intrahost.py and vphaser errors

[elasekness]

I am using the containerized version of viral-ngs (broadinstitute/viral-ngs) to run intrahost.py.

I have a coordinate sorted bam file (generated with bwa mem) with only properly paired reads included. I also added a readgroup although I only have one library per sample.

Regardless, when I execute intrahost.py with the following command:
docker run --rm -v $(pwd):/data -w /data quay.io/broadinstitute/viral-ngs intrahost.py vphaser_one_sample CTP10.rg.sorted.bam CTP10.fasta CTP10.tsv

I get an error "get_column_x: fail to identify mapping"

Full error message:
2023-11-08 20:36:05,207 - cmd:197:main_argparse - INFO - software version: v1.25.0-8-ge144969, python version: 3.6.7 | packaged by conda-forge | (default, Jul 2 2019, 02:18:42)
[GCC 7.3.0]
2023-11-08 20:36:05,207 - cmd:199:main_argparse - INFO - command: /opt/viral-ngs/source/intrahost.py vphaser_one_sample inBam=CTP10.rg.sorted.bam inConsFasta=CTP10.fasta outTab=CTP10.tsv vphaserNumThreads=None minReadsEach=0 maxBias=10 removeDoublyMappedReads=False loglevel=INFO
2023-11-08 20:36:12,698 - vphaser2:48:execute - ERROR - b'\n--------------------------------------------------------\nProgram runs with the following Parameter setting:\n\n\tinput BAM file\t=\tCTP10.rg.sorted.bam\n\toutput Directory\t=\t/tmp/tmpbdyy4c1_vphaser2\n\terrModel\t\t=\tpileup + phase\n\talpha\t\t=\t0.05\n\tignoreBases \t=\t0\n\t(var_matepair, var_cycle, var_dt, var_qt)\t=\t1,1,1,20\n\tpSample\t\t=\t30%\n\twindowSz\t=\t500\n\tdelta\t=\t2\n\n--------------------------------------------------------\n\n\n\t1 bam file(s) found: \n\t\tCTP10.rg.sorted.bam\n\n\nParse bam header: get refSeq info & sanity check\n\n\tCTP10 len =11029\n\n\t1 ref sequence(s) found: \n\t\tName: CTP10\n\t\t\tBamfileID = 0\tRefID = 0\n\n\n\t0 platform(s) found: \n\n\nGet maxQ, minQ, maxReadLen, avgFragSz, stdFragSz from bam files ...\n\n\tTotal Reads = 80726\n\t# Mapped Reads = 80726\n\t# Reads used for checking Q scores = 24132\n\tminQ = 35\tmaxQ=69\t\tmaxRL = 149\n\t(avgfragSz, std) = 205\t156\n\nGenerate qual -> quantile map ... \n\n\nSet up paired read map arrays ... \n\n\t# total mapped reads: 80726\n\t# mapped mate-pairs = 40363\n\nPrepare aln columns file...\n\n Ref: CTP10 , len = 11029\n\n\n\t\tcreate file: /tmp/tmpbdyy4c1_vphaser2/CTP10.0.499.region\n\n\t\tcreate file: /tmp/tmpbdyy4c1_vphaser2/CTP10.500.999.region\n[EXIT]: get_column_x: fail to identify mapping\n'
b'\n--------------------------------------------------------\nProgram runs with the following Parameter setting:\n\n\tinput BAM file\t=\tCTP10.rg.sorted.bam\n\toutput Directory\t=\t/tmp/tmpbdyy4c1_vphaser2\n\terrModel\t\t=\tpileup + phase\n\talpha\t\t=\t0.05\n\tignoreBases \t=\t0\n\t(var_matepair, var_cycle, var_dt, var_qt)\t=\t1,1,1,20\n\tpSample\t\t=\t30%\n\twindowSz\t=\t500\n\tdelta\t=\t2\n\n--------------------------------------------------------\n\n\n\t1 bam file(s) found: \n\t\tCTP10.rg.sorted.bam\n\n\nParse bam header: get refSeq info & sanity check\n\n\tCTP10 len =11029\n\n\t1 ref sequence(s) found: \n\t\tName: CTP10\n\t\t\tBamfileID = 0\tRefID = 0\n\n\n\t0 platform(s) found: \n\n\nGet maxQ, minQ, maxReadLen, avgFragSz, stdFragSz from bam files ...\n\n\tTotal Reads = 80726\n\t# Mapped Reads = 80726\n\t# Reads used for checking Q scores = 24132\n\tminQ = 35\tmaxQ=69\t\tmaxRL = 149\n\t(avgfragSz, std) = 205\t156\n\nGenerate qual -> quantile map ... \n\n\nSet up paired read map arrays ... \n\n\t# total mapped reads: 80726\n\t# mapped mate-pairs = 40363\n\nPrepare aln columns file...\n\n Ref: CTP10 , len = 11029\n\n\n\t\tcreate file: /tmp/tmpbdyy4c1_vphaser2/CTP10.0.499.region\n\n\t\tcreate file: /tmp/tmpbdyy4c1_vphaser2/CTP10.500.999.region\n[EXIT]: get_column_x: fail to identify mapping\n'
Traceback (most recent call last):
File "/opt/viral-ngs/source/intrahost.py", line 1203, in
util.cmd.main_argparse(commands, doc)
File "/opt/viral-ngs/source/util/cmd.py", line 224, in main_argparse
ret = args.func_main(args)
File "/opt/viral-ngs/source/util/cmd.py", line 106, in _main
mainfunc(**args2)
File "/opt/viral-ngs/source/intrahost.py", line 150, in vphaser_one_sample
for row in libraryFilteredIter:
File "/opt/viral-ngs/source/intrahost.py", line 226, in compute_library_bias
for row in isnvs:
File "/opt/viral-ngs/source/intrahost.py", line 163, in filter_strand_bias
for row in isnvs:
File "/opt/viral-ngs/source/tools/vphaser2.py", line 61, in iterate
self.execute(inBam, outdir, numThreads)
File "/opt/viral-ngs/source/tools/vphaser2.py", line 45, in execute
subprocess.check_output(cmd, env=envCopy, stderr=subprocess.STDOUT)
File "/opt/miniconda/envs/viral-ngs-env/lib/python3.6/subprocess.py", line 336, in check_output
**kwargs).stdout
File "/opt/miniconda/envs/viral-ngs-env/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['/opt/miniconda/envs/viral-ngs-env/bin/vphaser2', '-i', 'CTP10.rg.sorted.bam', '-o', '/tmp/tmpbdyy4c1_vphaser2']' returned non-zero exit status 1.

I tried to run vphaser, as the error seems to originate there:
command:
docker run --rm -v $(pwd):/data -w /data quay.io/broadinstitute/viral-ngs vphaser2 -i CTP10.rg.sorted.bam -o vphaser_output
error message:
create file: vphaser_output/CTP10.0.499.region
[EXIT]: create_output_file: can't open file vphaser_output/CTP10.0.499.region

There is read coverage over these regions.