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ndaniel / fusioncatcher

Finder of Somatic Fusion Genes in RNA-seq data
GNU General Public License v3.0
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FusionCatcher keeps crashing at step 255 #192

Open rituparna-13 opened 2 years ago

rituparna-13 commented 2 years ago

Hi, I am running the FusionCatcher version 1.33 on single end RNA seq data with the following command:

../fusioncatcher/bin/fusioncatcher -d ../fusioncatcher/data/current/ --single-end --input ../from_Julia/ACGI428/FGC1222/ --output ./fusionCatcher_output/

It started unzipping the fastq.gz files and suddenly it starts looking for file init-0_FGC1222_s_3_AAGAGGCAAAGGAGTA.fastq which does not exists and it throws the following error:

==> Current working directory: '/gpfs/research/fangroup/rk18g/JuliaData_exp'
fastqtk \
lengths  \
 /gpfs/research/fangroup/rk18g/JuliaData_exp/fusionCatcher_output/init-0_FGC1222_s_3_AAGAGGCAAAGGAGTA.fastq \
 /gpfs/research/fangroup/rk18g/JuliaData_exp/fusionCatcher_output/single/log_lengths_single_reads_0.txt
--------------------------------------------------------------------------------
+-->EXECUTING...

ERROR: Workflow execution failed at step 255 while executing:
----------------
   fastqtk \
   lengths  \
    /gpfs/research/fangroup/rk18g/JuliaData_exp/fusionCatcher_output/init-0_FGC1222_s_3_AAGAGGCAAAGGAGTA.fastq \
    /gpfs/research/fangroup/rk18g/JuliaData_exp/fusionCatcher_output/single/log_lengths_single_reads_0.txt
----------------
  * Size '/gpfs/research/fangroup/rk18g/JuliaData_exp/fusionCatcher_output/init-0_FGC1222_s_3_AAGAGGCAAAGGAGTA.fastq' = 0 bytes
  * Size '/gpfs/research/fangroup/rk18g/JuliaData_exp/fusionCatcher_output/single/log_lengths_single_reads_0.txt' = 0 bytes

Executing second time the same step/command in order to capture error messages (i.e. STDERR)...

-------------------------------------------
ERROR: Failed to open the file '/gpfs/research/fangroup/rk18g/JuliaData_exp/fusionCatcher_output/init-0_FGC1222_s_3_AAGAGGCAAAGGAGTA.fastq'!

I am not sure why is it trying to look for a file that does not exist or maybe I need to add some parameters to the command line for running it. Can you please help me solve this?

ndaniel commented 2 years ago

Hi @phoenix1391

How many input FASTQ files are there? How long the reads are?

rituparna-13 commented 2 years ago

Hello Daniel, There are 194 fastq files as input and the read length is 100.

rituparna-13 commented 2 years ago

Hi Daniel, I am commenting here again since I did not hear back from you. Please let me know if you need more information.

ndaniel commented 2 years ago

Hi,

sorry but FusionCatcher does not support single end reads of 100bp long.

Cheers, Daniel

rituparna-13 commented 2 years ago

Hi Daniel,

I see. Thank you so much for letting me know.

Thanks, Ritu