error while running translate6frames.sh

[TheWrightonLab]

I am trying to map transcript reads to a database of amino acid sequences. To do this I am converting the database into nt with this tool, and converting the reads to amino acids, and then to nt.

While converting the reads back to nt, I get the following error:

"java.lang.Exception: An input file appears to be misformatted: The character with ASCII code 76 appeared where a base was expected: 'L' Sequence #0 Sequence ID: 'HISEQ13:228:C8GY6ANXX:6:1101:6860:3216 1:N:0:CAGATC fr1' Sequence: '[71, 86, 83, 82, 76, 67, 84, 71, 84, 42, 71, 83, 80, 71, 84, 83, 42, 71, 81, 87, 68, 83, 72, 42, 83, 73, 72, 65, 83, 82, 81, 76, 83, 71, 75, 86, 76, 82, 89, 76, 75, 82, 86, 73] GVSRLCTGTGSPGTSGQWDSH*SIHASRQLSGKVLRYLKRVI' This can be bypassed with the flag 'tossjunk', 'fixjunk', or 'ignorejunk'"

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When I pass any of the recommendations (tossjunk, ignorejunk, fixjunk), I get another error.

"Exception in thread "main" java.lang.AssertionError: This read is not flagged as an amino acid sequence."

Any idea on what I am doing wrong? Command copied below. Thank you!

translate6frames.sh -Xmx30g in=R1_no_Ribo_trimmed_Plant_9_15_B_aa.fastq out=R1_no_Ribo_trimmed_Plant_9_15_B_aa_to_nt.fastq aaout=f aain=t overwrite=t

[feifeiyang123]

Hello, did you solve the problem? I am having the same problem as yours. Could you help me?

[edisagarcia]

Same here. Did you solve the problem?