morinlab / dellingr Goto Github PK

Hi @ckrushton,

I'm currently trying to run your Dellingr pipeline on fastq files with 4bp UMI which flank the insert (for example NNNN----------------------------NNNN). I've followed all the installation steps noted in the README. However when I run the following command:

python3.8 /path/to/Dellingr/DellingrPipeline.py \ --fastqs R1.fastq.gz R2.fastq.gz --reference REF_GENOME --outdir alignment --barcode_sequence NNNN --barcode_position 1111 --max_mismatch 0 --family_mask 1111 -fmm 0 --duplex_mask 1111 -dmm 0 --targets path/to/BED --tag_family_members --threshold 0.01 --bwa /path/to/bwa --samtools /path/to/samtools

The pipeline completes the trim and BWA tasks, but fails at the collapse stage:

DELLINGR-MAIN 16:29:38 Starting...
DELLINGR-MAIN D36466_R1 16:29:39 Processing Sample 'test_R1'
DELLINGR-TRIM D36466_R1 16:29:39 Starting...
DELLINGR-TRIM D36466_R1 16:29:56 Discard Rate:0.11% Count:100000
DELLINGR-TRIM D36466_R1 16:30:13 Discard Rate:0.09% Count:200000
DELLINGR-TRIM D36466_R1 16:30:30 Discard Rate:0.10% Count:300000
DELLINGR-TRIM D36466_R1 16:30:47 Discard Rate:0.07% Count:400000
DELLINGR-TRIM D36466_R1 16:31:04 Discard Rate:0.08% Count:500000
DELLINGR-TRIM D36466_R1 16:31:21 Discard Rate:0.08% Count:600000
DELLINGR-TRIM D36466_R1 16:31:39 Discard Rate:0.08% Count:700000
DELLINGR-TRIM D36466_R1 16:31:57 Discard Rate:0.07% Count:800000
DELLINGR-TRIM D36466_R1 16:32:14 Discard Rate:0.07% Count:900000
DELLINGR-TRIM D36466_R1 16:32:30 Discard Rate:0.07% Count:1000000
DELLINGR-TRIM D36466_R1 16:32:48 Discard Rate:0.07% Count:1100000
DELLINGR-TRIM D36466_R1 16:33:06 Discard Rate:0.07% Count:1200000
DELLINGR-TRIM D36466_R1 16:33:24 Discard Rate:0.07% Count:1300000
DELLINGR-TRIM D36466_R1 16:33:42 Discard Rate:0.07% Count:1400000
DELLINGR-TRIM D36466_R1 16:34:00 Discard Rate:0.07% Count:1500000
DELLINGR-TRIM D36466_R1 16:34:18 Discard Rate:0.06% Count:1600000
DELLINGR-TRIM D36466_R1 16:34:36 Discard Rate:0.06% Count:1700000
DELLINGR-TRIM D36466_R1 16:34:54 Discard Rate:0.07% Count:1800000
DELLINGR-TRIM D36466_R1 16:35:13 Discard Rate:0.06% Count:1900000
DELLINGR-TRIM D36466_R1 16:35:31 Discard Rate:0.06% Count:2000000
DELLINGR-TRIM D36466_R1 16:35:49 Discard Rate:0.06% Count:2100000
DELLINGR-TRIM D36466_R1 16:36:07 Discard Rate:0.06% Count:2200000
DELLINGR-TRIM D36466_R1 16:36:25 Discard Rate:0.06% Count:2300000
DELLINGR-TRIM D36466_R1 16:36:42 Discard Rate:0.06% Count:2400000
DELLINGR-TRIM D36466_R1 16:37:00 Discard Rate:0.06% Count:2500000
DELLINGR-TRIM D36466_R1 16:37:19 Discard Rate:0.05% Count:2600000
DELLINGR-TRIM D36466_R1 16:37:36 Discard Rate:0.05% Count:2700000
