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sestaton / tephra

A tool for discovering transposable elements and describing patterns of genome evolution
MIT License
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Error running tephra age command #38

Closed davidecarlson closed 5 years ago

davidecarlson commented 5 years ago

Hi Evan, Thanks for this tool. I wanted to report an error running the tephra age command to estimate tir age. I'm running this in a docker container. Here is the error:

Can't use an undefined value as an ARRAY reference at /usr/local/share/perl/5.26.1/Tephra/Role/GFF.pm line 234

Here is the command that I issued:

tephra age -f r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_tirs_classified.gff3 -g r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe.fasta -o tir_age.txt -i /db --type tir --all

Here are the contents of my db directory:

-rw-rw-r--. 1 1004 1004 897M May 29 15:54 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe.fasta -rw-rw-r--. 1 1004 1004 15M May 29 15:54 Repeats_noUnkown.lib -rw-rw-r--. 1 1004 1004 1.8K May 29 15:55 tephra_config.yml -rw-r--r--. 1 root root 347K Jun 1 13:30 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe.fasta.fai -rw-r--r--. 1 root root 665K Jun 2 07:16 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_masked.fasta.log -rw-r--r--. 1 root root 897M Jun 2 07:16 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_masked.fasta -rw-r--r--. 1 root root 347K Jun 2 16:03 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_masked.fasta.fai -rw-r--r--. 1 root root 22K Jun 2 16:24 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_ltrs_trims_gypsy_domain_org.tsv -rw-r--r--. 1 root root 41K Jun 2 16:24 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_ltrs_trims_copia_domain_org.tsv -rw-r--r--. 1 root root 13K Jun 2 16:24 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_ltrs_trims_unclassified_domain_org.tsv -rw-r--r--. 1 root root 3.6M Jun 2 18:42 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_ltrs_trims_classified_family-level_domain_org.tsv -rw-r--r--. 1 root root 85M Jun 2 18:42 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_ltrs_trims_classified.fasta -rw-r--r--. 1 root root 45M Jun 2 18:42 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_ltrs_trims_classified.gff3 -rw-------. 1 root root 13M Jun 4 17:47 tephra_transposons_hmmdb_tFoH.hmm -rw-------. 1 root root 0 Jun 4 17:47 tephra_suffixerator_errors_Iee6.err drwxr-x--x. 1 root root 72 Jun 4 17:58 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_ltrs_trims_classified_ltrages/ -rw-r--r--. 1 root root 41M Jun 7 13:42 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_ltrs.gff3 -rw-r--r--. 1 root root 587M Jun 7 13:42 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_ltrs.fasta -rw-r--r--. 1 root root 4.0M Jun 7 22:11 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_trims.gff3 -rw-------. 1 root root 4.1M Jun 7 22:11 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_trims.fasta -rw-r--r--. 1 root root 45M Jun 7 22:11 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_ltrs_trims.fasta -rw-r--r--. 1 root root 8.2K Jun 7 22:11 elata_r4_full.log -rw-r--r--. 1 root root 0 Jun 7 22:11 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_masked2.fasta drwxr-x--x. 1 root root 331K Jun 7 22:11 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_masked_tephra_masked_tmp/ -rw-r--r--. 1 root root 67K Jun 7 22:37 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_masked2.fasta.log -rw-r--r--. 1 root root 22K Jun 7 23:07 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_ltrs_gypsy_domain_org.tsv -rw-r--r--. 1 root root 41K Jun 7 23:07 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_ltrs_copia_domain_org.tsv -rw-r--r--. 1 root root 13K Jun 7 23:07 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_ltrs_unclassified_domain_org.tsv drwxr-x--x. 1 root root 452 Jun 7 23:07 ltrs_classified/ -rw-r--r--. 1 root root 3.6M Jun 8 00:14 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_ltrs_classified_family-level_domain_org.tsv -rw-r--r--. 1 root root 2.3K Jun 8 00:15 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_classifyltrs.log -rw-r--r--. 1 root root 295M Jun 8 00:15 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_ltrs_classified.fasta -rw-r--r--. 1 root root 42M Jun 8 00:15 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_ltrs_classified.gff3 -rw-r--r--. 1 root root 3.8M Jun 8 01:11 ltr_age.txt -rw-r--r--. 1 root root 20M Jun 8 19:05 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_tirs.gff3 -rw-r--r--. 1 root root 87M Jun 8 19:05 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_tirs.fasta -rw-r--r--. 1 root root 3.0K Jun 8 20:28 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_tirs_tc1-mariner_domain_org.tsv

Notably, I didn't encounter this issue when I ran the tephra age command on ltrs. Any idea what could be happening? Thanks! Dave

sestaton commented 5 years ago

Hi Dave,

Can you confirm you are using the latest version? I did make quite a few changes around the handling of TIR elements in the last update (v0.12.4). Updating the code may fix the issues.

Thanks, Evan

davidecarlson commented 5 years ago

Hi Evan, Thanks for your response. I was using v0.12.3, so I just updated the docker image and confirmed I'm now on v0.12.4. Unfortunately I'm still getting the same error when attempting to run tephra age fro TIRs:

Can't use an undefined value as an ARRAY reference at /usr/local/share/perl/5.26.1/Tephra/Role/GFF.pm line 234.

sestaton commented 5 years ago

In that case, would it be possible to share the input file and genome? You can email it or if the files are too large I'll suggest another approach.

sestaton commented 5 years ago

Any updates? My email, by the way, is evan@evanstaton.com and I'll try to respond as soon as I can.

davidecarlson commented 5 years ago

Hi Evan, Apologies, I haven't had a chance to follow up on this. To be honest, I'm mostly interested in the LTR ages, which I was able to get successfully. Estimating the TIR ages would just be a bonus. I will have more time in a couple weeks, and I'll follow up then. Thanks so much for your help! Dave

On Fri, Jun 14, 2019 at 5:01 PM Evan Staton notifications@github.com wrote:

Any updates? My email, by the way, is evan@evanstaton.com and I'll try to respond as soon as I can.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/sestaton/tephra/issues/38?email_source=notifications&email_token=AGDHTDDXJANJTZGRQEKBOADP2QBJDA5CNFSM4HWK2S22YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODXX6QRQ#issuecomment-502261830, or mute the thread https://github.com/notifications/unsubscribe-auth/AGDHTDG3T63PATL5RD5UR7DP2QBJDANCNFSM4HWK2S2Q .

-- Dave Carlson PhD Candidate Ecology and Evolution Department Stony Brook University

davidecarlson commented 5 years ago

Hi Evan, Sorry for the delay, but I wanted to report back that I updated my docker image to the latest version, reran the analysis, and it completed without issue this time. Either something in the update fixed my issue, or I was doing something wrong previously. In any case, I'll closing the ticket. Thanks, Dave