Closed michieitel closed 5 years ago
I think that I solved it. I need few days to make a new image.
That's awesome! Thanks! Looking forward to try again... Michael
Hi Luigi! Any updates on this? Best Michael
@michieitel i made a new image. Can you test it?
cheers Luigi
Hi Luigi!
Thanks for creating a new image. How can I check it is the latest?
I pulled with:
singularity pull docker://lfaino/lorean:noIPRS
when running 'lorean -h' it says 2017 in the last line...!?
cheers Michael
@michieitel please work with
singularity pull docker://lfaino/lorean:latest
cheers
ah I see. thanks. will try and report
I pulled using the link above... still says 2017 ;-)
But since I got the lorean_latest.sif I assume it should be the correct version...
i guess so. I never noticed
same error again:
Traceback (most recent call last): File "/opt/LoReAn/code/lorean.py", line 596, in
main() File "/opt/LoReAn/code/lorean.py", line 320, in main augustus_file, genemark_file = inputEvm.braker_folder_find(braker_folder) File "/opt/LoReAn/code/prepareEvmInputs.py", line 115, in braker_folder_find gff = [y for x in os.walk(location) for y in glob(os.path.join(x[0], "augustus.hints.gff"))][0] IndexError: list index out of range
PLUS all intermediated removed automatically again...
@michieitel can you send me the singularity command? thanks
singularity exec \
-B /home/ubuntu/cbas/lorean/config/:/opt/LoReAn/third_party/software/augustus/config/ \
-B /home/ubuntu/cbas/lorean/Libraries/:/usr/local/RepeatMasker/Libraries/ \
/home/ubuntu/cbas/lorean/lorean_latest.sif \
lorean -t 20 -sp cbas_masurca2 \
--stranded \
--proteins /home/ubuntu/cbas/lorean/data/PORI_Demo_Amphimedon_queenslandica_v2.1__P__FERNANDEZ-VALVERDE.fasta \
--short_reads /home/ubuntu/cbas/lorean/data/CBAS_Concatenated_RNAseq_Read1_Clean_Datasets.fastq,/home/ubuntu/cbas/lorean/data/CBAS_Concatenated_RNAseq_Read2_Clean_Datasets.fastq \
--long_reads /home/ubuntu/cbas/lorean/data/cbas_cDNA_polyA-guppy-3.1.5-hac.porechop_100bp_to_20kb_combined.fastq \
--adapter /home/ubuntu/cbas/lorean/data/TruSeq3-PE-2.fa \
--mask_genome \
--working_dir lorean_run1 \
--max_intron_length 40000 \
/home/ubuntu/cbas/lorean/data/CBAS_MASURCA-2_final.genome.scf.fasta 2> cbas_lorean_run1.log
we can try adding add --keep_tmp to lorean options. The folder will not disappear. do you have the geneMark key in the home folder of the user that run LoReAn?
ubuntu@lorean:~/cbas/lorean$ cat ~/.gm_key TTGTTCAATTAGCACGGATGTTTTTTTTTTTTTTTTCCGTCGCCATAAAGTTACTAACAGAATTCAAAAGGGAGCGCATA 520951310
If it helps to keep inmtermediates to find the error I can run again with the suggested option ...
ok I will test the image again to see if something is wrong.
should I run it on a dummy set?
can you include a test dataset in the repo that we can both run?
it is there.
oh there is one. I will try using that one!
not sure if I can ask here, but is it too difficult to implement an option that allows to pass user-defined options for the gmap step of long reads.... I am asking since I have figured out the settings that worked best for my set of nanopore reads.
which setting do you mean? can you tell me the option?
on the toy dataset all works fine... is /home/ubuntu/cbas/lorean/config/ folder writing accessible?
for gmap settings I am using:
-k 15 -B 4 --cross-species -A --exons=cdna --format=samse --npaths=0 --sam-extended-cigar
not sure which of these you included...
home/ubuntu/cbas/lorean/config/ is accessible
I got the same error for both example datasets ...
singularity exec \
-B /home/ubuntu/cbas/lorean/config/:/opt/LoReAn/third_party/software/augustus/config/ \
-B /home/ubuntu/cbas/lorean/Libraries/:/usr/local/RepeatMasker/Libraries/ \
/home/ubuntu/cbas/lorean/lorean_latest.sif \
lorean -a -d -f -mg -t 20 --keep_tmp -rp repeats.scaffold3.bed \
-sr /home/ubuntu/cbas/lorean/LoReAn_Example/Crispa/scaffold3.short_1.fastq,/home/ubuntu/cbas/lorean/LoReAn_Example/Crispa/scaffold3.short_2.fastq \
-lr /home/ubuntu/cbas/lorean/LoReAn_Example/Crispa/scaffold3.long.fasta \
-pr /home/ubuntu/cbas/lorean/LoReAn_Example/Crispa/scaffold3.prot.fasta \
-sp crispa \
--working_dir Plicaturopsis \
/home/ubuntu/cbas/lorean/LoReAn_Example/Crispa/scaffold3.fasta
singularity exec \
-B /home/ubuntu/cbas/lorean/config/:/opt/LoReAn/third_party/software/augustus/config/ \
-B /home/ubuntu/cbas/lorean/Libraries/:/usr/local/RepeatMasker/Libraries/ \
/home/ubuntu/cbas/lorean/lorean_latest.sif \
lorean -t 20 --keep_tmp -a -f -d \
-sr /home/ubuntu/cbas/lorean/LoReAn_Example/JR2/readsChr.subset.fastq \
-lr /home/ubuntu/cbas/lorean/LoReAn_Example/JR2/longReadsChr8.fastq \
-pr /home/ubuntu/cbas/lorean/LoReAn_Example/JR2/subset.prot.fasta \
-sp JR2 \
--working_dir Verticillium \
-mg /home/ubuntu/cbas/lorean/LoReAn_Example/JR2/chr8.fasta
In the beaker folder in run folder, you should see a genemark folder.
