Phasing fails

[csmoreno]

I am trying to run a pipeline and it gets through the generation of the snps, but then the phasing fails.
I get this error:

Traceback (most recent call last):
File "/Users/cmoreno/opt/anaconda3/envs/hatchet/bin/hatchet", line 33, in
sys.exit(load_entry_point('hatchet==1.1.1', 'console_scripts', 'hatchet')())
File "/Users/cmoreno/opt/anaconda3/envs/hatchet/lib/python3.10/site-packages/hatchet/main.py", line 61, in main
globals()command
File "/Users/cmoreno/opt/anaconda3/envs/hatchet/lib/python3.10/site-packages/hatchet/utils/run.py", line 155, in main
phase_snps(
File "/Users/cmoreno/opt/anaconda3/envs/hatchet/lib/python3.10/site-packages/hatchet/utils/phase_snps.py", line 88, in main
vcfs = phaser.run(work=phaser_args, n_instances=n_instances)
File "/Users/cmoreno/opt/anaconda3/envs/hatchet/lib/python3.10/site-packages/hatchet/utils/multiprocessing.py", line 98, in run
raise result.class(f'WORK {work_i} FAILED\n\n{error_string}')
RuntimeError: WORK 2 FAILED

Traceback (most recent call last):
File "/Users/cmoreno/opt/anaconda3/envs/hatchet/lib/python3.10/site-packages/hatchet/utils/multiprocessing.py", line 32, in run
result = self.worker.work(*args)
File "/Users/cmoreno/opt/anaconda3/envs/hatchet/lib/python3.10/site-packages/hatchet/utils/phase_snps.py", line 210, in work
vcf_phased = self.run_shapeit(infile=vcf_filtered, chromosome=chromosome) # phase
File "/Users/cmoreno/opt/anaconda3/envs/hatchet/lib/python3.10/site-packages/hatchet/utils/phase_snps.py", line 358, in run_shapeit
run(
File "/Users/cmoreno/opt/anaconda3/envs/hatchet/lib/python3.10/site-packages/hatchet/utils/Supporting.py", line 189, in run
error(error_msg.format(command=command), raise_exception=True)
File "/Users/cmoreno/opt/anaconda3/envs/hatchet/lib/python3.10/site-packages/hatchet/utils/Supporting.py", line 137, in error
return log(
File "/Users/cmoreno/opt/anaconda3/envs/hatchet/lib/python3.10/site-packages/hatchet/utils/Supporting.py", line 124, in log
raise exception_class(msg)
ValueError: Phasing failed on /Users/cmoreno/hatchet-master/PCM002.hatchet.output/phase/12_filtered.vcf.gz. Please check /Users/cmoreno/hatchet-master/PCM002.hatchet.output/phase/12_shapeit.log for possible hints.

12_shapeit.log says
Phaser mode : unrecognised option '--input-vcf'
Converter mode : unrecognised option '--output-vcf'
[bgzip] No such file or directory: /Users/cmoreno/hatchet-master/PCM002.hatchet.output/phase/12_phased.vcf
[E::hts_open_format] Failed to open file "/Users/cmoreno/hatchet-master/PCM002.hatchet.output/phase/12_phased.vcf.gz" : No such file or directory
index: failed to open "/Users/cmoreno/hatchet-master/PCM002.hatchet.output/phase/12_phased.vcf.gz"

If I try to run it with phase_snps = False, I get this error:

[2023-May-03 16:00:38]# Writing the total read counts for all samples in /Users/cmoreno/hatchet-master/output/rdr/total.tsv
NO PHASING FILE FOUND at /Users/cmoreno/hatchet-master/output/phase/phased.vcf.gz. Not including phasing in binning process.
[2023-May-03 16:00:38]# Parsing and checking input arguments
Identified 22 chromosomes.

