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Question: Error message after running FreeBayes
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gravatar for federico.bernuzzi
19 months ago by
federico.bernuzzi • 20
Quadram Institute of BioSciences
federico.bernuzzi • 20 wrote:

Hi,

I am quite new with Galaxy only been working with it for a month so please bare with me. I am trying to identify SNP variants from RNA-Seq data of prostate cancer tissue. All of the previous steps in the pipeline have successfully worked (FastQC, TrimGalore, FASTQC and HISAT2). When i launch FreeBayes on the results obtained from HISAT2 I get the following error. I was wondering whether someone has come across this error message before and could point me towards the right direction on what is causing the issue.

Fatal error: Exit code 3 () Exception: Unable to read reference sequence base past end of current cached sequence. KI270304.1:1047 1046-2166 alignment: GTTTCTGAGAATCGTTCTGTCTAGTTTCTATAGGAAGATATTTCCTATTCTACCATTGACCTCAAAGCGGCTGAAATCTCCACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGCAAATTCGACAAAAA currentSequence: TCTGTGAGTTGAACGAACACATCACAACGCAGTTTGAGGGAATGATTCTGTCTAGTTTTGAAACGAAGATATTTCCTTTTCTGCCATTGACATAAACGCTTGAAATCTACAGTTGCCAATTGCACAAATAGAGTGTTTCAAATCTGCTCTGTCTAAGGGAACGTTCAACTCTGTGAGTTGAATGCACACAACACAAGGAAGTTACTGGGAATTCTTCTGTCTAGCCTGACAGGAAAAAAACCCTTTTCCAACGAAGGCCTCTAAGTGGTCCAATTATCCACGTGCAGAGTTTACAAACAGAGTGTTTCAAACTGCTGAATGAAAAGAAAAGTTAAACTCTGAGAGTTGAACGCACACATCACAGAGCAGTTTCTGAGAATGATTCTGTCTAGTTTTTATACGACGATATTTACTTTTCTGCTTTTGGCCCCAAAGCGCTTGAAATCTCCACTTGCAAATCCAAAAAAACAGTGTTTCAAATCTGCTCTCTCTAAATGAAAGTTCAACTCTGTCAGTTGAATACACACAACACAAGGAAGTTACTGAGAATTCTTCTGTCTAGCCTTAAATGAAAAAAACCCGTTTCCAACGAAGGCCTCAAAGAAGTCCAAATATCCACGTGCAGACATTACAAACAGAGTGTTTCCTAACTGCTCTATGAAAAAAAGGTTAAACTCTGTGAGTTGAATGCCCACAGCACAAAGGAGTTTCTGAGAATCATTCTGTCTAGTTTTTATACGAAGATATTTCCTTTTCTACCATTGATCTCAAAGCGGCTGAAATCTCCACTTGCAAATTCCACAAAAAGAGTGTTTCAAGTCTGCTCTGTGTAAAGGATCGTTCAACTCTGTGAGTTGAACACACACAAAACAAGGAAGTTACTGAGAATTCTTCTGTCTAGCAGAATATGAAGAAATCCCGTTTCCAACGAAGGCCTCAAAGAGGTCTGAATATCCACTTGCAGACTTTTCAGAAAGAGTGTTTCCTAACTGCTCTATGAAAAGAAAGGTTAAACTCTGTGAGTTGAACGCACACATCACAAAGGAGTTTCTGAGAATCATTCTGTCTAGTTTCTATAGGAAGATATTTCCTATTCAACCATTGACCTCAAAGCGGCTGAAATCTCCACCTGCAAATTCCATAAAAAGAGTGTTTCAAGTCTGCTCTGTGTAAAGGATCGTACAACTCTGTGAGTTGAATACACACAACAAAAAGAAGTTACTGAGAATTCTTCTGTCTAGCAGAATATGAAGAAATCCCGCTTCCAACGAATGCCTCAAAGAGGTCTGAATATCCACTTGCAGACTTTTCAGAAAGAGTGTTTCCTAACTGCTCTATGAAAAGAAAGGTTAAACTCTGTGAGTTGAACGCACACATCACAAAGGAGTTTCTGAGAATCATTCTGTCTAGTTTTTATACGAAGATATTTCCTTTTCTATCATTGACCTCAAAGCGGCTGAAATCTCCACTTGCAAATTCCACAAATAGAGTGTTTCAAGTCTGCTCTGTGTAAAGGATCGTTCAACTCTGTGAGTTGAATACACACAACACAAGGAAGTTACTGAGAATTCTTCTGTGTAGCAGAAGATGAAGAAATCCCGTTTCCAACGAAGGCCACAAGATGTCAGAATATCCACTTACAGACTTTACAAACAGAGTGTTTCCTAACTGCTCTATGAACAGAAAGGTTAAACTCTGTGAGCTGAACGAACACATCACAACGCAGTTTGTGGGAATGATTCTGTCTAGTTTTGAAACGAAGATATTTCCTTTTCTGCCATTGACCTTAAAGCGCTTGAAATCTACACTTGCAAATTGCACAAATACAGTGTTTCAAATCTGCTCTGTCTAAGGGAACGTTCAACTCTGTGAGTTGAATGCACACAACACAAGGAAGTTACTGGGAATTCTTCTGTTTAGCCTTACATGAAAAAAACCCGTTTCCAACGAAGGCCTCTAAGTGGTCAAAATATCCACGTGCAGACTTTACAAACAGAGTGTTTCCAAACCGCTGAATGAAAAGAAAAGTAAAACTCTGAGAGGTAATCCCACACATCACGCAGCAGTTTCTGAGAATGATTCTGTCCAGTTTTTATACCAAGATATTTCCTTTTCTGCCTTTGTCCCCAAAGCGCTTGAAATCTCCACTTGCAAATTCCACAAAA