Question: (Closed) Error from HISAT2 when using fasta data retrieved from Get Data: EBI SRA
gravatar for Mo
12 weeks ago by
Mo40 wrote:

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:
FASTA/Q file #2 6: EBI SRA: SRX015657 File:
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)

ADD COMMENTlink written 12 weeks ago by Mo40

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.


PS: The imported data has the wrong datatype assigned (a bug we are working to fix). Please see the other post for how to correct.
ADD REPLYlink written 12 weeks ago by Jennifer Hillman Jackson25k

@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

ADD REPLYlink written 12 weeks ago by Mo40

Hi - let's keep your Q&A in the same thread -- I replied more here:

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.

ADD REPLYlink modified 12 weeks ago • written 12 weeks ago by Jennifer Hillman Jackson25k
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