Blastn warning: subject sequence contains no data, and final retained clean sequence: 0 about ltr_retriever

[oushujun]

Hi,

There is an open issue reporting the same bug. I am trying to reproduce this bug. Please indicate what versions of your dependent programs. Thank you!

Regards,
Shujun

[rimjhimroy]

Hi,
Thank you very much for your reply. Sorry, I should have commented on the open issue, but I thought the warning about the subject sequence was a bit different for me.
The versions of the dependent programs are:
BLAST+: 2.2.31+
HMMER: 3.1b2
CDHIT: 4.6
RepeatMasker: 4.0.5

[oushujun]

Hi,

Thanks for the information. Two things I need you to check:
less genome.fasta.retriever.scn.extend.fa, then search the following sequences:
chr5:12326794..12333995|chr5:12326844..12333945
chr6:21651306..21669448|chr6:21651356..21669398
chr7:25108611..25136833[1]
Please see if these sequences are really empty or look just like others.

Please also check with your sysadmin to see if RepeatMasker was installed using HMMER as the primary search engine. You should use rmblast instead if this is the case.
You can test run: RepeatMasker -q -pa 4 -no_is -norna -nolow -div 40 -lib genome.fasta.ltrTE.mask.lib -cutoff 225 genome.fasta.ltrTE.trunc

Thank you!

Regards,
Shujun

[oushujun]

Hi, Good observations! Yes, LTR_retriever is using an extended format of LTRharvest outputs. The beginning of the line is the coordinate information. LTR_retriever utilizes this information to generate extra details about the candidate and appended them at the end of each line. For lines that remained in the LTRharvest-like formats, those probably could not pass the initial screening and no further analysis is made. I kept them for the purpose of further checking. Best, Shujun

…

On Thu, Jun 8, 2017 at 5:19 AM, rimjhimroy ***@***.***> wrote: I have also noticed that there are many sequences that are still in LTR-harvest like format in the file genome.fasta.retriever.scn.adj like: 10 4550 4541 10 1974 1965 2553 4550 1998 97.90 12 129 12354 12226 129 2120 1992 10359 12354 1996 98.00 408 There are also few lines in the format: 10069 31145 21077 10069 11357 1289 29870 31145 1276 0.947 scaffold_316 scaffold_316 - CATA 10065..10068, 31146..31149 TG,TG,CA,CA 10090 18546 8457 10090 10517 428 18110 18546 437 0.922 scaffold_446 scaffold_446 + AGTG 10086..10089, 18547..18550 TG,TG,CA,CA Whereas other lines are in the format: 49618769 49624184 5416 49618769 49619172 404 49623781 49624184 404 0.9926 chr8 chr8 - GAGAA 49618764..49618768 49624185..49624189 TGCA LTR Gypsy 286029 1 10261 10261 1 763 763 9500 10261 762 0.9382 scaffold_586 scaffold_586 - GGTT -3..0 10262..10265 TGCA LTR Gypsy 2480588 I am not sure the program can handle such different row types in this file. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#4 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFt-NBmuvHI5N31bWoHdFNyCdoKFv7Suks5sB7yegaJpZM4NzOwH> .

[oushujun]

Hi,

I have fixed several bugs and pushed to the latest version (v1.3). Please update your program and rerun the analysis. Please let me know if you have further issues.

Thanks,
Shujun Ou