Subset of chromosome 1 json files have been added into chr X output when converting from VCF to JSON

[mugitty]

Output for chr X has a subdirectory chr1 which contains json files. Note not all chromosome1's files are in chrX directory. Only a subset.

/annoq/20241024_annoq_proj/annoq-database/output/top_med
]$ ls chrX.vcf/chr1.vcf
1009.json 1073.json 115.json 203.json 288.json 367.json 449.json 491.json 566.json 659.json 714.json 835.json 902.json 960.json
1011.json 1082.json 124.json 232.json 290.json 396.json 451.json 504.json 597.json 668.json 747.json 857.json 91.json 978.json
1020.json 1117.json 146.json 248.json 305.json 4.json 460.json 51.json 60.json 670.json 776.json 866.json 933.json 989.json
1038.json 1126.json 177.json 250.json 334.json 402.json 478.json 535.json 612.json 681.json 787.json 89.json 949.json
1042.json 1144.json 186.json 261.json 356.json 433.json 49.json 557.json 623.json 699.json 804.json 897.json 951.json

chromosome 1 also contains the json files
$ ls -latr chrX.vcf/chr1.vcf/1073.json
616899165 Oct 24 18:10 chrX.vcf/chr1.vcf/1073.json
ls -latr chr1.vcf/1073.json
616899165 Oct 24 16:59 chr1.vcf/1073.json

=====================================

Output from slurm job looks good. Counts also match

annoq-database]$ cat slurm-24086501.out

SLURM_JOB_ID = 24086501
SLURM_JOB_NODELIST = b11-20
TMPDIR = /tmp/SLURM_24086501

The following have been reloaded with a version change:

1. python/3.11.3 => python/3.9.12

Python 3.9.12
Starting JSON conversion: /20241024_annoq_proj//annoq-data-builder/wgsa_add/output/top_med/chr1.vcf -> /annoq/20241024_annoq_proj//annoq-database/output/top_med/chr1.vcf
Start time: Thu Oct 24 11:20:28 PDT 2024
Processed 57550000 records. Time elapsed: 21712.01637363434 simport records 57577226
used time 21719.3152821064 s
Process completed in 21719.359974622726 seconds
End time: Thu Oct 24 17:22:28 PDT 2024

annoq-database]$ cat slurm-24086523.out

SLURM_JOB_ID = 24086523
SLURM_JOB_NODELIST = b11-19
TMPDIR = /tmp/SLURM_24086523

The following have been reloaded with a version change:

1. python/3.11.3 => python/3.9.12

Python 3.9.12
Starting JSON conversion: /annoq/20241024_annoq_proj//annoq-data-builder/wgsa_add/output/top_med/chrX.vcf -> /annoq/20241024_annoq_proj//annoq-database/output/top_med/chrX.vcf
Start time: Thu Oct 24 11:20:32 PDT 2024
Processed 29100000 records. Time elapsed: 9015.62481713295 simport records 29114100
used time 9019.519134283066 s
Process completed in 9019.558532476425 seconds
End time: Thu Oct 24 13:50:51 PDT 2024