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<h3>
Liubov Chuprikova pushed to branch master
at <a href="https://salsa.debian.org/med-team/ncbi-tools6">Debian Med / ncbi-tools6</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/ncbi-tools6/commit/3bf173820570f09fad0d307020082755a813d111">3bf17382</a></strong>
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<span>by Liubov Chuprikova</span>
<i>at 2018-03-29T13:55:29+00:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Autopkgtest. More tests
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<h4>5 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<a href="#54a392406c9d7232b01a2248fc27eeb32eccbafc">
debian/ncbi-tools-bin.docs
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<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<a href="#d5a28aca73e03038ef6d2b2b036f5a2c218066f3">
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debian/tests/test-data/trnascan-se_sample.output
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/ncbi-tools6/commit/3bf173820570f09fad0d307020082755a813d111#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,7 +2,7 @@ ncbi-tools6 (6.1.20170106-3) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="mosel"> <span class="p">[</span> <span class="n" style="color: #333;">Liubov</span> <span class="n" style="color: #333;">Chuprikova</span> <span class="p">]</span></span>
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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Team</span> <span class="n" style="color: #333;">upload</span><span class="p">.</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Added</span> <span class="n" style="color: #333;">autopkgtest</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;"><span class="idiff left">part</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">of</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">ncbi</span><span class="p">-</span><span class="n" style="color: #333;">tools</span><span class="p">-</span><span class="n" style="color: #333;">bin</span><span class="p">.</span> </span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Added</span> <span class="n" style="color: #333;">autopkgtest</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">ncbi</span><span class="p">-</span><span class="n" style="color: #333;">tools</span><span class="p">-</span><span class="n" style="color: #333;">bin</span><span class="p">.</span> </span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="mosel"> <span class="n" style="color: #333;">Closes</span><span class="p">:</span> <span class="p">#</span><span class="m" style="color: #099;">879619</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="mosel"> <span class="p">[</span> <span class="n" style="color: #333;">Aaron</span> <span class="n" style="color: #333;">M</span><span class="p">.</span> <span class="n" style="color: #333;">Ucko</span> <span class="p">]</span></span>
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<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/ncbi-tools6/commit/3bf173820570f09fad0d307020082755a813d111#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,13 +13,19 @@ Copyright: 1998-1999 Stephane Bortzmeyer <bortzmeyer@pasteur.fr></td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> 2001-2017 Aaron M. Ucko <ucko@debian.org></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">License: public_domain</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">Files: debian/tests/test-data</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Files: debian/tests/test-data/nc0305.aso.gz</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> debian/tests/test-data/dsRNA_viruses.ags.gz</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Copyright: 1996-2018 NCBI </span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">License: public_domain</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">Comment: <span class="idiff left right">GenBank Release 224.0</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Comment: </span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> To dowload the files use:</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> wget ftp://ftp.ncbi.nih.gov/ncbi-asn1/daily-nc/nc0305.aso.gz</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> wget ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ASN_BINARY/Viruses/dsRNA_viruses.ags.gz</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> wget ftp://ftp.ncbi.nih.gov/ncbi-asn1/daily-nc/nc0305.aso.gz</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> wget ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ASN_BINARY/Viruses/dsRNA_viruses.ags.gz</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Files: debian/tests/test-data/trnascan-se_sample.output</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">Comment:</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> The file was generated by tRNAscan-SE 2.0:</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> tRNAscan-SE -d -y -o trnascan-se_sample.output /usr/share/doc/trnascan-se/examples/Example1.fa</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">License: public_domain</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> The NCBI toolkit has been put into the public domain, completely unfettered:</span>
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<li id="54a392406c9d7232b01a2248fc27eeb32eccbafc">
<a href="https://salsa.debian.org/med-team/ncbi-tools6/commit/3bf173820570f09fad0d307020082755a813d111#54a392406c9d7232b01a2248fc27eeb32eccbafc"><strong>debian/ncbi-tools-bin.docs</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,3 +4,5 @@ doc/tbl2asn.txt</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">debian/README.test</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">debian/tests/run-unit-test</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">debian/tests/test-data</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">asn/asnpub.all</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">demo/medline.ent</span></pre>
