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dan-landau / IronThrone-GoT

processes GoT amplicon data and generates a table of metrics
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File not found for test data #9

Closed grasshoffm closed 3 years ago

grasshoffm commented 3 years ago

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.

grasshoffm commented 3 years ago

I found the error.

The barcodes file is named 737K-august-2016_barcodes.txt

The script is looking for 737K-august-2016.txt