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Error loading data into sqlite database : died with ret 65280 at Trinotate line 126 #84

Open limengchen628 opened 2 years ago

limengchen628 commented 2 years ago

Hi Brian, When I import data into sqlite, it gives error: Error, cmd: /home/data/t120347/software/Trinotate/util/trinotateSeqLoader/TrinotateSeqLoader.pl --sqlite Trinotate.sqlite --gene_trans_map ../4.trinity/Trinity.fasta.gene_trans_map --transcript_fasta ../4.trinity/Trinity.fasta --tansdecoder_pep Trinity.fasta.transdecoder.pep --bulk_load died with ret 65280 at /home/data/t120347/software/Trinotate/Trinotate line 126.

Here is my gene_trans_map, and I think is correct. TRINITY_DN2391_c0_g1 TRINITY_DN2391_c0_g1_i1 TRINITY_DN2337_c0_g1 TRINITY_DN2337_c0_g1_i1 TRINITY_DN2321_c0_g1 TRINITY_DN2321_c0_g1_i1 TRINITY_DN2397_c0_g1 TRINITY_DN2397_c0_g1_i1 TRINITY_DN2363_c0_g1 TRINITY_DN2363_c0_g1_i1 TRINITY_DN2308_c0_g1 TRINITY_DN2308_c0_g1_i1 TRINITY_DN2385_c0_g1 TRINITY_DN2385_c0_g1_i1 TRINITY_DN2360_c0_g1 TRINITY_DN2360_c0_g1_i1 TRINITY_DN2333_c0_g1 TRINITY_DN2333_c0_g1_i1 TRINITY_DN2399_c0_g1 TRINITY_DN2399_c0_g1_i1 TRINITY_DN2369_c0_g1 TRINITY_DN2369_c0_g1_i1 TRINITY_DN2334_c0_g1 TRINITY_DN2334_c0_g1_i1 TRINITY_DN2342_c0_g1 TRINITY_DN2342_c0_g1_i1 TRINITY_DN2325_c0_g1 TRINITY_DN2325_c0_g1_i1 TRINITY_DN2351_c0_g1 TRINITY_DN2351_c0_g1_i1 TRINITY_DN2357_c0_g1 TRINITY_DN2357_c0_g1_i1 TRINITY_DN2389_c0_g1 TRINITY_DN2389_c0_g1_i1 TRINITY_DN2384_c0_g1 TRINITY_DN2384_c0_g1_i1

And I trying to use trinotate sampledata, it's run OK.

` CMD: /home/data/t120347/software/Trinotate/util/trinotateSeqLoader/TrinotateSeqLoader.pl --sqlite myTrinotate.sqlite --gene_trans_map data/Trinity.fasta.gene_to_trans_map --transcript_fasta data/Trinity.fasta --transdecoder_pep data/Trinity.fasta.transdecoder.pep --bulk_load -parsing gene/trans map file.... done. -loading Transcripts. [600]
done. -loading ORFs.

done.

CMD: echo "pragma journal_mode=memory; pragma synchronous=0; pragma cache_size=4000000; .mode tabs .import tmp.Transcript.bulk_load Transcript" | sqlite3 myTrinotate.sqlite memory CMD: echo "pragma journal_mode=memory; pragma synchronous=0; pragma cache_size=4000000; .mode tabs .import tmp.ORF.bulk_load ORF" | sqlite3 myTrinotate.sqlite memory

Loading complete `

So, I don't know how to solve this problem. Thank you inadvance

Moson

brianjohnhaas commented 2 years ago

Hi,

Are there other error messages shown in the log? If not, you could try running this directly:

/home/data/t120347/software/Trinotate/util/trinotateSeqLoader/TrinotateSeqLoader.pl --sqlite Trinotate.sqlite --gene_trans_map ../4.trinity/Trinity.fasta.gene_trans_map --transcript_fasta ../4.trinity/Trinity.fasta --tansdecoder_pep Trinity.fasta.transdecoder.pep --bulk_load d

and see if it provides any more context in errors.

best,

~brian

On Thu, Jul 21, 2022 at 12:27 PM Moson @.***> wrote:

Hi Brian, When I import data into sqlite, it gives error: Error, cmd: /home/data/t120347/software/Trinotate/util/trinotateSeqLoader/TrinotateSeqLoader.pl --sqlite Trinotate.sqlite --gene_trans_map ../4.trinity/Trinity.fasta.gene_trans_map --transcript_fasta ../4.trinity/Trinity.fasta --tansdecoder_pep Trinity.fasta.transdecoder.pep --bulk_load died with ret 65280 at /home/data/t120347/software/Trinotate/Trinotate line 126.

