debug_issue_31

gistfile1.txt

```
tar zxvf debug_issue_31.tar.gz
./test/test_task/ref_output/test_xcor/se/subsample/ENCFF439VSY.subsampled.400.trim.merged.nodup.tn5.no_chrM.5K.cc.qc
./test/test_task/ref_output/test_xcor/pe/subsample/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.no_chrM.R1.5K.cc.qc
./cromwell-executions/atac/5d7e30ce-d8eb-4658-a63c-4972a2b64eff/call-read_genome_tsv/execution/script
./cromwell-executions/atac/5d7e30ce-d8eb-4658-a63c-4972a2b64eff/call-read_genome_tsv/execution/stdout
./cromwell-executions/atac/5d7e30ce-d8eb-4658-a63c-4972a2b64eff/call-read_genome_tsv/execution/stderr
./cromwell-executions/atac/2a0d0464-f14a-4c4d-a994-cf084e712a66/call-read_genome_tsv/execution/script
./cromwell-executions/atac/22b7290b-b6b3-444f-aece-b9d0d367821b/call-read_genome_tsv/execution/script
./cromwell-executions/atac/22b7290b-b6b3-444f-aece-b9d0d367821b/call-read_genome_tsv/execution/stdout
./cromwell-executions/atac/22b7290b-b6b3-444f-aece-b9d0d367821b/call-read_genome_tsv/execution/stderr
./cromwell-executions/atac/9d936185-fae0-45ac-8bd8-bd22ceac4634/call-read_genome_tsv/execution/script
./cromwell-executions/atac/9d936185-fae0-45ac-8bd8-bd22ceac4634/call-read_genome_tsv/execution/stdout
./cromwell-executions/atac/9d936185-fae0-45ac-8bd8-bd22ceac4634/call-read_genome_tsv/execution/stderr
./cromwell-executions/atac/018d7f41-9161-4d4d-8a85-30b884e414c1/call-read_genome_tsv/execution/script
./cromwell-executions/atac/018d7f41-9161-4d4d-8a85-30b884e414c1/call-read_genome_tsv/execution/stdout
./cromwell-executions/atac/018d7f41-9161-4d4d-8a85-30b884e414c1/call-read_genome_tsv/execution/stderr
./cromwell-executions/atac/017cb8fd-6ee0-4b2d-b349-9303fe25cac8/call-bowtie2/shard-0/execution/script
./cromwell-executions/atac/017cb8fd-6ee0-4b2d-b349-9303fe25cac8/call-bowtie2/shard-1/execution/script
./cromwell-executions/atac/017cb8fd-6ee0-4b2d-b349-9303fe25cac8/call-read_genome_tsv/execution/script
./cromwell-executions/atac/017cb8fd-6ee0-4b2d-b349-9303fe25cac8/call-read_genome_tsv/execution/stdout
./cromwell-executions/atac/017cb8fd-6ee0-4b2d-b349-9303fe25cac8/call-read_genome_tsv/execution/stderr
./cromwell-executions/atac/017cb8fd-6ee0-4b2d-b349-9303fe25cac8/call-trim_adapter/shard-0/execution/script
./cromwell-executions/atac/017cb8fd-6ee0-4b2d-b349-9303fe25cac8/call-trim_adapter/shard-0/execution/stdout
./cromwell-executions/atac/017cb8fd-6ee0-4b2d-b349-9303fe25cac8/call-trim_adapter/shard-0/execution/stderr
./cromwell-executions/atac/017cb8fd-6ee0-4b2d-b349-9303fe25cac8/call-trim_adapter/shard-1/execution/script
./cromwell-executions/atac/017cb8fd-6ee0-4b2d-b349-9303fe25cac8/call-trim_adapter/shard-1/execution/stdout
./cromwell-executions/atac/017cb8fd-6ee0-4b2d-b349-9303fe25cac8/call-trim_adapter/shard-1/execution/stderr
./cromwell-executions/atac/89488399-9cda-4021-88c5-0ddb5e40b195/call-read_genome_tsv/execution/script
./cromwell-executions/atac/07ff48b1-5fb0-4f32-8386-5e29759c2ed6/call-read_genome_tsv/execution/script
./cromwell-executions/atac/07ff48b1-5fb0-4f32-8386-5e29759c2ed6/call-read_genome_tsv/execution/stdout
./cromwell-executions/atac/07ff48b1-5fb0-4f32-8386-5e29759c2ed6/call-read_genome_tsv/execution/stderr
