diff options
Diffstat (limited to 'debian/tests/test-data/trnascan-se_sample.output')
| -rw-r--r-- | debian/tests/test-data/trnascan-se_sample.output | 49 |
1 files changed, 49 insertions, 0 deletions
diff --git a/debian/tests/test-data/trnascan-se_sample.output b/debian/tests/test-data/trnascan-se_sample.output new file mode 100644 index 00000000..d4aa35c0 --- /dev/null +++ b/debian/tests/test-data/trnascan-se_sample.output @@ -0,0 +1,49 @@ +tRNAscan-SE v.2.0 (December 2017) - scan sequences for transfer RNAs +Copyright (C) 2017 Patricia Chan and Todd Lowe + University of California Santa Cruz +Freely distributed under the GNU General Public License (GPLv3) + +------------------------------------------------------------ +Sequence file(s) to search: /usr/share/doc/trnascan-se/examples/Example1.fa +Search Mode: Eukaryotic +Results written to: trnascan-se_sample.output +Output format: Tabular +Searching with: Infernal First Pass->Infernal +Isotype-specific model scan: Yes +Covariance model: /usr/share/trnascan-se/models/TRNAinf-euk.cm + /usr/share/trnascan-se/models/TRNAinf-euk-SeC.cm +Infernal first pass cutoff score: 10 + +Temporary directory: /tmp +------------------------------------------------------------ + +Status: Phase I: Searching for tRNAs with HMM-enabled Infernal +Status: Phase I: Searching for tRNAs with HMM-enabled Infernal +Scanned seqs: 0 (at CELF22B7) +/usr/bin/cmsearch -g --mid --notrunc -T 10 /usr/share/trnascan-se/models/TRNAinf-euk.cm /tmp/tscan26061.fa > /tmp/tscan26061_fp_cm_Domain.out +/usr/bin/cmsearch -g --mid --notrunc -T 10 /usr/share/trnascan-se/models/TRNAinf-euk-SeC.cm /tmp/tscan26061.fa > /tmp/tscan26061_fp_cm_SeC.out + +1 seqs scanned, 1 seqs had at least one hit. +5 total tRNAs predicted in first pass scans +Status: Phase II: Infernal verification of candidate tRNAs detected with first-pass scan +Status: Phase II: Infernal verification of candidate tRNAs detected with first-pass scan +Scanning CELF22B7 +/usr/bin/cmsearch -g --nohmm --toponly --notrunc /usr/share/trnascan-se/models/TRNAinf-euk.cm /tmp/tscan26061.trna > /tmp/tscan26061_cm_Domain.out +/usr/bin/cmsearch -g --nohmm --toponly --notrunc /usr/share/trnascan-se/models/TRNAinf-euk-SeC.cm /tmp/tscan26061.trna > /tmp/tscan26061_cm_SeC.out +/usr/bin/cmsearch -g --toponly --notextw /usr/share/trnascan-se/models/TRNAinf-euk.cm /tmp/tscan26061.trna > /tmp/tscan26061_trunc_cm_Domain.out +/usr/bin/cmscan -g --mid --toponly --notrunc --fmt 2 --tblout /tmp/tscan26061_iso_cm.tab -o /tmp/tscan26061_iso_cm.out /usr/share/trnascan-se/models/TRNAinf-euk-iso /tmp/tscan26061.trna +CELF22B7.tRNA1-LeuCAA: Infernal type= Leu Score= 74.2 +CELF22B7.tRNA2-SerAGA: Infernal type= Ser Score= 81.6 +CELF22B7.tRNA3-PheGAA: Infernal type= Phe Score= 82.5 +CELF22B7.tRNA4-PheGAA: Infernal type= Phe Score= 82.5 +CELF22B7.tRNA5-ProCGG: Infernal type= Pro Score= 71.5 + +End Time: Tue Mar 27 23:02:00 2018 +Sequence tRNA Bounds tRNA Anti Intron Bounds Inf Hit +Name tRNA # Begin End Type Codon Begin End Score Origin Note +-------- ------ ----- ------ ---- ----- ----- ---- ------ ------ ------ +CELF22B7 1 12619 12738 Leu CAA 12657 12692 74.2 Inf +CELF22B7 2 19480 19561 Ser AGA 0 0 81.6 Inf +CELF22B7 3 26367 26439 Phe GAA 0 0 82.5 Inf +CELF22B7 4 26992 26920 Phe GAA 0 0 82.5 Inf +CELF22B7 5 23765 23694 Pro CGG 0 0 71.5 Inf |