BLAT call failed with Aligngraph #17
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Hi, Meeta, This error message tells that neither PBLAT nor BLAT can be called, so I guess there would some problem in your $PATH. Maybe you can double check it. Best, From: meetasunil [[email protected]] Hello Bao, Thanks, — |
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Hi Bao, Jut for your information, the commands.txt is: --read1 Also, the tmp/_checkpoint.txt is empty.. Is that why --resume doesn't work Thanks again, Regards, On 24 December 2015 at 17:45, Bao [email protected] wrote:
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Hi, Meeta, Maybe it's because the contig file's format is something I didn't expect when I was writing the software, e.g. it contains many spaces between two continuous contigs? Let me know about it. Yes. If the _checkpoint.txt is empty, --resume doesn't work. Best, From: meetasunil [[email protected]] Hi Bao, Jut for your information, the commands.txt is: --read1 Also, the tmp/_checkpoint.txt is empty.. Is that why --resume doesn't work Thanks again, Regards, On 24 December 2015 at 17:45, Bao [email protected] wrote:
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ohk, I've attached the head -20 and tail outputs of my contigs.fasta; It's actually a concatenation of contigs from one assembly ranging in Best, Regards, On 26 December 2015 at 20:01, Bao [email protected] wrote:
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I can't find the attached file... Bao From: meetasunil [[email protected]] ohk, I've attached the head -20 and tail outputs of my contigs.fasta; It's actually a concatenation of contigs from one assembly ranging in Best, Regards, On 26 December 2015 at 20:01, Bao [email protected] wrote:
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Oh, I've attached them again. In case you don't receive them still, please head head.txt
head - 2 tail.txt
Best, Regards, On 26 December 2015 at 15:55, Bao [email protected] wrote:
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Hi, Meeta, Maybe you have an empty line somewhere in the file (probably between chaff contigs and long contigs)? Best, From: meetasunil [[email protected]] Oh, I've attached them again. In case you don't receive them still, please head head.txt
head - 2 tail.txt
Best, Regards, On 26 December 2015 at 15:55, Bao [email protected] wrote:
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Ohk thanks, I've re-merged the two fasta files I have and also removed On Tue, 29 Dec 2015 7:24 am Bao [email protected] wrote:
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Hi Bao, Also, It would be good to get a detailed log file for all the steps fie Regards, On 28 December 2015 at 19:14, Meeta Sunil [email protected] wrote:
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You mean the program is running, but all the files are empty? Maybe you could just wait for some time and check again? Best, From: meetasunil [[email protected]] Hi Bao, Also, It would be good to get a detailed log file for all the steps fie Regards, On 28 December 2015 at 19:14, Meeta Sunil [email protected] wrote:
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Yes, both aligngraph and pblat are running. I was thinking that blat writes Best, On Wed, 30 Dec 2015 4:03 pm Bao [email protected] wrote:
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Hi Bao, I see that AlignGraph is still running but I don't know if it's actually Thanks, Regards, On 30 December 2015 at 16:15, Meeta Sunil [email protected] wrote:
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Hi, Meeta, It looks weird that the files are empty. It means no contig has been aligned to the reference genome. But I remember you told me the contigs and the reference genome should be very close.
Happy new year! From: meetasunil [[email protected]] Hi Bao, I see that AlignGraph is still running but I don't know if it's actually Thanks, Regards, On 30 December 2015 at 16:15, Meeta Sunil [email protected] wrote:
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Dear Bao, My syntax is as follows: $HOME/AlignGraph/AlignGraph/AlignGraph --read1 TCGA-A7-A0CE-10A-01D-A017-09.paired1.fasta --read2 TCGA-A7-A0CE-10A-01D-A017-09.paired2.fasta --contig graph_prefix.scafSeq --genome /N/dc2/projects/radovlab/robin_06-17-2016/TCGA-A7-A0CE-01A-11R-A00Z-07/lincRNA/multo/MULTo1.0/src/hg19genome.fasta --distanceLow 550 --distanceHigh 1550 --extendedContig extendedContigs.fa --remainingContig remainingContigs.fa |
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Can you tell me which version of blat you used when you wrote Aligngraph? |
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Hi, It should be a version before v35. Please see FAQ 4 for details. Best, From: rop14009 [[email protected]] Can you tell me which version of blat you used when you wrote Aligngraph? — |
Hello Bao,
My $PATH contains all the three tools - bowtie2, blat and pblat but I still get BLAT CALL FAILED! error. How can I troubleshoot this? I'd like Aligngraph to use pblat preferably but it is trying to look for blat and that also it is not able to find.. Please help.
Thanks,
Meeta
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