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ages file has different LTR names #35

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juancresc opened this issue Feb 27, 2019 · 4 comments
Open

ages file has different LTR names #35

juancresc opened this issue Feb 27, 2019 · 4 comments

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@juancresc
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In ages file I see things like:
RLC_family0_exemplar

And in the fasta files, I got

RLG_singleton_family1616_LTR_12347_chr07_42270149_42278820
RLC_singleton_family1616_TRIM_2991_chr04_13871214_13872432

So it is quite hard to connect those elements, how can I figure out which one is which?
@sestaton
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Owner

Hi,

The exemplar ID will be in the FASTA file also, just grep for the ID.

grep RLC_family0_exemplar tephra_ltrs_classified.fasta

Should tell you the answer. Also, please show a few of the sequence IDs like so:

grep ">" tephra_ltrs_classified.fasta | head -5

because something does not look correct with those IDs. Last, can you confirm the version you are using is the latest?

Thanks.

@juancresc
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Author

Thank you for your response, within my files, I cannot find that ID

:~/tephra/tephra-0.12.2/config$ grep RLC_family0_exemplar ltr_class.fasta 
:~/tephra/tephra-0.12.2/config$ grep RLC_family0_exemplar potato_genome_transposons.fasta 
:~/tephra/tephra-0.12.2/config$ grep RLC_family0_exemplar potato_dm_v404_all_pm_un_tephra_ltrs.fasta

this is a list of output files, which on the following you think is the one you refer as tephra_ltrs_classified.fasta


