BLAT CALL FAILED! (New problem for existing issue)

[cistarsa]

Hello and thank you for this highly acclaimed software. I am attempting to use it, but keep receiving this error.

AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references
By Ergude Bao, CS Department, UC-Riverside. All Rights Reserved

BLAT CALL FAILED!

After reading up I've made sure to install a previous BLAT build (v34) and export its location to $PATH The transitional contigs do not seem to have large spaces, as was the issue with another user's data:

CGCCACTGGAATCAATGAAGTCGCCCCGGAGCGCCAATTAATTTTTATTGTTGTTTTTAT
TTTATTTTTATCGTTGTTTTGACAAAATAAAACTTACTTTTAACACAAATATCTTACAAA
GTGTTTTGTACAACTGTCCTGTTTTCATAATAAAATAAATAAATTCATTAAATTATTCCA
TATTTAAAAGTAGGAAACAAAAATATTCAACAATGATTGTGAATTTTTTTTAATCAGTGT
TCACATAGGGTGGTGAATTAGACACTTCTGATAGAGATTTTTCCATTGAGTCACCAGTCA
GCAATTGTTTTTCCAGGGATGGCAACATTATTAACCGAAAATAAAATAAAAACATAACCT
ACTTTTCTTGTAGATGTGCCAAAAATGGATAAGTATGTTTTGGTTGAATATTCAAGTAAT
TTAAATGCCGTGATATGCGAAACGTTCAAGTCTATGCAACGAATTAAGGTCAGTGAGAGG
AGTCAATATTTTTTATATAAAATAAAAAAAGCTTTTGATATAATTTCAGCTAATGAGTTT

But could there be an issue with my paired-end reads' headers?

TTCAGGTGTCCTCTAAGCGGACAATGACCGGTTAGTAGCCCTGTAATTATTCTGAGCCGATCCCTACTATATTGAAGTAGTTCTTCGGTTCTTTTCTCGGACGGTTCCCTAATGAAGGTTCTACT
+
B<BBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/BFFFFFFFFFFFFFFFFFFFFFFBFBFFFFFFF<<FFFFFFFFFFFFFBFFFFFFFBFF
@HWI-D00256:413:C7N5GANXX:1:1101:2404:2383 1:N:0:ATTACTCGCCTATCCT
GGAAAACAAAGTAAACCCAAATTCCAATTGAATGAAATTGTACGGATAAGTAAATACAAAAATATTTTTGAAAAGTCTTACACTGCGAATTTCACCACGGAGCTCTTCAAGATTGTTAAAATTAAT
+
///BBFFFFBFFBBFFFFFFFFFFFFFFFF/FFFFFFFFFFFFFFBFF<FFFFFFFFFFFFFFFFBBFFFBFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFBBFFFFFFFF/B/BFFFFFFFFB
@HWI-D00256:413:C7N5GANXX:1:1101:2445:2420 1:N:0:ATTACTCGCCTATCCT
TAATATGCCAATGCGTTAATCCCATCAGAGGTTGGAATCGAAAGTAGTTGGAAATGTATTATGTTGAATATGACGTTCGATAACTACAAGAAATGAATTACTTAGGTATATATGGAAAATTCAGAA

I hope you can help me resolve this issue and thanks again for your consideration

[baoe]

Hi,

I believe this is due to the file format. AlignGraph requires FASTA format, but looks like your file is in FASTQ format.

Regards,
Bao

[thsierocinski]

Hi there, I am having the same issue on fasta files:
AlignGraph --read1 ../S25_R1_trimmed.fasta --read2 ../S25_R2_trimmed.fasta --contig scaffold.fa --genome reference_sequence_20150113.fsa --distanceLow 35 --distanceHigh 1150 --extendedContig extended_scaffold.fa --remainingContig rmaining_scaffold.fa

but nothing more than this message as a result:
"By Ergude Bao, CS Department, UC-Riverside. All Rights Reserved

BLAT CALL FAILED!"

which is rather uninformative.
my BLAT installation works fine by itself.
is there a log that can be checked somewhere? what could be the issue?

[baoe]

Hi,

Sorry for reply late. Please use BLAT version v34 instead.

Bao

[rafaeltiveron]

@baoe , please, remake AlignGraph, there is no way to recompile blat v34, man! 2022!

[rafaeltiveron]

@cistarsa , do you have binary blat v34? Could you make a shared link to us??

[cistarsa]

alas, I do not have a blat binary as I no longer have access to the workstation I was using then....here's a repo of older blats

[rafaeltiveron]

@cistarsa , yes, thank you, but it is not compiling... I think new versions of kernel, gcc, build-essentials, etc using here.. that is the problem. Much work to do in blat v34 code to be compiled. Then, a new version of AlignGraph would be the best to do.

[rafaeltiveron]

Updating:

I've got it! Three things to compile blast v34:

1. In blastSrc/inc/common.mk:

Remove or comment from "# Stronger warning checks, and warnings-->errors, for libraries and CGIs:" to "endif # Apply the stronger checks to all code on our development machine:"

2. Type command line MACHTYPE=x86_64 ; export $MACHTYPE

3. Type command line mkdir ~/bin/$MACHTYPE ; cd blastSrc && make ; make MACHTYPE=$MACHTYPE

If any permission denied errors appears during cd blastSrc && make, just jump to make MACHTYPE=$MACHTYPE

[Hua-CM]

@rafaeltiveron Thanks!!!!!! That make a big help for me. For others who are looking for blat v34, here is the url https://users.soe.ucsc.edu/~kent/src/