Here is my gene_trans_map, and I think is correct. TRINITY_DN2391_c0_g1 TRINITY_DN2391_c0_g1_i1 TRINITY_DN2337_c0_g1 TRINITY_DN2337_c0_g1_i1 TRINITY_DN2321_c0_g1 TRINITY_DN2321_c0_g1_i1 TRINITY_DN2397_c0_g1 TRINITY_DN2397_c0_g1_i1 TRINITY_DN2363_c0_g1 TRINITY_DN2363_c0_g1_i1 TRINITY_DN2308_c0_g1 TRINITY_DN2308_c0_g1_i1 TRINITY_DN2385_c0_g1 TRINITY_DN2385_c0_g1_i1 TRINITY_DN2360_c0_g1 TRINITY_DN2360_c0_g1_i1 TRINITY_DN2333_c0_g1 TRINITY_DN2333_c0_g1_i1 TRINITY_DN2399_c0_g1 TRINITY_DN2399_c0_g1_i1 TRINITY_DN2369_c0_g1 TRINITY_DN2369_c0_g1_i1 TRINITY_DN2334_c0_g1 TRINITY_DN2334_c0_g1_i1 TRINITY_DN2342_c0_g1 TRINITY_DN2342_c0_g1_i1 TRINITY_DN2325_c0_g1 TRINITY_DN2325_c0_g1_i1 TRINITY_DN2351_c0_g1 TRINITY_DN2351_c0_g1_i1 TRINITY_DN2357_c0_g1 TRINITY_DN2357_c0_g1_i1 TRINITY_DN2389_c0_g1 TRINITY_DN2389_c0_g1_i1 TRINITY_DN2384_c0_g1 TRINITY_DN2384_c0_g1_i1

And I trying to use trinotate sampledata, it's run OK.

` CMD: /home/data/t120347/software/Trinotate/util/trinotateSeqLoader/TrinotateSeqLoader.pl --sqlite myTrinotate.sqlite --gene_trans_map data/Trinity.fasta.gene_to_trans_map --transcript_fasta data/Trinity.fasta --transdecoder_pep data/Trinity.fasta.transdecoder.pep --bulk_load -parsing gene/trans map file.... done. -loading Transcripts. [600] done. -loading ORFs.

done.

CMD: echo "pragma journal_mode=memory; pragma synchronous=0; pragma cache_size=4000000; .mode tabs .import tmp.Transcript.bulk_load Transcript" | sqlite3 myTrinotate.sqlite memory CMD: echo "pragma journal_mode=memory; pragma synchronous=0; pragma cache_size=4000000; .mode tabs .import tmp.ORF.bulk_load ORF" | sqlite3 myTrinotate.sqlite memory

Loading complete `

So, I don't know how to solve this problem. Thank you inadvance

Moson

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limengchen628 commented 2 years ago

Thank U brian, it's my wrong. I have found a solution to the problem. I'm sorry to bother you

pguarnizob commented 1 year ago

Hi Brian, I got a similar issue. I think I cannot populate my sqlite database.

These are my files in my wd after using chmod 644 on Trinotate.sqlite

(base) gsotil@gsotil-supi:~/Documents/transcriptomas/mushig_anotacion$ ls -l total 921336 -rwxrwxrwx 1 gsotil gsotil 216522927 feb 11 10:14 mushig.Trinity.fasta -rwxrwxrwx 1 gsotil gsotil 7048478 feb 11 10:14 mushig.Trinity.fasta.gene_trans_map -rwxrwxrwx 1 gsotil gsotil 36190931 feb 17 10:16 mushig.Trinity.fasta.transdecoder.pep -rw-r--r-- 1 gsotil gsotil 341835776 feb 21 11:25 sqlite.sqlite -rw-r--r-- 1 gsotil gsotil 341835776 feb 23 11:22 Trinotate.sqlite