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<a href="https://salsa.debian.org/med-team/ncbi-tools6/commit/3bf173820570f09fad0d307020082755a813d111#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,11 +7,9 @@ if [ "$AUTOPKGTEST_TMP" = "" ] ; then</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</span>mktemp <span class="nt" style="color: navy;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: navy;">-test</span>.XXXXXX<span class="k" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="shell"></span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell">cp <span class="nt" style="color: navy;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">pkg</span><span class="k" style="font-weight: 600;">}</span>/test-data/<span class="k" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">.</span></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell">gunzip <span class="k" style="font-weight: 600;"><span class="idiff left right">*</span></span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell">gunzip <span class="idiff left right">nc0305.aso.gz</span></span>
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15
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---asn2all test---'</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell">/usr/bin/asn2all <span class="nt" style="color: navy;">-i</span> nc0305.aso <span class="nt" style="color: navy;">-b</span> <span class="nt" style="color: navy;">-f</span> g <span class="nt" style="color: navy;">-o</span> nc0305.nuc <span class="nt" style="color: navy;">-v</span> nc0305.prt</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -58,12 +56,12 @@ echo '---debruijn test---'</td>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> debruijn.output <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---gene2xml test---'</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="shell">/usr/bin/gene2xml <span class="nt" style="color: navy;">-<span class="idiff left">b</span></span><span class="idiff"> </span><span class="nt" style="color: navy;"><span class="idiff">-i</span></span><span class="idiff right"> dsRNA_viruses.ags</span> <span class="nt" style="color: navy;">-o</span> dsRNA_viruses.xgs</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="shell">/usr/bin/gene2xml <span class="nt" style="color: navy;">-<span class="idiff left">c</span></span><span class="idiff"> </span><span class="nt" style="color: navy;"><span class="idiff">-b</span></span><span class="idiff"> </span><span class="nt" style="color: navy;"><span class="idiff">-i</span></span><span class="idiff right"> dsRNA_viruses.ags.gz</span> <span class="nt" style="color: navy;">-o</span> dsRNA_viruses.xgs</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> dsRNA_viruses.xgs <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="shell"><span class="nb" style="color: #0086b3;">grep</span> <span class="s1" style="color: #d14;">'GI:'</span> nc0305.gbk | head | sed <span class="s1" style="color: #d14;">'s/.*GI://'</span> <span class="o" style="font-weight: 600;">></span> GIs.txt</span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <span class="idiff left right">insdseqget and idfetch testing requires internet connection. Comment lines below</span></span></span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># to skip the testing.</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <span class="idiff left right">_insdseqget_ and _idfetch_ testing requires internet connection.</span></span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <span class="idiff left right">Comment the lines below </span>to skip the testing.</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---insdseqget test---'</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="shell">/usr/bin/insdseqget <span class="nt" style="color: navy;">-n</span> <span class="nt" style="color: navy;">-i</span> GIs.txt <span class="o" style="font-weight: 600;">></span> insdset.xml</span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> insdset.xml <span class="o" style="font-weight: 600;">]</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -71,3 +69,16 @@ echo '---idfetch test---'</td>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="shell">/usr/bin/idfetch <span class="nt" style="color: navy;">-G</span> GIs.txt <span class="nt" style="color: navy;">-t</span> 2 <span class="nt" style="color: navy;">-o</span> idfetch.aso</span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> idfetch.aso <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---trna2sap test---'</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="shell">/usr/bin/trna2sap < trnascan-se_sample.output <span class="o" style="font-weight: 600;">></span> trna2sap.output</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> trna2sap.output <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---trna2tbl test---'</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="shell">/usr/bin/trna2tbl < trnascan-se_sample.output <span class="o" style="font-weight: 600;">></span> trna2tbl.output</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> trna2tbl.output <span class="o" style="font-weight: 600;">]</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="shell">cp /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">pkg</span><span class="k" style="font-weight: 600;">}</span>/<span class="o" style="font-weight: 600;">{</span>asnpub.all.gz,medline.ent<span class="o" style="font-weight: 600;">}</span> <span class="nb" style="color: #0086b3;">.</span> </span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="shell">gunzip asnpub.all.gz</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---asntool test---'</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="shell">/usr/bin/asntool <span class="nt" style="color: navy;">-m</span> asnpub.all <span class="nt" style="color: navy;">-v</span> medline.ent <span class="nt" style="color: navy;">-p</span> asntool.output</span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> asntool.output <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="shell"></span></pre>