DELLINGR-TRIM D36466_R1 16:37:54 Discard Rate:0.05% Count:2800000
DELLINGR-TRIM D36466_R1 16:38:13 Discard Rate:0.05% Count:2900000
DELLINGR-TRIM D36466_R1 16:38:31 Discard Rate:0.05% Count:3000000
DELLINGR-TRIM D36466_R1 16:38:49 Discard Rate:0.05% Count:3100000
DELLINGR-TRIM D36466_R1 16:39:07 Discard Rate:0.05% Count:3200000
DELLINGR-TRIM D36466_R1 16:39:25 Discard Rate:0.05% Count:3300000
DELLINGR-TRIM D36466_R1 16:39:43 Discard Rate:0.05% Count:3400000
DELLINGR-TRIM D36466_R1 16:40:02 Discard Rate:0.05% Count:3500000
DELLINGR-TRIM D36466_R1 16:40:20 Discard Rate:0.05% Count:3600000
DELLINGR-TRIM D36466_R1 16:40:37 Discard Rate:0.05% Count:3700000
DELLINGR-TRIM D36466_R1 16:40:56 Discard Rate:0.04% Count:3800000
DELLINGR-TRIM D36466_R1 16:41:14 Discard Rate:0.04% Count:3900000
DELLINGR-TRIM D36466_R1 16:41:28 Discard Rate:0.04% Count:3977336
DELLINGR-TRIM D36466_R1 16:41:28 Trimming Complete
DELLINGR-MAIN D36466_R1 16:41:28 Running BWA...
DELLINGR-MAIN D36466_R1 16:43:03 Reads Processed:68494
DELLINGR-MAIN D36466_R1 16:43:49 Reads Processed:136988
DELLINGR-MAIN D36466_R1 16:44:35 Reads Processed:205482
DELLINGR-MAIN D36466_R1 16:45:18 Reads Processed:273976
DELLINGR-MAIN D36466_R1 16:46:04 Reads Processed:342470
DELLINGR-MAIN D36466_R1 16:46:48 Reads Processed:410964
DELLINGR-MAIN D36466_R1 16:47:34 Reads Processed:479458
DELLINGR-MAIN D36466_R1 16:48:18 Reads Processed:547952
DELLINGR-MAIN D36466_R1 16:49:03 Reads Processed:616446
DELLINGR-MAIN D36466_R1 16:49:48 Reads Processed:684940
DELLINGR-MAIN D36466_R1 16:50:33 Reads Processed:753434
DELLINGR-MAIN D36466_R1 16:51:18 Reads Processed:821928
DELLINGR-MAIN D36466_R1 16:52:03 Reads Processed:890422
DELLINGR-MAIN D36466_R1 16:52:48 Reads Processed:958916
DELLINGR-MAIN D36466_R1 16:53:33 Reads Processed:1027410
DELLINGR-MAIN D36466_R1 16:54:17 Reads Processed:1095904
DELLINGR-MAIN D36466_R1 16:55:01 Reads Processed:1164398
DELLINGR-MAIN D36466_R1 16:55:47 Reads Processed:1232892
DELLINGR-MAIN D36466_R1 16:56:32 Reads Processed:1301386
DELLINGR-MAIN D36466_R1 16:57:16 Reads Processed:1369880
DELLINGR-MAIN D36466_R1 16:58:00 Reads Processed:1438374
DELLINGR-MAIN D36466_R1 16:58:45 Reads Processed:1506868
DELLINGR-MAIN D36466_R1 16:59:28 Reads Processed:1575362
DELLINGR-MAIN D36466_R1 17:00:13 Reads Processed:1643856
DELLINGR-MAIN D36466_R1 17:00:57 Reads Processed:1712350
DELLINGR-MAIN D36466_R1 17:01:41 Reads Processed:1780844
DELLINGR-MAIN D36466_R1 17:02:26 Reads Processed:1849338
DELLINGR-MAIN D36466_R1 17:03:09 Reads Processed:1917832
DELLINGR-MAIN D36466_R1 17:03:53 Reads Processed:1986326
