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Unrecognized STAR-Fusion input #14

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zaqnq opened this issue Feb 6, 2022 · 0 comments
Open

Unrecognized STAR-Fusion input #14

zaqnq opened this issue Feb 6, 2022 · 0 comments

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@zaqnq
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zaqnq commented Feb 6, 2022

Hi,

I input the tsv file from STAR fusion on Linux server but it is not working. The slurm output shows:

assert line[4] == 'LeftGene', 'Unrecognized STAR-Fusion input'
AssertionError: Unrecognized STAR-Fusion input

Then I tried uploading the tsv file to the webapp, it pops up input errors:

Line 1: does not have enough columns. Expected at least: 4.
Line 2: 5' gene junction must be an integer: HISEQ2000-03:523:C5HJFACXX:6:2104:17156:8138;
Line 3: 5' gene junction must be an integer: HISEQ2000-05:462:C5HJ6ACXX:8:2108:10586:9477;
Line 4: 5' gene junction must be an integer: HISEQ2500-02:564:C5HJLACXX:8:2107:15460:6701;
Line 5: 5' gene junction must be an integer: HISEQ2000-05:462:C5HJ6ACXX:8:1305:12805:25454;
...

Here is my script:
agfusion batch
-f star-fusion.fusion_predictions.abridged.tsv
-a starfusion
-db /mnt/beegfs/hassan/Resources/agfusion.homo_sapiens.87.db
-o AGFusion_out
--middlestar
--noncanonical

Are these errors caused by an incompatibility of files or versions?

Thank you.
-q

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