issue with 'align'

Question

issue with 'align'

yongshes opened this issue 3 years ago · 7 comments

Hi,

I tried to align sequences and got the following error message. I'd appreciate your help.

[vast align]: Input RNA-seq file(s): READ1.fa.gz
Use of uninitialized value $length in concatenation (.) or string at /home/Scripts/vast-tools/bin/RunDBS_1.pl line 489.
Use of uninitialized value $percF in concatenation (.) or string at /home/Scripts/vast-tools/bin/RunDBS_1.pl line 489.
[vast align]: Most common read length detected for fq1: (%)
[vast align]: Sample name: READ1
[vast align]: Using VASTDB -> /home/vast-tools/VASTDB/Hsa
[vast align]: Setting output directory to /home/FASTQ/vast_out
[vast align]: Setting tmp directory..
[vast align]: Set tmp directory to /home/FASTQ/vast_out/tmp!
Use of uninitialized value $length in subtraction (-) at /home/Scripts/vast-tools/bin/RunDBS_1.pl line 522.
Use of uninitialized value $length in concatenation (.) or string at /home/Scripts/vast-tools/bin/RunDBS_1.pl line 523.
[vast align error]: Trim5 (0) cannot be applied for reads of length

Use of uninitialized value $length in numeric ge (>=) at /home/Scripts/vast-tools/bin/RunDBS_1.pl line 531.
[vast align error]: Minimum reads length has to be 50nt

Answer 1 · 2021-09-01T07:47:20.000Z

Hello,

It's strange; it's not detecting the reads at all. Can you please paste the first few reads of your file? (I'm assuming they are >= 50 in FASTA format?)

Thanks
Manu

Answer 2 · 2021-09-01T14:32:28.000Z

Hi Manu, Thanks for you quick reply. Here is a couple of reads from the fastq file that I am using: @K00339:125:HWJH7BBXX:1:1101:1529:1578 1:N:0:ATCACG GGGCGATGCGGCGCGCCTTGGCTTGCCGGGCCTTACGTCTGCGGATCTTACGGGCCGGCTGGTTGAACCACGTGGCCACGCGCCGCTGCCAGTCCTTGTG + AAFFFFJJJJJJJAJJFJJJJJJJJJJJJFJJJJJJJJJJJJJJF7F7<JJJFJJJJAFJJJJJFJJJJJJJ<JF<AFJJJJJJJJJJJJJJJJJJJJJJ @K00339:125:HWJH7BBXX:1:1101:2301:1578 1:N:0:ATCACG CCCCACAGCAGCCCCTGGAGGTTGTGGTAGGCGGAAAATGCAGAAACTTCTCTCAAAAGCGTCCATGTGGCTCTGTTGGGCCAGGCGGGTAGGGGACTCA + AAFFFJJJJJJJJJFJJJJJJAFJJJJJJJJJJJJJJJJJJJJJJJF<JJ<AAJJJJJJJJ<<AFJJ<FJJFF-FAAAFJFJJJFAJJAAJJJJJJJFJJ It doesn’t have the length information in it. Do you know of any tools that can convert my file to the required format? Thanks.

…

On Sep 1, 2021, at 12:47 AM, Manuel Irimia ***@***.***> wrote: Hello, It's strange; it's not detecting the reads at all. Can you please paste the first few reads of your file? (I'm assuming they are >= 50 in FASTA format?) Thanks Manu — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#100 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALIBGF2TBVZP4K7M3EXAEJLT7XLBFANCNFSM5DFVQQHA>. Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

Answer 3 · 2021-09-01T14:34:52.000Z

OK. I think this is because you're using FASTQ files but your file extension is .fa.gz (for FASTA). If you rename them to .fq.gz or .fastq.gz it should work.

M

Answer 4 · 2021-09-01T17:56:10.000Z

Thanks, that solved the problem! But now I get a new error: gzip: stdout: Disk quota exceeded gzip: write error: Disk quota exceeded There is plenty of disk space on my server. Sorry for bothering you with these small things, but I’d really appreciate your advice. Thanks again!

…

On Sep 1, 2021, at 7:35 AM, Manuel Irimia ***@***.***> wrote: OK. I think this is because you're using FASTQ files but your file extension is .fa.gz (for FASTA). If you rename them to .fq.gz or .fastq.gz it should work. M — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#100 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALIBGF3EUZFVF2YTOLX3G4DT7Y2ZPANCNFSM5DFVQQHA>. Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

Answer 5 · 2021-09-01T18:06:01.000Z

By the way, there was one warning message when I ran ./install.R: Using R version 4.0.4 (2021-02-15) Looking for VAST Database [VASTDB] Found 'VASTDB'.. Do you want to download yet uninstalled datasets or update installed datasets? [y/n]: n Trying to load required package: MASS Trying to load required package: getopt Trying to load required package: optparse Trying to load required package: RColorBrewer Trying to load required package: reshape2 Trying to load required package: ggplot2 Trying to load required package: grid Trying to load required package: parallel Trying to load required package: devtools Warning message: In for (i in seq_along(cenv$extra)) { : closing unused connection 3 (stdin) Loading required package: psiplot Setting vast-tools permissions... success! /dfs4/som/yongshes/Scripts/bowtie-1.0.0/bowtie Found bowtie... Everything looks --OK I am not sure if this warning message is normal. Thanks.

…

On Sep 1, 2021, at 10:56 AM, Yongsheng Shi ***@***.***> wrote: Thanks, that solved the problem! But now I get a new error: gzip: stdout: Disk quota exceeded gzip: write error: Disk quota exceeded There is plenty of disk space on my server. Sorry for bothering you with these small things, but I’d really appreciate your advice. Thanks again! > On Sep 1, 2021, at 7:35 AM, Manuel Irimia ***@***.*** ***@***.***>> wrote: > > > OK. I think this is because you're using FASTQ files but your file extension is .fa.gz (for FASTA). If you rename them to .fq.gz or .fastq.gz it should work. > > M > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub <#100 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALIBGF3EUZFVF2YTOLX3G4DT7Y2ZPANCNFSM5DFVQQHA>. > Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. >

Answer 6 · 2021-09-01T18:12:29.000Z

Good.

Re the new errors, I doubt they are related to vast-tools (?). Ie. It seems a gzip issue somehow, so I have no clue why it could be...

Re the installation warning, we are changing that script, so perhaps is not working well. In any case, this is just to install R libraries and R is not used in align.

Answer 7 · 2021-09-01T18:19:25.000Z

OK, thanks again for all your help!

…

On Sep 1, 2021, at 11:12 AM, Manuel Irimia ***@***.***> wrote: Good. Re the new errors, I doubt they are related to vast-tools (?). Ie. It seems a gzip issue somehow, so I have no clue why it could be... Re the installation warning, we are changing that script, so perhaps is not working well. In any case, this is just to install R libraries and R is not used in align. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#100 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALIBGF3A45HB24332FGBDKDT7ZUJRANCNFSM5DFVQQHA>. Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.