./cromwell-executions/atac/fdb1feb7-85f0-40f3-ac70-bc8162d0c046/call-read_genome_tsv/execution/script
./cromwell-executions/atac/fdb1feb7-85f0-40f3-ac70-bc8162d0c046/call-read_genome_tsv/execution/stdout
./cromwell-executions/atac/fdb1feb7-85f0-40f3-ac70-bc8162d0c046/call-read_genome_tsv/execution/stderr
./cromwell-executions/atac/aa1a0c24-8044-4b9f-bfa4-d9f1df86ebaa/call-read_genome_tsv/execution/script
./cromwell-executions/atac/aa1a0c24-8044-4b9f-bfa4-d9f1df86ebaa/call-read_genome_tsv/execution/stdout
./cromwell-executions/atac/aa1a0c24-8044-4b9f-bfa4-d9f1df86ebaa/call-read_genome_tsv/execution/stderr
./cromwell-executions/atac/e0efd905-c9b4-4b2a-8feb-b144ace88b66/call-read_genome_tsv/execution/script
./cromwell-executions/atac/e0efd905-c9b4-4b2a-8feb-b144ace88b66/call-read_genome_tsv/execution/stdout
./cromwell-executions/atac/e0efd905-c9b4-4b2a-8feb-b144ace88b66/call-read_genome_tsv/execution/stderr
./cromwell-executions/atac/b1447aab-533b-4922-b0ee-8f359254d27c/call-read_genome_tsv/execution/script
./cromwell-executions/atac/b1447aab-533b-4922-b0ee-8f359254d27c/call-read_genome_tsv/execution/stdout
./cromwell-executions/atac/b1447aab-533b-4922-b0ee-8f359254d27c/call-read_genome_tsv/execution/stderr
./cromwell-executions/atac/5bb912e0-4078-4b8b-b1a8-617191f897d3/call-bowtie2/shard-0/execution/script
./cromwell-executions/atac/5bb912e0-4078-4b8b-b1a8-617191f897d3/call-read_genome_tsv/execution/script
./cromwell-executions/atac/5bb912e0-4078-4b8b-b1a8-617191f897d3/call-read_genome_tsv/execution/stdout
./cromwell-executions/atac/5bb912e0-4078-4b8b-b1a8-617191f897d3/call-read_genome_tsv/execution/stderr
./cromwell-executions/atac/5bb912e0-4078-4b8b-b1a8-617191f897d3/call-trim_adapter/shard-0/execution/script
./cromwell-executions/atac/5bb912e0-4078-4b8b-b1a8-617191f897d3/call-trim_adapter/shard-0/execution/stdout
./cromwell-executions/atac/5bb912e0-4078-4b8b-b1a8-617191f897d3/call-trim_adapter/shard-0/execution/stderr
./cromwell-executions/atac/5bb912e0-4078-4b8b-b1a8-617191f897d3/call-trim_adapter/shard-1/execution/script
./cromwell-executions/atac/5bb912e0-4078-4b8b-b1a8-617191f897d3/call-trim_adapter/shard-1/execution/stdout
./cromwell-executions/atac/5bb912e0-4078-4b8b-b1a8-617191f897d3/call-trim_adapter/shard-1/execution/stderr
./cromwell-executions/atac/2386aadb-26d5-40d6-862f-1b698f292652/call-read_genome_tsv/execution/script
./cromwell-executions/atac/2386aadb-26d5-40d6-862f-1b698f292652/call-read_genome_tsv/execution/stdout
./cromwell-executions/atac/2386aadb-26d5-40d6-862f-1b698f292652/call-read_genome_tsv/execution/stderr
./cromwell-executions/atac/a6746e89-56e0-4fa7-bac7-7c869ee6b589/call-read_genome_tsv/execution/script
./cromwell-executions/atac/a6746e89-56e0-4fa7-bac7-7c869ee6b589/call-read_genome_tsv/execution/stdout
./cromwell-executions/atac/a6746e89-56e0-4fa7-bac7-7c869ee6b589/call-read_genome_tsv/execution/stderr
./cromwell-executions/atac/1a39602d-0119-4882-ba4d-eb0f49c3c2cc/call-read_genome_tsv/execution/script
./cromwell-executions/atac/1a39602d-0119-4882-ba4d-eb0f49c3c2cc/call-read_genome_tsv/execution/stdout
./cromwell-executions/atac/1a39602d-0119-4882-ba4d-eb0f49c3c2cc/call-read_genome_tsv/execution/stderr
