATTTGTTCGTGATCAGCCCCACACCTGTTAGAATGGAAGCTGCAGGCAGCAGGAACCAGT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBBBBB NM:i:0 MD:Z:98 AS:i:98 XS:i:0 RG:Z:None RX:Z:CAAGGGCATCCAAC QX:Z:BBBBBFFFFFFFF/ BX:Z:CAAGGGCATCCAAC-1 BC:Z:GACTAAAC QT:Z:BBBBBFFF PS:Z:10843405 HP:i:2
HISEQ-002:393:C7A29ANXX:2:1210:20066:36242 99 chr1 844235 60 88M = 844352 215 TGGCCCTGCAGCAGGTGGGATTCTGCTCAGCCCATTTCCTGGGCCACGGGATTCATGAAGGGCACGGGGTCAGGCCCCCCGGGCGCAC F/BFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NM:i:1 MD:Z:65C22 AS:i:83 XS:i:24 RG:Z:None RX:Z:TGCTTTCATACCTG QX:Z:BBBBBFFFFFBBF< BX:Z:TGCTTTCATACCTG-1 BC:Z:CTTGTGTA QT:Z:BBBBBFFF PS:Z:10843405HP:i:2
HISEQ-002:393:C7A29ANXX:2:1210:20066:36242 147 chr1 844352 1 98M = 844235 -215 AGGCCCCCGGGCGCACCTTTGCTGGTATATGCGGGGGTCGGGGTCAGGCCCCCGGGCGCACCTTTGCTGGTATATGCGGGGGTCGGGGTCAGGCCCCC /BB<BBB/7/BB///<B/F/B/<BFBB</BB/FB//</BFFF<FBB</FFFFFFFFFB<FBFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBBBBB NM:i:1 MD:Z:62G35 AS:i:93 XS:i:93 RG:Z:None RX:Z:TGCTTTCATACCTG QX:Z:BBBBBFFFFFBBF< BX:Z:TGCTTTCATACCTG-1 BC:Z:CTTGTGTA QT:Z:BBBBBFFFPS:Z:10843405 HP:i:2
HISEQ-002:393:C7A29ANXX:5:1104:8117:50815 99 chr1 844374 6 88M = 844525 243 TGGTATATGCGGGGGTCGGGGTCAGGCCCCCGGGCGCACCGTTGCTGGTATATGCGGGGGTCGGGGTCAGGCCCCCGGGCGCACCGTT BFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFBFFB/FFFBB</7BBFBFFBFFF// NM:i:0 MD:Z:88 AS:i:88 XS:i:83 RG:Z:None RX:Z:TGCTTTCATACCTG QX:Z:BB<BBFFFFFFFFB BX:Z:TGCTTTCATACCTG-1 BC:Z:ACGACCGT QT:Z:BBBBBFFF PS:Z:10843405 HP:i:2
HISEQ-002:393:C7A29ANXX:4:1111:6966:5186 163 chr1 844524 0 6S92M = 844542 106 GCAGGAGTCGGGGTCAGGCCCCCGGGCGCACCTTTGCTGGTATATGCGGGGGTCGGGGTCAGGCCCCCGGGCGCACCGTTGCTGGTATATGCGGGGGT BBBBBBFFFF<BBFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFF</<F/7//B7FFFFF<<7///BBFBBFFFFFFBF<//<F<FFF/F/BFBBBBB/ NM:i:0 MD:Z:92 AS:i:92 XS:i:92 RG:Z:None XA:Z:chr1,+844880,6S92M,0;chr1,+844344,7S91M,0;chr1,+844699,6S92M,2;chr1,+844382,98M,4; RX:Z:TCGTCCCAGTCCTA QX:Z://B<B/B/<<BFB/ BX:Z:TCGTCCCAGTCCTA-1 BC:Z:TGACGTCG QT:Z:BBBBBB<F PS:Z:10843405 HP:i:2

Do you have any idea what could be causing the issue?

Best,
Pierre