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chadlaing / Panseq

Pan-genomic sequence analysis
http://lfz.corefacility.ca/panseq
GNU General Public License v3.0
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Cannot open settings.txt #24

Closed rupesh-sinha closed 5 years ago

rupesh-sinha commented 5 years ago

I have created a tab-delimited configuration file and named it as settings.txt and placed it in 'lib' directory. When I am giving the command perl lib/panseq.pl settings.txt the following result is returned: No such file or directory at /home/rks/Downloads/Panseq-master/lib/Modules/Setup/Settings.pm line 284. Whats the issue?

My configuration file "settings.txt" has the following contents: queryDirectory /home/rks/Downloads/Panseq-master/16_genome_panseq/ baseDirectory /home/rks/Downloads/Panseq-master/output_panseq_P_pel/ numberOfCores 4 minimumNovelRegionSize 500 novelRegionFinderMode no_duplicates fragmentationSize 500 percentIdentityCutoff 85 coreGenomeThreshold 3 runMode pan cdhitDirectory /home/rks/Downloads/cdhit-master/ storeAlleles 1 allelesToKeep 2 nameOrId name frameshift 1 overwrite 1 maxNumberResultsInMemory 500 blastWordSize 11 nucB 200 nucC 65 nucD 0.12 nucG 90 nucL 20 cdhit 1 sha1 1

Please let me know the solution for this issue

chadlaing commented 5 years ago

Hi @rupesh-sinha,

From the way you described your situation, it sounds like you are launching the program from the Panseq-master directory, and your settings.txt file is in Panseq-master/lib/. If this is the case, try running: perl lib/panseq.pl lib/settings.txt

If that doesn't work, let me know.

Thanks, Chad

rupesh-sinha commented 5 years ago

Hi, I did according to your suggestion. But this time it comes as:

rks@rks-VirtualBox:~/Downloads/Panseq-master$ perl lib/panseq.pl lib/settings.txt Settings file: lib/settings.txt Please suggest.

Thanks, Rupesh

chadlaing commented 5 years ago

Do the tests work when you run perl t/output.t?

rupesh-sinha commented 5 years ago

Hi, I am pasting the output of perl t/output.t: rks@rks-VirtualBox:~/Downloads/Panseq-master$ ./Build installdeps All prerequisites satisfied rks@rks-VirtualBox:~/Downloads/Panseq-master$ perl t/output.t

Seeded srand with seed '20181120' from local date.