currentSequence matching: Exception: Unable to read reference sequence base past end of current cached sequence. KI270304.1:1053 1052-2171 alignment: GAGAATCATTCTGTCTAGTTTCTATAGGAAGATATTTCCTATTCTACCATTGACCTCAAAGCGGCTGAAATCTCCACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGCAAATTCCACAAAAAGAGTG currentSequence: TCTGTGAGTTGAACGAACACATCACAACGCAGTTTGAGGGAATGATTCTGTCTAGTTTTGAAACGAAGATATTTCCTTTTCTGCCATTGACATAAACGCTTGAAATCTACAGTTGCCAATTGCACAAATAGAGTGTTTCAAATCTGCTCTGTCTAAGGGAACGTTCAACTCTGTGAGTTGAATGCACACAACACAAGGAAGTTACTGGGAATTCTTCTGTCTAGCCTGACAGGAAAAAAACCCTTTTCCAACGAAGGCCTCTAAGTGGTCCAATTATCCACGTGCAGAGTTTACAAACAGAGTGTTTCAAACTGCTGAATGAAAAGAAAAGTTAAACTCTGAGAGTTGAACGCACACATCACAGAGCAGTTTCTGAGAATGATTCTGTCTAGTTTTTATACGACGATATTTACTTTTCTGCTTTTGGCCCCAAAGCGCTTGAAATCTCCACTTGCAAATCCAAAAAAACAGTGTTTCAAATCTGCTCTCTCTAAATGAAAGTTCAACTCTGTCAGTTGAATACACACAACACAAGGAAGTTACTGAGAATTCTTCTGTCTAGCCTTAAATGAAAAAAACCCGTTTCCAACGAAGGCCTCAAAGAAGTCCAAATATCCACGTGCAGACATTACAAACAGAGTGTTTCCTAACTGCTCTATGAAAAAAAGGTTAAACTCTGTGAGTTGAATGCCCACAGCACAAAGGAGTTTCTGAGAATCATTCTGTCTAGTTTTTATACGAAGATATTTCCTTTTCTACCATTGATCTCAAAGCGGCTGAAATCTCCACTTGCAAATTCCACAAAAAGAGTGTTTCAAGTCTGCTCTGTGTAAAGGATCGTTCAACTCTGTGAGTTGAACACACACAAAACAAGGAAGTTACTGAGAATTCTTCTGTCTAGCAGAATATGAAGAAATCCCGTTTCCAACGAAGGCCTCAAAGAGGTCTGAATATCCACTTGCAGACTTTTCAGAAAGAGTGTTTCCTAACTGCTCTATGAAAAGAAAGGTTAAACTCTGTGAGTTGAACGCACACATCACAAAGGAGTTTCTGAGAATCATTCTGTCTAGTTTCTATAGGAAGATATTTCCTATTCAACCATTGACCTCAAAGCGGCTGAAATCTCCACCTGCAAATTCCATAAAAAGAGTGTTTCAAGTCTGCTCTGTGTAAAGGATCGTACAACTCTGTGAGTTGAATACACACAACAAAAAGAAGTTACTGAGAATTCTTCTGTCTAGCAGAATATGAAGAAATCCCGCTTCCAACGAATGCCTCAAAGAGGTCTGAATATCCACTTGCAGACTTTTCAGAAAGAGTGTTTCCTAACTGCTCTATGAAAAGAAAGGTTAAACTCTGTGAGTTGAACGCACACATCACAAAGGAGTTTCTGAGAATCATTCTGTCTAGTTTTTATACGAAGATATTTCCTTTTCTATCATTGACCTCAAAGCGGCTGAAATCTCCACTTGCAAATTCCACAAATAGAGTGTTTCAAGTCTGCTCTGTGTAAAGGATCGTTCAACTCTGTGAGTTGAATACACACAACACAAGGAAGTTACTGAGAATTCTTCTGTGTAGCAGAAGATGAAGAAATCCCGTTTCCAACGAAGGCCACAAGATGTCAGAATATCCACTTACAGACTTTACAAACAGAGTGTTTCCTAACTGCTCTATGAACAGAAAGGTTAAACTCTGTGAGCTGAACGAACACATCACAACGCAGTTTGTGGGAATGATTCTGTCTAGTTTTGAAACGAAGATATTTCCTTTTCTGCCATTGACCTTAAAGCGCTTGAAATCTACACTTGCAAATTGCACAAATACAGTGTTTCAAATCTGCTCTGTCTAAGGGAACGTTCAACTCTGTGAGTTGAATGCACACAACACAAGGAAGTTACTGGGAATTCTTCTGTTTAGCCTTACATGAAAAAAACCCGTTTCCAACGAAGGCCTCTAAGTGGTCAAAATATCCACGTGCAGACTTTACAAACAGAGTGTTTCCAAACCGCTGAATGAAAAGAAAAGTAAAACTCTGAGAGGTAATCCCACACATCACGCAGCAGTTTCTGAGAATGATTCTGTCCAGTTTTTATACCAAGATATTTCCTTTTCTGCCTTTGTCCCCAAAGCGCTTGAAATCTCCACTTGCAAATTCCACAAAA currentSequence matching:

Many thanks for the help and support.

Federico B
snp software error galaxy rna-seq • 770 views
ADD COMMENT • link •
modified 19 months ago by Anton Nekrutenko ♦ 1.7k • written 19 months ago by federico.bernuzzi • 20
0
gravatar for Jennifer Hillman Jackson
19 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Formatting might be the source of the problem. Places to look for problems: the original fastq data (not really in fastqsanger format), the custom genome fasta format needs to be modified (if one is being used), other inputs need to be sorted (BAM) or are missing data (header incomplete on SAM), etc.

The Troubleshooting section of the Galaxy support wiki has how-to help for resolving errors.

A google search with the error message brings up many similar reported issues at the Freebayes Github site and it looks like input format is almost always the root issues when this message results (line-command usage, but remember that Galaxy is just that same tool wrapped). You could also review those. If after checking you cannot determine the root problem, a bug report can be sent in (how-to is also described on the support page above, at the link "Issues").

That said, there was a bug in an earlier version of the software. The authors explains it here. You are not the only one to run into this issue. https://github.com/ekg/freebayes/issues/6

Thanks, Jen, Galaxy team
ADD COMMENT • link modified 19 months ago • written 19 months ago by Jennifer Hillman Jackson ♦ 25k
0
gravatar for federico.bernuzzi
19 months ago by
federico.bernuzzi • 20
Quadram Institute of BioSciences
federico.bernuzzi • 20 wrote:

Hi Jen,

Many thanks for the advice and help Kind regards

FB
ADD COMMENT • link written 19 months ago by federico.bernuzzi • 20
0
gravatar for Anton Nekrutenko
19 months ago by
Anton Nekrutenko ♦ 1.7k
Penn State
Anton Nekrutenko ♦ 1.7k wrote:

Federico B:

HISAT is a spliced mapper and it is possible that FreeBayes does not like BAM files generated by HISAT. Can you try Naive Varinat Caller instead and see if you will be getting valid VCF.

ADD COMMENT • link written 19 months ago by Anton Nekrutenko ♦ 1.7k

Hi Anton,

You raised a very good point. I thought that maybe HISAT2 might cause the problem and was thinking of running TopHat and then putting the results (the accepted hits file) into FreeBayes to see whether that would work. I have not come across Naive Variant Caller so I am not exactly sure how it works.

Many thanks for the help and advice. Much appreciated

Best wishes

FB

ADD REPLY • link written 19 months ago by federico.bernuzzi • 20

Naive Variant Caller is ... naive. It just tabulates the number of differences. But since calling variants in RNAseq does not necessary follow diplod assumption it may work for you (FreeBayes also has pooled continuous function for such cases). It is the NGS: Variant Analysis section on the tool panel,

ADD REPLY • link written 19 months ago by Anton Nekrutenko ♦ 1.7k
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