DELLINGR-MAIN D36466_R1 17:04:37 Reads Processed:2054820
DELLINGR-MAIN D36466_R1 17:05:21 Reads Processed:2123314
DELLINGR-MAIN D36466_R1 17:06:05 Reads Processed:2191808
DELLINGR-MAIN D36466_R1 17:06:50 Reads Processed:2260302
DELLINGR-MAIN D36466_R1 17:07:34 Reads Processed:2328796
DELLINGR-MAIN D36466_R1 17:08:19 Reads Processed:2397290
DELLINGR-MAIN D36466_R1 17:09:03 Reads Processed:2465784
DELLINGR-MAIN D36466_R1 17:09:49 Reads Processed:2534278
DELLINGR-MAIN D36466_R1 17:10:32 Reads Processed:2602772
DELLINGR-MAIN D36466_R1 17:11:17 Reads Processed:2671266
DELLINGR-MAIN D36466_R1 17:12:01 Reads Processed:2739760
DELLINGR-MAIN D36466_R1 17:12:45 Reads Processed:2808254
DELLINGR-MAIN D36466_R1 17:13:29 Reads Processed:2876748
DELLINGR-MAIN D36466_R1 17:14:13 Reads Processed:2945242
DELLINGR-MAIN D36466_R1 17:14:56 Reads Processed:3013736
DELLINGR-MAIN D36466_R1 17:15:39 Reads Processed:3082230
DELLINGR-MAIN D36466_R1 17:16:24 Reads Processed:3150724
DELLINGR-MAIN D36466_R1 17:17:07 Reads Processed:3219218
DELLINGR-MAIN D36466_R1 17:17:49 Reads Processed:3287712
DELLINGR-MAIN D36466_R1 17:18:31 Reads Processed:3356206
DELLINGR-MAIN D36466_R1 17:19:15 Reads Processed:3424700
DELLINGR-MAIN D36466_R1 17:19:58 Reads Processed:3493194
DELLINGR-MAIN D36466_R1 17:20:41 Reads Processed:3561688
DELLINGR-MAIN D36466_R1 17:21:23 Reads Processed:3630182
DELLINGR-MAIN D36466_R1 17:22:06 Reads Processed:3698676
DELLINGR-MAIN D36466_R1 17:22:48 Reads Processed:3767170
DELLINGR-MAIN D36466_R1 17:23:30 Reads Processed:3835664
DELLINGR-MAIN D36466_R1 17:24:13 Reads Processed:3904158
DELLINGR-MAIN D36466_R1 17:24:54 Reads Processed:3972652
DELLINGR-MAIN D36466_R1 17:24:56 Reads Processed:3975418
DELLINGR-MAIN D36466_R1 17:26:41 Mapping Complete
usage: DellingrPipeline.py [-h] [-c INI] -i SAM/BAM/CRAM -o SAM/BAM/CRAM
[-t BED] [--no_barcodes] [--collapse_duplexes]
[-fm 0001111111111110] [-dm 0000000001111110]
[-fmm INT] [-dmm INT] [--tag_family_members]
[--plot_prefix DIR] -r REFERENCE
[--input_format SAM/BAM/CRAM]
DellingrPipeline.py: error: the following arguments are required: (-fmm/--family_mismatch, -dmm/--duplex_mismatch) OR --no_barcodes

I tried the above command using -fmm/--family_mismatch and -dmm/--duplex_mismatch 0, but the program fails with the same error message. I ran the command using -fmm 1 and -dmm 1 and the program ran to completion. I looked into the Collapse code and saw https://github.com/morinlab/Dellingr/blob/master/Dellingr/Collapse.py#L1489-L1495 that the -fmm/-dmm can be 0, but the program fails when run with a 0. Am I doing something wrong on my end, or is there an issue with the validateArgs?

Best,
Chad