drwxr-xr-x 9    85 Dec  3 13:01 .
drwxr-xr-x 9    23 Nov  1 10:42 ..
-rw-r--r-- 1   64K Nov 30 11:32 ages
-rw-r--r-- 1     0 Nov  7 12:41 data.txt
-rw-r--r-- 1  1.5K Nov  6 07:01 DTX_singleton_family1278.fasta
-rw-r--r-- 1   19M Nov 30 10:21 ltr_class
drwxr-x--x 5     6 Nov 30 09:49 ltr_class_dir
drwxr-x--x 3     3 Nov 30 11:32 ltr_class_dir_ltrages
-rw-r--r-- 1  1.7M Nov 30 10:11 ltr_class_family-level_domain_org.tsv
-rw-r--r-- 1  144M Nov 30 10:21 ltr_class.fasta
drwxr-x--x 2     2 Nov 30 09:47 ltr_class_ltrages
-rw------- 1   20K Nov  6 07:01 nohup.out.txt
drwxr-xr-x 2     2 Nov 23 09:25 outclass
-rwxr-xr-x 1  856M Nov  1 12:27 potato_dm_v404_all_pm_un.fasta
-rw-r--r-- 1   426 Nov  4 03:23 potato_dm_v404_all_pm_un.fasta.fai
-rw-r--r-- 1  2.7K Nov 30 10:21 potato_dm_v404_all_pm_un_tephra_classifyltrs.log
-rw-r--r-- 1  858M Nov  6 00:05 potato_dm_v404_all_pm_un_tephra_genome_masked.fasta
-rw-r--r-- 1   14K Nov  6 00:04 potato_dm_v404_all_pm_un_tephra_genome_masked.fasta.log
-rw------- 1   11M Nov  5 17:01 potato_dm_v404_all_pm_un_tephra_helitrons.fasta
-rw-r--r-- 1  157K Nov  5 17:01 potato_dm_v404_all_pm_un_tephra_helitrons.gff3
-rw-r--r-- 1  1.0K Nov  6 15:38 .potato_dm_v404_all_pm_un_tephra_helitrons.gff3.swp
-rw-r--r-- 1 1001K Nov  5 10:35 potato_dm_v404_all_pm_un_tephra_illrecomb.fasta
-rw-r--r-- 1  2.6M Nov  5 10:35 potato_dm_v404_all_pm_un_tephra_illrecomb_rep.tsv
-rw-r--r-- 1   63K Nov  5 10:35 potato_dm_v404_all_pm_un_tephra_illrecomb_stats.tsv
-rw-r--r-- 1   55K Nov  5 01:20 potato_dm_v404_all_pm_un_tephra_ltrages.tsv
-rw-r--r-- 1   61K Nov 30 09:49 potato_dm_v404_all_pm_un_tephra_ltrs_copia_domain_org.tsv
-rw-r--r-- 1  143M Nov  4 03:23 potato_dm_v404_all_pm_un_tephra_ltrs.fasta
-rw-r--r-- 1   18M Nov  4 03:23 potato_dm_v404_all_pm_un_tephra_ltrs.gff3
-rw-r--r-- 1   28K Nov 30 09:49 potato_dm_v404_all_pm_un_tephra_ltrs_gypsy_domain_org.tsv
-rw-r--r-- 1  1.7M Nov  5 01:18 potato_dm_v404_all_pm_un_tephra_ltrs_trims_classified_family-level_domain_org.tsv
-rw-r--r-- 1  1.7M Nov 28 14:57 potato_dm_v404_all_pm_un_tephra_ltrs_trims_classified_family-level_domain_org.tsv.save
-rw-r--r-- 1  1.0K Nov 28 14:56 .potato_dm_v404_all_pm_un_tephra_ltrs_trims_classified_family-level_domain_org.tsv.swp
-rw-r--r-- 1  150M Nov  5 01:18 potato_dm_v404_all_pm_un_tephra_ltrs_trims_classified.fasta.txt
-rw-r--r-- 1   24M Nov  5 01:19 potato_dm_v404_all_pm_un_tephra_ltrs_trims_classified.gff3.txt
drwxr-x--x 5     6 Nov  5 09:12 potato_dm_v404_all_pm_un_tephra_ltrs_trims_classified_results
drwxr-x--x 3   341 Nov 30 09:45 potato_dm_v404_all_pm_un_tephra_ltrs_trims_classified_results_ltrages
-rw-r--r-- 1   61K Nov  5 00:54 potato_dm_v404_all_pm_un_tephra_ltrs_trims_copia_domain_org.tsv
-rw-r--r-- 1   23M Nov  5 00:53 potato_dm_v404_all_pm_un_tephra_ltrs_trims.fasta
-rw-r--r-- 1  1.0K Nov  8 10:03 .potato_dm_v404_all_pm_un_tephra_ltrs_trims.fasta.swp
-rw-r--r-- 1   28K Nov  5 00:54 potato_dm_v404_all_pm_un_tephra_ltrs_trims_gypsy_domain_org.tsv
-rw-r--r-- 1   15K Nov  5 00:54 potato_dm_v404_all_pm_un_tephra_ltrs_trims_unclassified_domain_org.tsv
-rw-r--r-- 1   15K Nov 30 09:49 potato_dm_v404_all_pm_un_tephra_ltrs_unclassified_domain_org.tsv
-rw-r--r-- 1  858M Nov  5 02:36 potato_dm_v404_all_pm_un_tephra_masked2.fasta
-rw-r--r-- 1   14K Nov  5 02:35 potato_dm_v404_all_pm_un_tephra_masked2.fasta.log
-rw-r--r-- 1  858M Nov  5 17:11 potato_dm_v404_all_pm_un_tephra_masked3.fasta
-rw-r--r-- 1   427 Nov  5 18:00 potato_dm_v404_all_pm_un_tephra_masked3.fasta.fai
-rw-r--r-- 1   462 Nov  5 17:11 potato_dm_v404_all_pm_un_tephra_masked3.fasta.index.md5