Then I run /home/gsotil/Documentos/Trinotate-Trinotate-v3.2.2/Trinotate Trinotate.sqlite init --gene_trans_map mushig.Trinity.fasta.gene_trans_map --transcripts_fasta mushig.Trinity.fasta --transdecoder_pep mushig.Trinity.fasta.transdecoder.pep

and got this error message

CMD: /home/gsotil/Documentos/Trinotate-Trinotate-v3.2.2/util/trinotateSeqLoader/TrinotateSeqLoader.pl --sqlite Trinotate.sqlite --gene_trans_map mushig.Trinity.fasta.gene_trans_map --transcripts_fasta mushig.Trinity.fasta --transdecoder_pep mushig.Trinity.fasta.transdecoder.pep --bulk_load

########################################################## Required:

--sqlite Trinotate sqlite database file

--gene_trans_map text file indicating "genetrans" for each trans-gene relationship.

--transcript_fasta transcripts fasta file

--transdecoder_pep transcdecoder-generated peptide file

Optional:

--bulk_load for faster loading ############################################################

Error, cmd: /home/gsotil/Documentos/Trinotate-Trinotate-v3.2.2/util/trinotateSeqLoader/TrinotateSeqLoader.pl --sqlite Trinotate.sqlite --gene_trans_map mushig.Trinity.fasta.gene_trans_map --transcripts_fasta mushig.Trinity.fasta --transdecoder_pep mushig.Trinity.fasta.transdecoder.pep --bulk_load died with ret 65280 at /home/gsotil/Documentos/Trinotate-Trinotate-v3.2.2/Trinotate line 126.

I will appreciate your comments.

Regards

brianjohnhaas commented 1 year ago

Hi,

The --transcripts_fasta should be --transcript_fasta (no plural).

hope this helps,

~b

On Thu, Feb 23, 2023 at 11:35 AM pguarnizob @.***> wrote:

Hi Brian, I got a similar issue. I think I cannot populate my sqlite database.

These are my files in my wd after using chmod 644 on Trinotate.sqlite

(base) @.***:~/Documents/transcriptomas/mushig_anotacion$ ls -l total 921336 -rwxrwxrwx 1 gsotil gsotil 216522927 feb 11 10:14 mushig.Trinity.fasta -rwxrwxrwx 1 gsotil gsotil 7048478 feb 11 10:14 mushig.Trinity.fasta.gene_trans_map -rwxrwxrwx 1 gsotil gsotil 36190931 feb 17 10:16 mushig.Trinity.fasta.transdecoder.pep -rw-r--r-- 1 gsotil gsotil 341835776 feb 21 11:25 sqlite.sqlite -rw-r--r-- 1 gsotil gsotil 341835776 feb 23 11:22 Trinotate.sqlite

Then I run /home/gsotil/Documentos/Trinotate-Trinotate-v3.2.2/Trinotate Trinotate.sqlite init --gene_trans_map mushig.Trinity.fasta.gene_trans_map --transcripts_fasta mushig.Trinity.fasta --transdecoder_pep mushig.Trinity.fasta.transdecoder.pep

and got this error message

CMD: /home/gsotil/Documentos/Trinotate-Trinotate-v3.2.2/util/trinotateSeqLoader/TrinotateSeqLoader.pl --sqlite Trinotate.sqlite --gene_trans_map mushig.Trinity.fasta.gene_trans_map --transcripts_fasta mushig.Trinity.fasta --transdecoder_pep mushig.Trinity.fasta.transdecoder.pep --bulk_load

########################################################## Required:

--sqlite Trinotate sqlite database file

--gene_trans_map text file indicating "genetrans" for each trans-gene relationship.

--transcript_fasta transcripts fasta file

--transdecoder_pep transcdecoder-generated peptide file

Optional:

--bulk_load for faster loading ############################################################

Error, cmd: /home/gsotil/Documentos/Trinotate-Trinotate-v3.2.2/util/trinotateSeqLoader/TrinotateSeqLoader.pl --sqlite Trinotate.sqlite --gene_trans_map mushig.Trinity.fasta.gene_trans_map --transcripts_fasta mushig.Trinity.fasta --transdecoder_pep mushig.Trinity.fasta.transdecoder.pep --bulk_load died with ret 65280 at /home/gsotil/Documentos/Trinotate-Trinotate-v3.2.2/Trinotate line 126.

