I have uploaded files from EBI then I run the HIST with the following setting
Source for the reference genome indexed
Select a reference genome hg19
Single-end or paired-end reads? paired
FASTA/Q file #1 5: EBI SRA: SRX015657 File: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR033/SRR033795/SRR033795_1.fastq.gz
FASTA/Q file #2 6: EBI SRA: SRX015657 File: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR033/SRR033795/SRR033795_2.fastq.gz
Specify strand information Unstranded
Paired-end options defaults
sum
Output alignment summary in a more machine-friendly style. False
Print alignment summary to a file. False
adv
Input options defaults
Alignment options defaults
Scoring options defaults
Spliced alignment options defaults
Reporting options defaults
Output options defaults
Other options defaults
Job Resource Parameters no
and I get the following errors, why would it be an error?
Fatal error: Exit code 1 () Error: reads file does not look like a FASTQ file terminate called after throwing an instance of 'int' (ERR): hisat2-align died with signal 6 (ABRT) (core dumped)
Hello Mo!
Questions similar to yours can already be found at:
We have closed your question to allow us to keep similar content in the same thread.
If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.
Cheers!
@Jennifer Hillman Jackson what should I do now ? I don't know how to reassign the fastq datatype to be fastqsanger.gz. I simply get them uploaded from the SRA. can you please guide me what I must do to resolve it because the post did not help much
Hi - let's keep your Q&A in the same thread -- I replied more here: https://biostar.usegalaxy.org/p/29256/#29260
How to make the metadata change is explained in the linked ticket as a workaround, however, that won't apply for your situation now that we know more about it. I also added the workaround directly to the other post for others that might not know how to review the issue ticket for the workaround.
I hadn't seen this particular problem before so the original reply in this Q&A was based on the known issues with the tool. The error message returned by the tool turned out to be the same for both cases but your solution will be different and color-space specific.