Open cistarsa opened 7 years ago
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
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?
Hi,
Sorry for reply late. Please use BLAT version v34 instead.
Bao
@baoe , please, remake AlignGraph, there is no way to recompile blat v34, man! 2022!
@cistarsa , do you have binary blat v34? Could you make a shared link to us??
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
@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.
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
@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/
Hello and thank you for this highly acclaimed software. I am attempting to use it, but keep receiving this error.
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:But could there be an issue with my paired-end reads' headers?
I hope you can help me resolve this issue and thanks again for your consideration