-rw-r--r-- 1   14K Nov  5 17:11 potato_dm_v404_all_pm_un_tephra_masked3.fasta.log
-rw-r--r-- 1  858M Nov  5 18:18 potato_dm_v404_all_pm_un_tephra_masked4.fasta
-rw-r--r-- 1   14K Nov  5 18:18 potato_dm_v404_all_pm_un_tephra_masked4.fasta.log
-rw-r--r-- 1  858M Nov  4 04:44 potato_dm_v404_all_pm_un_tephra_masked.fasta
-rw-r--r-- 1   427 Nov  5 00:53 potato_dm_v404_all_pm_un_tephra_masked.fasta.fai
-rw-r--r-- 1   14K Nov  4 04:44 potato_dm_v404_all_pm_un_tephra_masked.fasta.log
-rw-r--r-- 1   11M Nov  5 06:57 potato_dm_v404_all_pm_un_tephra_sololtrs.gff3
-rw-r--r-- 1  7.4M Nov  5 06:57 potato_dm_v404_all_pm_un_tephra_sololtrs_rep.tsv
-rw-r--r-- 1  1.0K Nov  5 08:48 .potato_dm_v404_all_pm_un_tephra_sololtrs_rep.tsv.swp
-rw-r--r-- 1   35M Nov  5 06:57 potato_dm_v404_all_pm_un_tephra_sololtrs_seqs.fasta
-rw-r--r-- 1   220 Nov  5 18:00 potato_dm_v404_all_pm_un_tephra_tirs_cacta_domain_org.tsv
-rw-r--r-- 1   33K Nov  5 18:01 potato_dm_v404_all_pm_un_tephra_tirs_classified_family-level_domain_org.tsv
-rw-r--r-- 1   30M Nov  5 18:02 potato_dm_v404_all_pm_un_tephra_tirs_classified.fasta
-rw-r--r-- 1  7.9M Nov  5 18:02 potato_dm_v404_all_pm_un_tephra_tirs_classified.gff3
drwxr-x--x 8     9 Nov  5 18:00 potato_dm_v404_all_pm_un_tephra_tirs_classified_results
-rw-r--r-- 1   30M Nov  7 12:44 potato_dm_v404_all_pm_un_tephra_tirs.fasta
-rw-r--r-- 1  7.8M Nov  5 18:00 potato_dm_v404_all_pm_un_tephra_tirs.gff3
-rw-r--r-- 1   228 Nov  5 18:00 potato_dm_v404_all_pm_un_tephra_tirs_hAT_domain_org.tsv
-rw-r--r-- 1  1.0K Nov 30 06:05 .potato_dm_v404_all_pm_un_tephra_tirs_hAT_domain_org.tsv.swp
-rw-r--r-- 1   646 Nov  5 18:00 potato_dm_v404_all_pm_un_tephra_tirs_mutator_domain_org.tsv
-rw-r--r-- 1   895 Nov  5 18:00 potato_dm_v404_all_pm_un_tephra_tirs_tc1-mariner_domain_org.tsv
-rw-r--r-- 1  1.7M Nov  5 18:00 potato_dm_v404_all_pm_un_tephra_tirs_unclassified_domain_org.tsv
-rw-r--r-- 1  303M Nov  6 03:09 potato_dm_v404_all_pm_un_tephra_transposon_fragments.fasta
-rw-r--r-- 1   77M Nov  6 03:09 potato_dm_v404_all_pm_un_tephra_transposon_fragments.gff3
-rw------- 1  5.8M Nov  5 00:53 potato_dm_v404_all_pm_un_tephra_trims.fasta
-rw-r--r-- 1  1.0K Nov  8 10:03 .potato_dm_v404_all_pm_un_tephra_trims.fasta.swp
-rw-r--r-- 1  4.9M Nov  5 00:53 potato_dm_v404_all_pm_un_tephra_trims.gff3
-rw-r--r-- 1  189M Nov  5 22:26 potato_genome_transposons_complete.fasta
-rw-r--r-- 1  492M Nov  6 03:09 potato_genome_transposons.fasta
-rw-r--r-- 1  120M Nov  6 03:09 potato_genome_transposons.gff3
-rw-r--r-- 1  1.0K Nov  6 07:45 .potato_genome_transposons.gff3.swp
-rw-r--r-- 1  1.8K Nov  1 10:57 tephra_config.yml
-rw-r--r-- 1  1.3K Nov  6 03:09 tephra_fragment_searches.log
-rw-r--r-- 1   16K Nov  6 03:09 tephra_potato_genome.log
-rw-r--r-- 1  1.0K Nov  2 08:53 .tephra_potato_genome.log.swp
-rw------- 1     0 Nov  1 15:09 tephra_suffixerator_errors_V7wj.err
-rw------- 1   13M Nov  1 15:09 tephra_transposons_hmmdb_Nd8V.hmm
-rw-r--r-- 1  1.2M Nov  1 10:55 TEs_all_Repbase_St.fasta

@sestaton
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Owner

Hi,

Based on the files you show it looks like one or more of the steps failed, or the processes were not complete with you ran other analysis commands? It is hard to say.

Can you share the log with me? You can send it privately if you want ([email protected]).

Thanks.

@sestaton
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Owner

Was this issue resolved? I believe it was in the end, but please let me know if something was left undone so I can update this issue.

Thanks.

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@sestaton @juancresc