./cromwell-executions/atac/b8a759e6-e30f-43be-9d7a-03cd9a75ab73/call-read_genome_tsv/execution/script
./cromwell-executions/atac/b8a759e6-e30f-43be-9d7a-03cd9a75ab73/call-read_genome_tsv/execution/stderr
./cromwell-executions/atac/4b8b70c5-d3c5-4e7e-9166-09e3e68ddac6/call-read_genome_tsv/execution/script
./cromwell-executions/atac/4b8b70c5-d3c5-4e7e-9166-09e3e68ddac6/call-read_genome_tsv/execution/stdout
./cromwell-executions/atac/4b8b70c5-d3c5-4e7e-9166-09e3e68ddac6/call-read_genome_tsv/execution/stderr
./cromwell-executions/atac/0f43a90d-fc9b-449b-9e2c-946d022665ef/call-bowtie2/shard-0/execution/script
./cromwell-executions/atac/0f43a90d-fc9b-449b-9e2c-946d022665ef/call-read_genome_tsv/execution/script
./cromwell-executions/atac/0f43a90d-fc9b-449b-9e2c-946d022665ef/call-read_genome_tsv/execution/stdout
./cromwell-executions/atac/0f43a90d-fc9b-449b-9e2c-946d022665ef/call-read_genome_tsv/execution/stderr
./cromwell-executions/atac/0f43a90d-fc9b-449b-9e2c-946d022665ef/call-trim_adapter/shard-0/execution/script
./cromwell-executions/atac/0f43a90d-fc9b-449b-9e2c-946d022665ef/call-trim_adapter/shard-0/execution/stdout
./cromwell-executions/atac/0f43a90d-fc9b-449b-9e2c-946d022665ef/call-trim_adapter/shard-0/execution/stderr
./cromwell-executions/atac/0f43a90d-fc9b-449b-9e2c-946d022665ef/call-trim_adapter/shard-1/execution/script
./cromwell-executions/atac/0f43a90d-fc9b-449b-9e2c-946d022665ef/call-trim_adapter/shard-1/execution/stdout
./cromwell-executions/atac/0f43a90d-fc9b-449b-9e2c-946d022665ef/call-trim_adapter/shard-1/execution/stderr
./cromwell-executions/atac/8faa9164-43cd-4f7c-aea5-215472407045/call-bowtie2/shard-0/execution/script
./cromwell-executions/atac/8faa9164-43cd-4f7c-aea5-215472407045/call-read_genome_tsv/execution/script
./cromwell-executions/atac/8faa9164-43cd-4f7c-aea5-215472407045/call-read_genome_tsv/execution/stdout
./cromwell-executions/atac/8faa9164-43cd-4f7c-aea5-215472407045/call-read_genome_tsv/execution/stderr
./cromwell-executions/atac/8faa9164-43cd-4f7c-aea5-215472407045/call-trim_adapter/shard-0/execution/script
./cromwell-executions/atac/8faa9164-43cd-4f7c-aea5-215472407045/call-trim_adapter/shard-0/execution/stdout
./cromwell-executions/atac/8faa9164-43cd-4f7c-aea5-215472407045/call-trim_adapter/shard-0/execution/stderr
./cromwell-executions/atac/8faa9164-43cd-4f7c-aea5-215472407045/call-trim_adapter/shard-1/execution/script
./cromwell-executions/atac/8faa9164-43cd-4f7c-aea5-215472407045/call-trim_adapter/shard-1/execution/stdout
./cromwell-executions/atac/8faa9164-43cd-4f7c-aea5-215472407045/call-trim_adapter/shard-1/execution/stderr
./cromwell-executions/atac/de4502fb-addf-43ba-811f-92c77476c3f9/call-read_genome_tsv/execution/script
./cromwell-executions/atac/de4502fb-addf-43ba-811f-92c77476c3f9/call-read_genome_tsv/execution/stdout
./cromwell-executions/atac/de4502fb-addf-43ba-811f-92c77476c3f9/call-read_genome_tsv/execution/stderr
./cromwell-executions/atac/fb4329fe-c5ef-46e4-9c2a-93ecbfe24e1b/call-bowtie2/shard-0/execution/script
./cromwell-executions/atac/fb4329fe-c5ef-46e4-9c2a-93ecbfe24e1b/call-read_genome_tsv/execution/script
./cromwell-executions/atac/fb4329fe-c5ef-46e4-9c2a-93ecbfe24e1b/call-read_genome_tsv/execution/stdout