I will appreciate your comments.

Regards

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pguarnizob commented 1 year ago

So dumb. I did not notice. Thank you very much.

Can you help me with a Trinotate web problem? I cannot launch the Trinotate web server because of the CGI.pm

I got this error: /usr/sbin/lighttpd -D -f /home/gsotil/Documentos/Trinotate-Trinotate-v3.2.2/TrinotateWeb.conf/lighttpd.conf.port8080 2023-02-23 11:47:08: (configfile.c.426) Warning: mod_auth should be listed in server.modules before dynamic backends such as mod_cgi 2023-02-23 11:47:08: (server.c.1551) server started (lighttpd/1.4.63) Can't locate CGI.pm in @INC (you may need to install the CGI module) (@INC contains: /home/gsotil/perl5/lib/perl5/x86_64-linux-thread-multi /home/gsotil/perl5/lib/perl5 /home/gsotil/miniconda3/lib/perl5/5.32/site_perl /home/gsotil/miniconda3/lib/perl5/site_perl /home/gsotil/miniconda3/lib/perl5/5.32/vendor_perl /home/gsotil/miniconda3/lib/perl5/vendor_perl /home/gsotil/miniconda3/lib/perl5/5.32/core_perl /home/gsotil/miniconda3/lib/perl5/core_perl .) at /home/gsotil/Documentos/Trinotate-Trinotate-v3.2.2/TrinotateWeb/cgi-bin/index.cgi line 7. BEGIN failed--compilation aborted at /home/gsotil/Documentos/Trinotate-Trinotate-v3.2.2/TrinotateWeb/cgi-bin/index.cgi line 7.

I've tried to install this module without success. Any ideas?

Thank you

brianjohnhaas commented 1 year ago

The CGI module usually installs without too much trouble.

You can try this:

cpanm install CGI

if you have cpanm installed (or can install it). That's the easiest way.

Otherwise, you can try to do it directly via:

perl -MCPAN -e shell install CGI

and then 'exit' to get out of the perl shell.

best,

~b

On Thu, Feb 23, 2023 at 11:49 AM Paul @.***> wrote:

So dumb. I did not notice. Thank you very much.

Can you help me with a Trinotate web problem? I cannot launch the Trinotate web server because of the CGI.pm

I got this error: /usr/sbin/lighttpd -D -f /home/gsotil/Documentos/Trinotate-Trinotate-v3.2.2/TrinotateWeb.conf/lighttpd.conf.port8080 2023-02-23 11:47:08: (configfile.c.426) Warning: mod_auth should be listed in server.modules before dynamic backends such as mod_cgi 2023-02-23 11:47:08: (server.c.1551) server started (lighttpd/1.4.63) Can't locate CGI.pm in @inc https://github.com/inc (you may need to install the CGI module) @.*** https://github.com/inc contains: /home/gsotil/perl5/lib/perl5/x86_64-linux-thread-multi /home/gsotil/perl5/lib/perl5 /home/gsotil/miniconda3/lib/perl5/5.32/site_perl /home/gsotil/miniconda3/lib/perl5/site_perl /home/gsotil/miniconda3/lib/perl5/5.32/vendor_perl /home/gsotil/miniconda3/lib/perl5/vendor_perl /home/gsotil/miniconda3/lib/perl5/5.32/core_perl /home/gsotil/miniconda3/lib/perl5/core_perl .) at /home/gsotil/Documentos/Trinotate-Trinotate-v3.2.2/TrinotateWeb/cgi-bin/index.cgi line 7. BEGIN failed--compilation aborted at /home/gsotil/Documentos/Trinotate-Trinotate-v3.2.2/TrinotateWeb/cgi-bin/index.cgi line 7.

I've tried to install this module without success. Any ideas?