Can you see any error or log file?
Can you check if you get any errors?
what I did not understand for the examples was you specify adaptors with '-a' but then don't pürovide a file? what is the default?
There is a module that looks for them
so I don't have to specify the adaptor file? it is included in the image?
how can I access the braker folder of the image?
It is better if you specify but without it will work.
Can you find out if genemark worked in the braker folder?
how can I access the braker folder of the image?
It is not in the image. In the folder where you run there is a LoReAn folder. Can you see it?
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how can I access the braker folder of the image?
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error log for example 1:
Use of uninitialized value $epath in concatenation (.) or string at /opt/LoReAn/third_party/software/BRAKER/scripts//braker.pl line 2370. ERROR in file /opt/LoReAn/third_party/software/BRAKER/scripts//braker.pl at line 5616 Failed to execute: perl /opt/LoReAn/third_party/software/gm_et_linux_64/gmes_petap//gmes_petap.pl --verbose --sequence=/home/ubuntu/cbas/lorean/LoReAn_Plicaturopsis/run/braker/genome.fa --ET=/home/ubuntu/cbas/lorean/LoReAn_Plicaturopsis/run/braker/genemark_hintsfile.gff --et_score 10 --max_intergenic 50000 --cores=9 --fungus 1>/home/ubuntu/cbas/lorean/LoReAn_Plicaturopsis/run/braker/GeneMark-ET.stdout 2>/home/ubuntu/cbas/lorean/LoReAn_Plicaturopsis/run/braker/errors/GeneMark-ET.stderr
looks like genemark cannot be fired up? key-related?
Can you check the .error file of genemark?
What is inside?
no .err in GenMark folder. content:
drwxr-xr-x 6 ubuntu ubuntu 4.0K Jul 30 17:55 GeneMark-ET -rw-r--r-- 1 ubuntu ubuntu 1.5K Jul 30 17:55 GeneMark-ET.stdout -rw-r--r-- 1 ubuntu ubuntu 10 Jul 30 17:54 bam_header.map -rw-r--r-- 1 ubuntu ubuntu 714 Jul 30 17:55 braker.error.log -rw-r--r-- 1 ubuntu ubuntu 9.0K Jul 30 17:54 braker.log drwxr-xr-x 2 ubuntu ubuntu 4.0K Jul 30 17:54 errors -rw-r--r-- 1 ubuntu ubuntu 436K Jul 30 17:54 genemark_hintsfile.gff -rw-r--r-- 1 ubuntu ubuntu 2.4M Jul 30 17:54 genome.fa -rw-r--r-- 1 ubuntu ubuntu 10 Jul 30 17:54 genome_header.map -rw-r--r-- 1 ubuntu ubuntu 436K Jul 30 17:54 hintsfile.gff drwxr-xr-x 2 ubuntu ubuntu 4.0K Jul 30 17:54 species
This
/home/ubuntu/cbas/lorean/LoReAn_Plicaturopsis/run/braker/errors/GeneMark-ET.stderr
GeneMark.hmm eukaryotic 3 GeneMark.hmm eukaryotic 3 Your license period has ended. We hope that you found this Your license period has ended. We hope that you found this software useful. If you would like to renew this license, software useful. If you would like to renew this license, please contact GeneProbe, Inc. at custserv@genepro.com please contact GeneProbe, Inc. at custserv@genepro.com
(in cleanup) Can't call method "FETCH" on an undefined value at /usr/local/share/perl/5.22.1/Object/InsideOut.pm line 1953 during global destruction. (in cleanup) Can't call method "FETCH" on an undefined value at /usr/local/share/perl/5.22.1/Object/InsideOut.pm line 1953 during global destruction. (in cleanup) Can't call method "FETCH" on an undefined value at /usr/local/share/perl/5.22.1/Object/InsideOut.pm line 1953 during global destruction.
The key of genemark is expired. You need a new one
I feel stupid now... let me get it and run again. many thanks for now
Hi Luigi,
the pipeline finished. It was that error. Now playing with weighings of the datasets.
Many Thanks for your help! Michael
Hi Luigi!
I ran the pipeline (options: --stranded --proteins --short_reads --adapter --mask_genome --max_intron_length 10000 ) and it created an error: Traceback (most recent call last):
Any suggestions?
Unfortunately, I cannot provide much more details of the run since all intermediate files (outputs of previous tools) were deleted with this crash...
Is it possible to include intermediates in future versions and restart from where the pipeline crashed?!
Thanks for your help Michael