./cromwell-executions/atac/fb4329fe-c5ef-46e4-9c2a-93ecbfe24e1b/call-read_genome_tsv/execution/stderr
./cromwell-executions/atac/fb4329fe-c5ef-46e4-9c2a-93ecbfe24e1b/call-trim_adapter/shard-0/execution/script
./cromwell-executions/atac/fb4329fe-c5ef-46e4-9c2a-93ecbfe24e1b/call-trim_adapter/shard-0/execution/stdout
./cromwell-executions/atac/fb4329fe-c5ef-46e4-9c2a-93ecbfe24e1b/call-trim_adapter/shard-0/execution/stderr
./cromwell-executions/atac/fb4329fe-c5ef-46e4-9c2a-93ecbfe24e1b/call-trim_adapter/shard-1/execution/script
./cromwell-executions/atac/fb4329fe-c5ef-46e4-9c2a-93ecbfe24e1b/call-trim_adapter/shard-1/execution/stdout
./cromwell-executions/atac/fb4329fe-c5ef-46e4-9c2a-93ecbfe24e1b/call-trim_adapter/shard-1/execution/stderr
./cromwell-executions/atac/40bbc13e-fb59-4ec8-baa8-4671533629f9/call-read_genome_tsv/execution/script
./cromwell-executions/atac/40bbc13e-fb59-4ec8-baa8-4671533629f9/call-read_genome_tsv/execution/stdout
./cromwell-executions/atac/40bbc13e-fb59-4ec8-baa8-4671533629f9/call-read_genome_tsv/execution/stderr
./cromwell-executions/atac/09eb9431-23e8-46e3-9174-1d8dfb002956/call-read_genome_tsv/execution/script
./cromwell-executions/atac/09eb9431-23e8-46e3-9174-1d8dfb002956/call-read_genome_tsv/execution/stdout
./cromwell-executions/atac/09eb9431-23e8-46e3-9174-1d8dfb002956/call-read_genome_tsv/execution/stderr
./cromwell-executions/atac/3a05bcad-9123-4cc6-8f20-eea9df4b786d/call-read_genome_tsv/execution/script
./cromwell-executions/atac/3a05bcad-9123-4cc6-8f20-eea9df4b786d/call-read_genome_tsv/execution/stdout
./cromwell-executions/atac/3a05bcad-9123-4cc6-8f20-eea9df4b786d/call-read_genome_tsv/execution/stderr
./cromwell-executions/atac/10560b82-8ecd-448e-b349-ac54606d07c3/call-read_genome_tsv/execution/script
./cromwell-executions/atac/10560b82-8ecd-448e-b349-ac54606d07c3/call-read_genome_tsv/execution/stdout
./cromwell-executions/atac/10560b82-8ecd-448e-b349-ac54606d07c3/call-read_genome_tsv/execution/stderr
./cromwell-executions/atac/2a0ed041-872c-4e5f-b2b5-54735758a707/call-bowtie2/shard-0/execution/script
./cromwell-executions/atac/2a0ed041-872c-4e5f-b2b5-54735758a707/call-read_genome_tsv/execution/script
./cromwell-executions/atac/2a0ed041-872c-4e5f-b2b5-54735758a707/call-read_genome_tsv/execution/stdout
./cromwell-executions/atac/2a0ed041-872c-4e5f-b2b5-54735758a707/call-read_genome_tsv/execution/stderr
./cromwell-executions/atac/2a0ed041-872c-4e5f-b2b5-54735758a707/call-trim_adapter/shard-0/execution/script
./cromwell-executions/atac/2a0ed041-872c-4e5f-b2b5-54735758a707/call-trim_adapter/shard-0/execution/stdout
./cromwell-executions/atac/2a0ed041-872c-4e5f-b2b5-54735758a707/call-trim_adapter/shard-0/execution/stderr
./cromwell-executions/atac/2a0ed041-872c-4e5f-b2b5-54735758a707/call-trim_adapter/shard-1/execution/script
./cromwell-executions/atac/2a0ed041-872c-4e5f-b2b5-54735758a707/call-trim_adapter/shard-1/execution/stdout
./cromwell-executions/atac/2a0ed041-872c-4e5f-b2b5-54735758a707/call-trim_adapter/shard-1/execution/stderr
./cromwell-executions/atac/8823cc11-5e71-4004-b8d4-edf40eb38cd6/call-read_genome_tsv/execution/script
./conda/requirements_py3.txt
./conda/requirements.txt
```