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Question: Fastq to fasta failure -- truncated uploaded datasets
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gravatar for fiona.walsh
9 weeks ago by
fiona.walsh • 0
fiona.walsh • 0 wrote:
fatal error: Exit code 1 ()
fastq_to_fasta: Error: invalid quality score data on line 4 (quality_tok = "&+(35165<<A7//?3.>"

Any idea how to fix this error? It's not just this file but another one too.
error upload ftp galaxy fastq • 99 views
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modified 9 weeks ago by Jennifer Hillman Jackson ♦ 25k • written 9 weeks ago by fiona.walsh • 0
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gravatar for Jennifer Hillman Jackson
9 weeks ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

It looks like several of your uploaded fastq datasets are truncated, triggering this error and a few others. I used the tool Tail to examine the last few lines of these to discover that the data did not end with a complete, intact, fastq read record. You can do this too, next time an error comes up with comments about poor fastq formatting (usually reported by the first tool using the newly uploaded dataset as an input).

To resolve the problem:

  • First, double check that the original files are intact (before they were uploaded to Galaxy). Correct problems as needed.
  • Then try using FTP to Upload the full intact datasets. You'll get direct information about the state of the upload including warnings about an interrupted connection/partial upload. If a connection is interrupted for some reason, the transfer can be resumed.

Resources: https://galaxyproject.org/support/

Thanks! Jen, Galaxy team
ADD COMMENT • link written 9 weeks ago by Jennifer Hillman Jackson ♦ 25k
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