baffile: /Users/cmoreno/hatchet-master/output/baf/tumor.1bed
outfile: /Users/cmoreno/hatchet-master/output/bb/bulk.bb
sample_names: ['normal', 'PCM002P1_bwa_mem_alignments_MARKDUPS.bam', 'PCM002P3_bwa_mem_alignments_MARKDUPS.bam']
min_snp_reads: 5000
min_total_reads: 5000
use_chr: True
processes: 4
chromosomes: ['chr1', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr2', 'chr20', 'chr21', 'chr22', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9']
array: /Users/cmoreno/hatchet-master/output/rdr
totalcounts: /Users/cmoreno/hatchet-master/output/rdr/total.tsv
phase: None
blocksize: 25000
max_snps_per_block: 10
test_alpha: 0.1
multisample: True
ref_version: hg38

Loading intermediate files for chromosome chr13
Loading intermediate files for chromosome chr1
Loading intermediate files for chromosome chr11
Loading intermediate files for chromosome chr15
Binning p arm of chromosome chr15
No SNPs found in p arm for chr15
Binning q arm of chromosome chr15
Error in chromosome chr15:
(2184, 2166)
Binning p arm of chromosome chr11
Error in chromosome chr11:
(1537, 1467)
Binning p arm of chromosome chr1
Traceback (most recent call last):
Traceback (most recent call last):
File "/Users/cmoreno/opt/anaconda3/envs/hatchet/lib/python3.10/site-packages/hatchet/utils/combine_counts.py", line 948, in run_chromosome
bins_p = adaptive_bins_arm(
File "/Users/cmoreno/opt/anaconda3/envs/hatchet/lib/python3.10/site-packages/hatchet/utils/combine_counts.py", line 270, in adaptive_bins_arm
assert len(snp_positions) == len(snp_thresholds) - 1, (
File "/Users/cmoreno/opt/anaconda3/envs/hatchet/lib/python3.10/site-packages/hatchet/utils/combine_counts.py", line 1009, in run_chromosome
bins_q = adaptive_bins_arm(
File "/Users/cmoreno/opt/anaconda3/envs/hatchet/lib/python3.10/site-packages/hatchet/utils/combine_counts.py", line 270, in adaptive_bins_arm
assert len(snp_positions) == len(snp_thresholds) - 1, (
AssertionError: (1537, 1467)
AssertionError: (2184, 2166)
Error in chromosome chr1:
(3255, 3312)
Traceback (most recent call last):
File "/Users/cmoreno/opt/anaconda3/envs/hatchet/lib/python3.10/site-packages/hatchet/utils/combine_counts.py", line 948, in run_chromosome
bins_p = adaptive_bins_arm(
File "/Users/cmoreno/opt/anaconda3/envs/hatchet/lib/python3.10/site-packages/hatchet/utils/combine_counts.py", line 270, in adaptive_bins_arm
assert len(snp_positions) == len(snp_thresholds) - 1, (
AssertionError: (3255, 3312)

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/Users/cmoreno/opt/anaconda3/envs/hatchet/bin/hatchet", line 33, in
sys.exit(load_entry_point('hatchet==1.1.1', 'console_scripts', 'hatchet')())
File "/Users/cmoreno/opt/anaconda3/envs/hatchet/lib/python3.10/site-packages/hatchet/main.py", line 61, in main
globals()command
File "/Users/cmoreno/opt/anaconda3/envs/hatchet/lib/python3.10/site-packages/hatchet/utils/run.py", line 253, in main
combine_counts(args)
File "/Users/cmoreno/opt/anaconda3/envs/hatchet/lib/python3.10/site-packages/hatchet/utils/combine_counts.py", line 98, in main
p.map(run_chromosome_wrapper, params)
File "/Users/cmoreno/opt/anaconda3/envs/hatchet/lib/python3.10/multiprocessing/pool.py", line 367, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/Users/cmoreno/opt/anaconda3/envs/hatchet/lib/python3.10/multiprocessing/pool.py", line 774, in get
raise self._value
AssertionError: (1537, 1467)