mask gff error: list index out of range

Question

mask gff error: list index out of range

iwangtoknow opened this issue 6 years ago · 9 comments

Hi Luigi,
Recently I pulled the image tagged dev_cli,
a problem raised at the mask step,
here is the log:

###RUNNNG REPEATSCOUT AND REPEATMASK TO MASK THE GENOME STARTED AT:	14:07:53 24-12	###
	###RUNNING REPEATSCOUT TO FIND REPETITIVE ELEMENTS###
	###RUNNING REPEATMASKER TO MASK THE GENOME###
Traceback (most recent call last):
  File "/opt/LoReAn/code/lorean.py", line 552, in <module>
    main()
  File "/opt/LoReAn/code/lorean.py", line 144, in main
    masked_ref = mseq.repeatsfind(ref_link, wd_split, args.repeat_lenght, threads_use, args.verbose)
  File "/opt/LoReAn/code/manipulateSeq.py", line 252, in repeatsfind
    gff = [y for x in os.walk(working_dir) for y in glob(os.path.join(x[0], name_gff))][0]
IndexError: list index out of range

content in split folder

ls LoReAn_20181224/run/split/
BJCHM5.nuclear.fasta.freq           RM_144740.MonDec241413472018  tmp4_49nifo  tmphshwq69c  tmptx_v8m9j
BJCHM5.nuclear.fasta.repeats.fasta  tmp05pzu06l                   tmph0t2lha5  tmpk5dl_073

Thanks
WANG

iwangtoknow commented 6 years ago

Thanks

Answer 1 · 2018-12-27T08:25:22.000Z

Hi Wang,
can you please try to run the image with the tag latest? additionally, which are you using Singularity or Docker?

Cheers
Luigi

Answer 2 · 2018-12-29T02:59:04.000Z

Hi Luigi,
I'm using Docker. I'll try latest.
Thanks!

Happy New Year!

WANG

Answer 3 · 2018-12-30T12:17:16.000Z

Hi Luigi,
Do you think it is necessary to fill gene id with 0, such as ID=gene000001 instead ID=gene1?
WANG

Answer 4 · 2019-01-04T10:49:51.000Z

Why do you want to do something like this?

luigi

Answer 5 · 2019-01-04T13:22:24.000Z

Hi Luigi,
For example, if you sort the gene name, could have the result like below:
gene1
gene10
gene2
...
gene9

But if you filled into the same length with 0, then it could be this:
gene01
gene02
...
gene10

That's why I have that thought.

WANG

Answer 6 · 2019-01-08T03:18:13.000Z

you can use {id:0{width}d}.format(id=id,width=width) in python, do this. just an example, detail you should read python doc.

Answer 7 · 2019-06-08T00:57:58.000Z

Hi.
the Verticillium example (/opt/singularity/bin/singularity exec ../../lorean_noIPRS.sif lorean -t 7 --keep_tmp -a -f -d -sr readsChr.subset.fastq -lr longReadsChr8.fastq -pr subset.prot.fasta -sp JR2 -mg chr8.fasta), and in fact any command line that has the -mg option, exits with this error:

RUNNING IN STRAND MODE AND USING ADAPTER PROVIDED

LOREAN IS CHECKING THAT GMAP IS CORRECTLY BUILD

###GMAP MAPPING STARTED AT: 00:50:41 08-06 ###
###BUILD INDEX###
###MAP###

GMAP IS CORRECTLY BUILD

###RUNNNG REPEATSCOUT AND REPEATMASK TO MASK THE GENOME STARTED AT: 00:50:41 08-06 ###
###RUNNING REPEATSCOUT TO FIND REPETITIVE ELEMENTS###
###RUNNING REPEATMASKER TO MASK THE GENOME###
Traceback (most recent call last):
File "/opt/LoReAn/code/lorean.py", line 560, in
main()
File "/opt/LoReAn/code/lorean.py", line 149, in main
masked_ref = mseq.repeatsfind(ref_link, wd_split, args.repeat_lenght, threads_use, args.verbose)
File "/opt/LoReAn/code/manipulateSeq.py", line 258, in repeatsfind
gff = [y for x in os.walk(working_dir) for y in glob(os.path.join(x[0], name_gff))][0]
IndexError: list index out of range

Answer 8 · 2019-06-08T06:04:10.000Z

@rchavez-langebio ,
I think that you did not follow very well the instruction. You need to download the two files and link the folders to the image as written in the instructions. Repeatmasker and Augustus need to be able to write to a file and it is not possible in the image.

please folow point 2 and 3 in the installation steps.

Cheers
Luigi