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<li id="d5a28aca73e03038ef6d2b2b036f5a2c218066f3">
<a href="https://salsa.debian.org/med-team/ncbi-tools6/commit/3bf173820570f09fad0d307020082755a813d111#d5a28aca73e03038ef6d2b2b036f5a2c218066f3"><strong>debian/tests/test-data/trnascan-se_sample.output</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">tRNAscan-SE v.2.0 (December 2017) - scan sequences for transfer RNAs</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Copyright (C) 2017 Patricia Chan and Todd Lowe</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> University of California Santa Cruz</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Freely distributed under the GNU General Public License (GPLv3)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">------------------------------------------------------------</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Sequence file(s) to search: /usr/share/doc/trnascan-se/examples/Example1.fa</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Search Mode: Eukaryotic</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Results written to: testrun.out</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Output format: Tabular</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Searching with: Infernal First Pass->Infernal</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Isotype-specific model scan: Yes</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Covariance model: /usr/share/trnascan-se/models/TRNAinf-euk.cm</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> /usr/share/trnascan-se/models/TRNAinf-euk-SeC.cm</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Infernal first pass cutoff score: 10</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Temporary directory: /tmp</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">------------------------------------------------------------</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Status: Phase I: Searching for tRNAs with HMM-enabled Infernal</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">Status: Phase I: Searching for tRNAs with HMM-enabled Infernal</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Scanned seqs: 0 (at CELF22B7)</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">/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</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">/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</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">1 seqs scanned, 1 seqs had at least one hit.</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">5 total tRNAs predicted in first pass scans</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">Status: Phase II: Infernal verification of candidate tRNAs detected with first-pass scan</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">Status: Phase II: Infernal verification of candidate tRNAs detected with first-pass scan</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">Scanning CELF22B7</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">/usr/bin/cmsearch -g --nohmm --toponly --notrunc /usr/share/trnascan-se/models/TRNAinf-euk.cm /tmp/tscan26061.trna > /tmp/tscan26061_cm_Domain.out</span>
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<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">/usr/bin/cmsearch -g --nohmm --toponly --notrunc /usr/share/trnascan-se/models/TRNAinf-euk-SeC.cm /tmp/tscan26061.trna > /tmp/tscan26061_cm_SeC.out</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">/usr/bin/cmsearch -g --toponly --notextw /usr/share/trnascan-se/models/TRNAinf-euk.cm /tmp/tscan26061.trna > /tmp/tscan26061_trunc_cm_Domain.out</span>
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<td class="diff-line-num new new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">/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</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">CELF22B7.tRNA1-LeuCAA: Infernal type= Leu Score= 74.2</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">CELF22B7.tRNA2-SerAGA: Infernal type= Ser Score= 81.6</span>
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<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">CELF22B7.tRNA3-PheGAA: Infernal type= Phe Score= 82.5</span>
</pre>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">CELF22B7.tRNA4-PheGAA: Infernal type= Phe Score= 82.5</span>
</pre>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">CELF22B7.tRNA5-ProCGG: Infernal type= Pro Score= 71.5</span>
</pre>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">End Time: Tue Mar 27 23:02:00 2018</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">Sequence tRNA Bounds tRNA Anti Intron Bounds Inf Hit </span>
</pre>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">Name tRNA # Begin End Type Codon Begin End Score Origin Note</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">-------- ------ ----- ------ ---- ----- ----- ---- ------ ------ ------</span>
</pre>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">CELF22B7 1 12619 12738 Leu CAA 12657 12692 74.2 Inf </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">CELF22B7 2 19480 19561 Ser AGA 0 0 81.6 Inf </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">CELF22B7 3 26367 26439 Phe GAA 0 0 82.5 Inf </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">CELF22B7 4 26992 26920 Phe GAA 0 0 82.5 Inf </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">CELF22B7 5 23765 23694 Pro CGG 0 0 71.5 Inf </span></pre>
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