Unable to start analysis
VikasDT opened this issue · 2 comments
(enrich2) vikastrivedi@Vikass-MacBook-Pro ~ % enrich_gui
2020-10-30 23:58:19,598 [enrich2.experiment.Experiment - PAL] Found existing HDF5 data store "/Users/vikastrivedi/Downloads/Sad/PAL_exp.h5"
2020-10-30 23:58:19,862 [numexpr.utils] NumExpr defaulting to 4 threads.
2020-10-30 23:58:19,940 [enrich2.selection.Selection - Rep1] Found existing HDF5 data store "/Users/vikastrivedi/Downloads/Sad/Rep1_sel.h5"
2020-10-30 23:58:19,943 [enrich2.basic.BasicSeqLib - Naive] Found existing HDF5 data store "/Users/vikastrivedi/Downloads/Sad/Naive_lib.h5"
2020-10-30 23:58:19,946 [enrich2.basic.BasicSeqLib - Gen1] Found existing HDF5 data store "/Users/vikastrivedi/Downloads/Sad/Gen1_lib.h5"
2020-10-30 23:58:19,949 [enrich2.basic.BasicSeqLib - Gen2] Found existing HDF5 data store "/Users/vikastrivedi/Downloads/Sad/Gen2_lib.h5"
2020-10-30 23:58:19,951 [enrich2.basic.BasicSeqLib - Gen3] Found existing HDF5 data store "/Users/vikastrivedi/Downloads/Sad/Gen3_lib.h5"
2020-10-30 23:58:19,955 [enrich2.selection.Selection - Rep1] Counting for each time point (variants)
2020-10-30 23:58:19,955 [enrich2.basic.BasicSeqLib - Naive] Counting variants
2020-10-30 23:58:58,771 [enrich2.gui.runner_window] Failed to count variants [Naive]
This is the configuration file
{
"conditions": [
{
"name": "Phe",
"selections": [
{
"libraries": [
{
"fastq": {
"filters": {
"min quality": 20
},
"length": 20,
"reads": "/Users/vikastrivedi/Downloads/Deep Seq data/Trimmed/Naive2.fastq",
"reverse": false
},
"name": "Naive",
"report filtered reads": false,
"timepoint": 0,
"variants": {
"use aligner": false,
"wild type": {
"coding": true,
"reference offset": 0,
"sequence": "ATGGCACATCACCACCACCATCACAAAACCCTGAGCCAGGCACAGAGCAAAACCAGCAGCCAGCAGTTTAGCTTTACCGGCAATAGCAGCGCAAATGTGATTATTGGTAATCAGAAACTGACCATCAATGATGTTGCACGTGTTGCCCGTAATGGCACCCTGGTTAGCCTGACCAATAATACCGATATTCTGCAGGGTATTCAGGCCAGCTGTGATTATATCAATAATGCAGTTGAAAGCGGTGAACCGATTTATGGTGTTACCAGCGGTTTTGGTGGTATGGCAAATGTTGCAATTAGCCGTGAACAGGCAAGCGAACTGCAGACCAATCTGGTTTGGTTTCTGAAAACCGGTGCAGGTAATAAACTGCCGCTGGCAGATGTTCGTGCAGCAATGCTGCTGCGTGCAAATAGCCACATGCGTGGTGCAAGCGGTATTCGTCTGGAACTGATTAAACGCATGGAAATCTTTCTGAATGCCGGTGTTACCCCGTATGTTTATGAATTTGGTAGCATTGGTGCCAGCGGTGATCTGGTTCCGCTGAGCTATATTACCGGTAGCCTGATTGGCCTGGACCCGAGCTTTAAAGTTGATTTTAATGGCAAAGAAATGGACGCACCGACCGCACTGCGTCAGCTGAATCTGAGTCCGCTGACCCTGCTGCCGAAAGAAGGTCTGGCAATGATGAATGGCACCAGCGTTATGACCGGTATTGCAGCAAATTGTGTTTATGATACCCAGATTCTGACCGCAATTGCAATGGGTGTTCATGCACTGGATATTCAGGCACTGAATGGTACAAATCAGAGCTTTCATCCGTTTATCCATAACAGCAAACCGCATCCGGGTCAGCTGTGGGCAGCAGATCAGATGATTAGCCTGCTGGCCAATAGCCAGCTGGTTCGTGATGAACTGGATGGTAAACATGATTATCGTGATCATGAACTGATCCAGGATCGTTATAGCCTGCGTTGTCTGCCGCAGTATCTGGGTCCGATTGTTGATGGTATTAGCCAGATTGCCAAACAAATCGAAATTGAGATTAACAGCGTTACCGATAACCCGCTGATTGATGTTGATAATCAGGCAAGCTATCATGGTGGTAATTTTCTGGGTCAGTATGTTGGTATGGGTATGGATCATCTGCGCTATTATATCGGTCTGCTGGCAAAACATCTGGATGTTCAGATTGCACTGCTGGCATCACCGGAATTTAGCAATGGTCTGCCTCCGAGTCTGCTGGGTAATCGTGAACGTAAAGTTAATATGGGTCTGAAAGGTCTGCAGATTTGCGGTAATAGCATTATGCCGCTGCTGACCTTTTATGGTAATAGTATTGCAGATCGTTTTCCGACCCATGCCGAACAGTTTAACCAGAATATTAACAGCCAGGGTTATACCAGCGCAACCCTGGCACGTCGTAGCGTTGATATTTTTCAGAATTATGTTGCCATTGCCCTGATGTTTGGTGTTCAGGCAGTTGATCTGCGTACCTACAAAAAAACCGGTCATTATGATGCACGTGCCTCTCTGTCACCGGCAACCGAACGTCTGTATAGCGCAGTTCGTCATGTTGTTGGTCAGAAACCGACCTCAGATCGTCCGTATATTTGGAATGATAATGAACAGGGTCTGGATGAACATATTGCACGTATTAGTGCAGATATTGCAGCCGGTGGTGTTATTGTTCAGGCCGTTCAGGACATTCTGCCGTCTCTGCAT"
}
}
},
{
"fastq": {
"filters": {
"min quality": 20
},
"length": 20,
"reads": "/Users/vikastrivedi/Downloads/Deep Seq data/Trimmed/Gen12.fastq",
"reverse": false
},
"name": "Gen1",
"report filtered reads": false,
"timepoint": 1,
"variants": {
"use aligner": false,
"wild type": {
"coding": true,
"reference offset": 0,
"sequence": "ATGGCACATCACCACCACCATCACAAAACCCTGAGCCAGGCACAGAGCAAAACCAGCAGCCAGCAGTTTAGCTTTACCGGCAATAGCAGCGCAAATGTGATTATTGGTAATCAGAAACTGACCATCAATGATGTTGCACGTGTTGCCCGTAATGGCACCCTGGTTAGCCTGACCAATAATACCGATATTCTGCAGGGTATTCAGGCCAGCTGTGATTATATCAATAATGCAGTTGAAAGCGGTGAACCGATTTATGGTGTTACCAGCGGTTTTGGTGGTATGGCAAATGTTGCAATTAGCCGTGAACAGGCAAGCGAACTGCAGACCAATCTGGTTTGGTTTCTGAAAACCGGTGCAGGTAATAAACTGCCGCTGGCAGATGTTCGTGCAGCAATGCTGCTGCGTGCAAATAGCCACATGCGTGGTGCAAGCGGTATTCGTCTGGAACTGATTAAACGCATGGAAATCTTTCTGAATGCCGGTGTTACCCCGTATGTTTATGAATTTGGTAGCATTGGTGCCAGCGGTGATCTGGTTCCGCTGAGCTATATTACCGGTAGCCTGATTGGCCTGGACCCGAGCTTTAAAGTTGATTTTAATGGCAAAGAAATGGACGCACCGACCGCACTGCGTCAGCTGAATCTGAGTCCGCTGACCCTGCTGCCGAAAGAAGGTCTGGCAATGATGAATGGCACCAGCGTTATGACCGGTATTGCAGCAAATTGTGTTTATGATACCCAGATTCTGACCGCAATTGCAATGGGTGTTCATGCACTGGATATTCAGGCACTGAATGGTACAAATCAGAGCTTTCATCCGTTTATCCATAACAGCAAACCGCATCCGGGTCAGCTGTGGGCAGCAGATCAGATGATTAGCCTGCTGGCCAATAGCCAGCTGGTTCGTGATGAACTGGATGGTAAACATGATTATCGTGATCATGAACTGATCCAGGATCGTTATAGCCTGCGTTGTCTGCCGCAGTATCTGGGTCCGATTGTTGATGGTATTAGCCAGATTGCCAAACAAATCGAAATTGAGATTAACAGCGTTACCGATAACCCGCTGATTGATGTTGATAATCAGGCAAGCTATCATGGTGGTAATTTTCTGGGTCAGTATGTTGGTATGGGTATGGATCATCTGCGCTATTATATCGGTCTGCTGGCAAAACATCTGGATGTTCAGATTGCACTGCTGGCATCACCGGAATTTAGCAATGGTCTGCCTCCGAGTCTGCTGGGTAATCGTGAACGTAAAGTTAATATGGGTCTGAAAGGTCTGCAGATTTGCGGTAATAGCATTATGCCGCTGCTGACCTTTTATGGTAATAGTATTGCAGATCGTTTTCCGACCCATGCCGAACAGTTTAACCAGAATATTAACAGCCAGGGTTATACCAGCGCAACCCTGGCACGTCGTAGCGTTGATATTTTTCAGAATTATGTTGCCATTGCCCTGATGTTTGGTGTTCAGGCAGTTGATCTGCGTACCTACAAAAAAACCGGTCATTATGATGCACGTGCCTCTCTGTCACCGGCAACCGAACGTCTGTATAGCGCAGTTCGTCATGTTGTTGGTCAGAAACCGACCTCAGATCGTCCGTATATTTGGAATGATAATGAACAGGGTCTGGATGAACATATTGCACGTATTAGTGCAGATATTGCAGCCGGTGGTGTTATTGTTCAGGCCGTTCAGGACATTCTGCCGTCTCTGCAT"
}
}
},
{
"fastq": {
"filters": {
"min quality": 20
},
"length": 20,
"reads": "/Users/vikastrivedi/Downloads/Deep Seq data/Trimmed/Gen22.fastq",
"reverse": false
},
"name": "Gen2",
"report filtered reads": false,
"timepoint": 2,
"variants": {
"use aligner": false,
"wild type": {
"coding": true,
"reference offset": 0,
"sequence": "ATGGCACATCACCACCACCATCACAAAACCCTGAGCCAGGCACAGAGCAAAACCAGCAGCCAGCAGTTTAGCTTTACCGGCAATAGCAGCGCAAATGTGATTATTGGTAATCAGAAACTGACCATCAATGATGTTGCACGTGTTGCCCGTAATGGCACCCTGGTTAGCCTGACCAATAATACCGATATTCTGCAGGGTATTCAGGCCAGCTGTGATTATATCAATAATGCAGTTGAAAGCGGTGAACCGATTTATGGTGTTACCAGCGGTTTTGGTGGTATGGCAAATGTTGCAATTAGCCGTGAACAGGCAAGCGAACTGCAGACCAATCTGGTTTGGTTTCTGAAAACCGGTGCAGGTAATAAACTGCCGCTGGCAGATGTTCGTGCAGCAATGCTGCTGCGTGCAAATAGCCACATGCGTGGTGCAAGCGGTATTCGTCTGGAACTGATTAAACGCATGGAAATCTTTCTGAATGCCGGTGTTACCCCGTATGTTTATGAATTTGGTAGCATTGGTGCCAGCGGTGATCTGGTTCCGCTGAGCTATATTACCGGTAGCCTGATTGGCCTGGACCCGAGCTTTAAAGTTGATTTTAATGGCAAAGAAATGGACGCACCGACCGCACTGCGTCAGCTGAATCTGAGTCCGCTGACCCTGCTGCCGAAAGAAGGTCTGGCAATGATGAATGGCACCAGCGTTATGACCGGTATTGCAGCAAATTGTGTTTATGATACCCAGATTCTGACCGCAATTGCAATGGGTGTTCATGCACTGGATATTCAGGCACTGAATGGTACAAATCAGAGCTTTCATCCGTTTATCCATAACAGCAAACCGCATCCGGGTCAGCTGTGGGCAGCAGATCAGATGATTAGCCTGCTGGCCAATAGCCAGCTGGTTCGTGATGAACTGGATGGTAAACATGATTATCGTGATCATGAACTGATCCAGGATCGTTATAGCCTGCGTTGTCTGCCGCAGTATCTGGGTCCGATTGTTGATGGTATTAGCCAGATTGCCAAACAAATCGAAATTGAGATTAACAGCGTTACCGATAACCCGCTGATTGATGTTGATAATCAGGCAAGCTATCATGGTGGTAATTTTCTGGGTCAGTATGTTGGTATGGGTATGGATCATCTGCGCTATTATATCGGTCTGCTGGCAAAACATCTGGATGTTCAGATTGCACTGCTGGCATCACCGGAATTTAGCAATGGTCTGCCTCCGAGTCTGCTGGGTAATCGTGAACGTAAAGTTAATATGGGTCTGAAAGGTCTGCAGATTTGCGGTAATAGCATTATGCCGCTGCTGACCTTTTATGGTAATAGTATTGCAGATCGTTTTCCGACCCATGCCGAACAGTTTAACCAGAATATTAACAGCCAGGGTTATACCAGCGCAACCCTGGCACGTCGTAGCGTTGATATTTTTCAGAATTATGTTGCCATTGCCCTGATGTTTGGTGTTCAGGCAGTTGATCTGCGTACCTACAAAAAAACCGGTCATTATGATGCACGTGCCTCTCTGTCACCGGCAACCGAACGTCTGTATAGCGCAGTTCGTCATGTTGTTGGTCAGAAACCGACCTCAGATCGTCCGTATATTTGGAATGATAATGAACAGGGTCTGGATGAACATATTGCACGTATTAGTGCAGATATTGCAGCCGGTGGTGTTATTGTTCAGGCCGTTCAGGACATTCTGCCGTCTCTGCAT"
}
}
},
{
"fastq": {
"filters": {
"min quality": 20
},
"length": 20,
"reads": "/Users/vikastrivedi/Downloads/Deep Seq data/Trimmed/Gen32.fastq",
"reverse": false
},
"name": "Gen3",
"report filtered reads": false,
"timepoint": 3,
"variants": {
"use aligner": false,
"wild type": {
"coding": true,
"reference offset": 0,
"sequence": "ATGGCACATCACCACCACCATCACAAAACCCTGAGCCAGGCACAGAGCAAAACCAGCAGCCAGCAGTTTAGCTTTACCGGCAATAGCAGCGCAAATGTGATTATTGGTAATCAGAAACTGACCATCAATGATGTTGCACGTGTTGCCCGTAATGGCACCCTGGTTAGCCTGACCAATAATACCGATATTCTGCAGGGTATTCAGGCCAGCTGTGATTATATCAATAATGCAGTTGAAAGCGGTGAACCGATTTATGGTGTTACCAGCGGTTTTGGTGGTATGGCAAATGTTGCAATTAGCCGTGAACAGGCAAGCGAACTGCAGACCAATCTGGTTTGGTTTCTGAAAACCGGTGCAGGTAATAAACTGCCGCTGGCAGATGTTCGTGCAGCAATGCTGCTGCGTGCAAATAGCCACATGCGTGGTGCAAGCGGTATTCGTCTGGAACTGATTAAACGCATGGAAATCTTTCTGAATGCCGGTGTTACCCCGTATGTTTATGAATTTGGTAGCATTGGTGCCAGCGGTGATCTGGTTCCGCTGAGCTATATTACCGGTAGCCTGATTGGCCTGGACCCGAGCTTTAAAGTTGATTTTAATGGCAAAGAAATGGACGCACCGACCGCACTGCGTCAGCTGAATCTGAGTCCGCTGACCCTGCTGCCGAAAGAAGGTCTGGCAATGATGAATGGCACCAGCGTTATGACCGGTATTGCAGCAAATTGTGTTTATGATACCCAGATTCTGACCGCAATTGCAATGGGTGTTCATGCACTGGATATTCAGGCACTGAATGGTACAAATCAGAGCTTTCATCCGTTTATCCATAACAGCAAACCGCATCCGGGTCAGCTGTGGGCAGCAGATCAGATGATTAGCCTGCTGGCCAATAGCCAGCTGGTTCGTGATGAACTGGATGGTAAACATGATTATCGTGATCATGAACTGATCCAGGATCGTTATAGCCTGCGTTGTCTGCCGCAGTATCTGGGTCCGATTGTTGATGGTATTAGCCAGATTGCCAAACAAATCGAAATTGAGATTAACAGCGTTACCGATAACCCGCTGATTGATGTTGATAATCAGGCAAGCTATCATGGTGGTAATTTTCTGGGTCAGTATGTTGGTATGGGTATGGATCATCTGCGCTATTATATCGGTCTGCTGGCAAAACATCTGGATGTTCAGATTGCACTGCTGGCATCACCGGAATTTAGCAATGGTCTGCCTCCGAGTCTGCTGGGTAATCGTGAACGTAAAGTTAATATGGGTCTGAAAGGTCTGCAGATTTGCGGTAATAGCATTATGCCGCTGCTGACCTTTTATGGTAATAGTATTGCAGATCGTTTTCCGACCCATGCCGAACAGTTTAACCAGAATATTAACAGCCAGGGTTATACCAGCGCAACCCTGGCACGTCGTAGCGTTGATATTTTTCAGAATTATGTTGCCATTGCCCTGATGTTTGGTGTTCAGGCAGTTGATCTGCGTACCTACAAAAAAACCGGTCATTATGATGCACGTGCCTCTCTGTCACCGGCAACCGAACGTCTGTATAGCGCAGTTCGTCATGTTGTTGGTCAGAAACCGACCTCAGATCGTCCGTATATTTGGAATGATAATGAACAGGGTCTGGATGAACATATTGCACGTATTAGTGCAGATATTGCAGCCGGTGGTGTTATTGTTCAGGCCGTTCAGGACATTCTGCCGTCTCTGCAT"
}
}
}
],
"name": "Rep1"
}
]
}
],
"name": "PAL",
"output directory": "/Users/vikastrivedi/Downloads/Sad"
}
Help is appreciated
Also the sequencing company that provided us the data says they have already trimmed the barcode. I tried to run the analysis with and without trimming.
This is a snippet of one of the one of the fast data file I am using for analysis
@NGSNJ-086:367:GW200810681st:1:2169:23276:13088_1:N:0:TCCTGAGC+CTATTAAG
GAAATCATAAAAAATTTATTTGCTTTGTGAGCGGATAACAAGTACTAGAGAAAGAGGAGAAATACTAGATGGCACATCACCACCACCATCACAATACCCTGAGCCAGGCACAGAGCAAAACCAGCAGCCAGCAGTTTAGCTTTACCGGCAATAGCAGCGCAAATGTGATTATTGGTAATCAGAAACTGACCATCAATGATGTTGCACGTGTTGCCCGTAATGGCACCCTGGTTAGCCTGACCAATAAT
+
FFFF,FFFFFFFFFFF::FFF:,F,FFFF:FFFFF:::F,F,FFFFFFFF:FFFF::F,F,:FFFFFF:F,FFFF,FFFFFFFFFFFF:FFFFF,,FFF:FFFF:FFFFFFFF,FFFFFF,FFFFFFFFFFF,FFF::FFFFFFFF,FFFFFFFFFFFFF,:,FFFF,FFF:FFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF,FFFFF,FFFFFF:FFFFFFFFFFFFFFFF:
@NGSNJ-086:367:GW200810681st:1:2125:29514:9424_1:N:0:TCCTGAGC+CTATTAAG
AAATCATAAAAAAATGACTTGCTGTGTGAGCGGAGAACAATTACTAGAGACAGAGGCGAAATACTCGATGGCACCTCACCACCACCATCACACAACCCAGAGCCAGGCACAGAGCAAAACCAGCAGCCAGCAGTTTAGCTTTACCGGCAATAGCAGCGCAAATGTGATTATTGGTAATCAGAAACTGACCATCAATGATGTTGCACGTGTTGCCCGTAATGGCACCCTGGTTAGCCTGACCAATAA
+
FF:FF:,F:,FFF,,,F,F,FF:,FF:FF::F:F,F,FFFF,F:,,FFFF:,,,F,,:F,:,,FF,F::FFF,F,F:,FF,FFFFFF,FFF:,:FFF:,,FF:FFFF:F:FFFFFF,FFFFFFF::FFFFFF:FFFFF:FFFF:FFFFFFF:FF,FFFFFFFFFFFF,F:FFFF,,F,FFFFFFFFFFFF,,FF,FFFFF:FFFF:FFFFFFFFFFFFFFFF::FFFF,FFFFFFFF:FFFFFFFF