Thank you

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pguarnizob commented 1 year ago

Using the cpanm command I get:

install is up to date. (0.01) CGI is up to date. (4.55)

But the same message showed up when running the run_TrinotateWebserver.pl

I tried using perl -MCPAN command but I got this message:

Test Summary Report

t/autoescape.t (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 18 tests but ran 0. t/checkbox_group.t (Wstat: 512 Tests: 1 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 3 tests but ran 1. t/compiles_pod.t (Wstat: 0 Tests: 18 Failed: 0) TODO passed: 3, 6 t/Dump.t (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 t/end_form.t (Wstat: 512 Tests: 1 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 2 tests but ran 1. t/form.t (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 t/function.t (Wstat: 0 Tests: 24 Failed: 0) Parse errors: Bad plan. You planned 33 tests but ran 24. t/headers.t (Wstat: 1024 Tests: 11 Failed: 4) Failed tests: 8-11 Non-zero exit status: 4 t/hidden.t (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 t/html.t (Wstat: 512 Tests: 13 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 40 tests but ran 13. t/no_tabindex.t (Wstat: 512 Tests: 3 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 18 tests but ran 3. t/popup_menu.t (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 t/push.t (Wstat: 512 Tests: 2 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 12 tests but ran 2. t/sorted.t (Wstat: 512 Tests: 3 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 5 tests but ran 3. t/unescapeHTML.t (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 7 tests but ran 0. Files=64, Tests=1447, 5 wallclock secs ( 0.32 usr 0.10 sys + 4.01 cusr 0.57 csys = 5.00 CPU) Result: FAIL Failed 14/64 test programs. 4/1447 subtests failed. make: *** [Makefile:943: test_dynamic] Error 255 Terminal does not support GetHistory. Lockfile removed. LEEJO/CGI-4.55.tar.gz one dependency not OK (HTML::Entities); additionally test harness failed /home/gsotil/miniconda3/bin/make test -- NOT OK //hint// to see the cpan-testers results for installing this module, try: reports LEEJO/CGI-4.55.tar.gz Failed during this command: OALDERS/HTML-Parser-3.81.tar.gz : make NO LEEJO/CGI-4.55.tar.gz : make_test NO one dependency not OK (HTML::Entities); additionally test harness failed

It seems like something is wrong with CGI. What can I do?

brianjohnhaas commented 1 year ago

Can you post the results of running both:

cpanm -V

and

perl -V

?

On Thu, Feb 23, 2023 at 12:21 PM Paul @.***> wrote:

Using the cpanm command I get:

install is up to date. (0.01) CGI is up to date. (4.55)

But the same message showed up when running the run_TrinotateWebserver.pl

I tried using perl -MCPAN command but I got this message: Test Summary Report

t/autoescape.t (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 18 tests but ran 0. t/checkbox_group.t (Wstat: 512 Tests: 1 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 3 tests but ran 1. t/compiles_pod.t (Wstat: 0 Tests: 18 Failed: 0) TODO passed: 3, 6 t/Dump.t (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 t/end_form.t (Wstat: 512 Tests: 1 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 2 tests but ran 1. t/form.t (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 t/function.t (Wstat: 0 Tests: 24 Failed: 0) Parse errors: Bad plan. You planned 33 tests but ran 24. t/headers.t (Wstat: 1024 Tests: 11 Failed: 4) Failed tests: 8-11 Non-zero exit status: 4 t/hidden.t (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 t/html.t (Wstat: 512 Tests: 13 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 40 tests but ran 13. t/no_tabindex.t (Wstat: 512 Tests: 3 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 18 tests but ran 3. t/popup_menu.t (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 t/push.t (Wstat: 512 Tests: 2 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 12 tests but ran 2. t/sorted.t (Wstat: 512 Tests: 3 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 5 tests but ran 3. t/unescapeHTML.t (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 7 tests but ran 0. Files=64, Tests=1447, 5 wallclock secs ( 0.32 usr 0.10 sys + 4.01 cusr 0.57 csys = 5.00 CPU) Result: FAIL Failed 14/64 test programs. 4/1447 subtests failed. make: *** [Makefile:943: test_dynamic] Error 255 Terminal does not support GetHistory. Lockfile removed. LEEJO/CGI-4.55.tar.gz one dependency not OK (HTML::Entities); additionally test harness failed /home/gsotil/miniconda3/bin/make test -- NOT OK //hint// to see the cpan-testers results for installing this module, try: reports LEEJO/CGI-4.55.tar.gz Failed during this command: OALDERS/HTML-Parser-3.81.tar.gz : make NO LEEJO/CGI-4.55.tar.gz : make_test NO one dependency not OK (HTML::Entities); additionally test harness failed

It seems like something is wrong with CGI. What can I do?

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