../IronThrone-GoT --run linear --config linear_example.config --fastqR1 linear_example.R1.fastq --fastqR2 linear_example.R2.fastq --outdir game --log of --sample throne
I got the following error:
No such file or directory at ../IronThrone-GoT line 1035.
The entire output was:
[Mon Mar 8 14:25:43 2021] [game/throne.SEQ_Qnum] created[Mon Mar 8 14:25:43 2021] Matrix(paste_cols_out) index added: index(0), name(0)[Mon Mar 8 14:25:43 2021] File read: game/throne.BARCODE (size: 424999, lines: 25000)[Mon Mar 8 14:25:43 2021] Matrix(paste_cols_out) index added: index(1), name(1)[Mon Mar 8 14:25:43 2021] File read: game/throne.BARCODE_Qnum (size: 1224976, lines: 25000)[Mon Mar 8 14:25:43 2021] Matrix(paste_cols_out) index added: index(2), name(2)[Mon Mar 8 14:25:43 2021] File read: game/throne.UMI (size: 274999, lines: 25000)[Mon Mar 8 14:25:43 2021] Matrix(paste_cols_out) index added: index(3), name(3)[Mon Mar 8 14:25:43 2021] File read: game/throne.SEQ (size: 2474999, lines: 25000)[Mon Mar 8 14:25:43 2021] Matrix(paste_cols_out) index added: index(4), name(4)[Mon Mar 8 14:25:43 2021] File read: game/throne.SEQ_Qnum (size: 19625000, lines: 25000)[Mon Mar 8 14:25:43 2021] Matrix(paste_cols_out) index added: index(5), name(5)[Mon Mar 8 14:25:43 2021] File read: game/throne.SEQ_Q.P_errors_SUM (size: 269693, lines: 25000)[Mon Mar 8 14:25:43 2021] Matrix file saved: game/throne.SEQUENCE (25000 rows x 6 cols)[Mon Mar 8 14:25:43 2021] File read: game/throne.SEQUENCE (size: 24294669, lines: 25000)[Mon Mar 8 14:25:45 2021] seeking for mismatches from 25000 lines | Primer<= 5 | Shared<= 4[Mon Mar 8 14:25:45 2021] -> 7759 found from 25000 linesNo such file or directory at ../IronThrone-GoT line 1035.
I ran IronThrone like this in the testdata folder
../IronThrone-GoT --run linear --config linear_example.config --fastqR1 linear_example.R1.fastq --fastqR2 linear_example.R2.fastq --outdir game --log of --sample throne
I got the following error:
No such file or directory at ../IronThrone-GoT line 1035.
The entire output was:
[Mon Mar 8 14:25:43 2021] [game/throne.SEQ_Qnum] created
[Mon Mar 8 14:25:43 2021] Matrix(paste_cols_out) index added: index(0), name(0)
[Mon Mar 8 14:25:43 2021] File read: game/throne.BARCODE (size: 424999, lines: 25000)
[Mon Mar 8 14:25:43 2021] Matrix(paste_cols_out) index added: index(1), name(1)
[Mon Mar 8 14:25:43 2021] File read: game/throne.BARCODE_Qnum (size: 1224976, lines: 25000)
[Mon Mar 8 14:25:43 2021] Matrix(paste_cols_out) index added: index(2), name(2)
[Mon Mar 8 14:25:43 2021] File read: game/throne.UMI (size: 274999, lines: 25000)
[Mon Mar 8 14:25:43 2021] Matrix(paste_cols_out) index added: index(3), name(3)
[Mon Mar 8 14:25:43 2021] File read: game/throne.SEQ (size: 2474999, lines: 25000)
[Mon Mar 8 14:25:43 2021] Matrix(paste_cols_out) index added: index(4), name(4)
[Mon Mar 8 14:25:43 2021] File read: game/throne.SEQ_Qnum (size: 19625000, lines: 25000)
[Mon Mar 8 14:25:43 2021] Matrix(paste_cols_out) index added: index(5), name(5)
[Mon Mar 8 14:25:43 2021] File read: game/throne.SEQ_Q.P_errors_SUM (size: 269693, lines: 25000)
[Mon Mar 8 14:25:43 2021] Matrix file saved: game/throne.SEQUENCE (25000 rows x 6 cols)
[Mon Mar 8 14:25:43 2021] File read: game/throne.SEQUENCE (size: 24294669, lines: 25000)
[Mon Mar 8 14:25:45 2021] seeking for mismatches from 25000 lines | Primer<= 5 | Shared<= 4
[Mon Mar 8 14:25:45 2021] -> 7759 found from 25000 lines
No such file or directory at ../IronThrone-GoT line 1035.