1..35 cd-hit not found SCRIPT_LOCATION: t Systemline: perl t/../lib/panseq.pl t/plasmids.batch Loading setting overwrite with value 1 Loading setting fragmentationSize with value 500 Loading setting numberOfCores with value 1 Loading setting allelesToKeep with value 2 Loading setting nameOrId with value name Loading setting storeAlleles with value 1 Loading setting baseDirectory with value t/plasmids/ Loading setting coreGenomeThreshold with value 2 Loading setting minimumNovelRegionSize with value 500 Loading setting queryDirectory with value t/data/plasmids/ Loading setting percentIdentityCutoff with value 90 Loading setting runMode with value pan Settings file: t/plasmids.batch 2018/11/20 21:49:54 INFO | NovelIterator.pm:186> We have 5 genomes this run 2018/11/20 21:49:58 INFO | Panseq.pm:268> Panseq mode set as pan 2018/11/20 21:49:58 INFO | SegmentMaker.pm:164> Segmenting t/plasmids/83cebb2c6208952b05599fd6693a5813_26f912cf187ef5c0e270e34f6bf2044a into 500bp segments 2018/11/20 21:49:58 INFO | FastaFileSplitter.pm:127> Splitting t/plasmids/pangenome_fragments.fasta into 1 files 2018/11/20 21:49:59 INFO | PanGenome.pm:210> Analyzing the pan-genome 2018/11/20 21:49:59 INFO | PanGenome.pm:215> Processing Blast output files 2018/11/20 21:50:11 INFO | PanGenome.pm:543> Total results: 897 2018/11/20 21:50:11 INFO | PanGenome.pm:303> Processing blast output files complete 2018/11/20 21:50:11 INFO | PanGenome.pm:304> Pan-genome generation complete 2018/11/20 21:50:11 INFO | Panseq.pm:524> Creating zip file Systemline: perl t/../lib/panseq.pl t/query.batch Loading setting overwrite with value 1 Loading setting numberOfCores with value 1 Loading setting fragmentationSize with value 0 Loading setting nameOrId with value name Loading setting queryFile with value t/data/testfragments.fasta Loading setting baseDirectory with value t/query/ Loading setting storeAlleles with value 1 Loading setting coreGenomeThreshold with value 2 Loading setting minimumNovelRegionSize with value 1 Loading setting queryDirectory with value t/data/genomes/ Loading setting percentIdentityCutoff with value 90 Loading setting runMode with value pan Settings file: t/query.batch 2018/11/20 21:50:13 INFO | Panseq.pm:268> Panseq mode set as pan 2018/11/20 21:50:13 INFO | FastaFileSplitter.pm:127> Splitting t/query/sanitized_queryFile.fasta into 1 files 2018/11/20 21:50:14 INFO | PanGenome.pm:210> Analyzing the pan-genome 2018/11/20 21:50:14 INFO | PanGenome.pm:215> Processing Blast output files 2018/11/20 21:50:14 INFO | PanGenome.pm:543> Total results: 10 2018/11/20 21:50:15 WARN | CombineFilesIntoSingleFile.pm:83> Skipping t/query/1_accessoryGenomeFragments as it has size of 0 2018/11/20 21:50:15 INFO | PanGenome.pm:303> Processing blast output files complete 2018/11/20 21:50:15 INFO | PanGenome.pm:304> Pan-genome generation complete 2018/11/20 21:50:15 INFO | Panseq.pm:524> Creating zip file Systemline: perl t/../lib/panseq.pl t/genomes.batch Loading setting minimumNovelRegionSize with value 1000 Loading setting coreGenomeThreshold with value 3 Loading setting queryDirectory with value t/data/genomes/ Loading setting percentIdentityCutoff with value 90 Loading setting runMode with value pan Loading setting baseDirectory with value t/genomes/ Loading setting numberOfCores with value 1 Loading setting fragmentationSize with value 1000 Loading setting nameOrId with value name Loading setting overwrite with value 1 Settings file: t/genomes.batch 2018/11/20 21:50:16 INFO | NovelIterator.pm:186> We have 6 genomes this run 2018/11/20 21:50:22 INFO | Panseq.pm:268> Panseq mode set as pan 2018/11/20 21:50:22 INFO | SegmentMaker.pm:164> Segmenting t/genomes/edfc6cac3fd4427a802625d82d978a4e_055fa1515be783d915e9dd57167d00f2 into 1000bp segments 2018/11/20 21:50:24 INFO | FastaFileSplitter.pm:127> Splitting t/genomes/pangenome_fragments.fasta into 1 files 2018/11/20 21:50:57 INFO | PanGenome.pm:210> Analyzing the pan-genome 2018/11/20 21:50:57 INFO | PanGenome.pm:215> Processing Blast output files

2018/11/20 22:01:56 INFO | PanGenome.pm:543> Total results: 15849 2018/11/20 22:02:00 WARN | CombineFilesIntoSingleFile.pm:83> Skipping t/genomes/1_locus_alleles as it has size of 0 2018/11/20 22:02:00 INFO | PanGenome.pm:303> Processing blast output files complete 2018/11/20 22:02:00 INFO | PanGenome.pm:304> Pan-genome generation complete 2018/11/20 22:02:00 INFO | Panseq.pm:524> Creating zip file Systemline: perl t/../lib/panseq.pl t/sha1.batch Loading setting runMode with value pan Loading setting percentIdentityCutoff with value 90 Loading setting sha1 with value 1 Loading setting queryDirectory with value t/data/plasmids/ Loading setting minimumNovelRegionSize with value 500 Loading setting coreGenomeThreshold with value 2 Loading setting baseDirectory with value t/sha1/ Loading setting storeAlleles with value 1 Loading setting nameOrId with value name Loading setting numberOfCores with value 1 Loading setting fragmentationSize with value 500 Loading setting allelesToKeep with value 2 Loading setting overwrite with value 1 Settings file: t/sha1.batch 2018/11/20 22:02:12 INFO | NovelIterator.pm:186> We have 5 genomes this run 2018/11/20 22:02:16 INFO | Panseq.pm:268> Panseq mode set as pan 2018/11/20 22:02:16 INFO | SegmentMaker.pm:164> Segmenting t/sha1/322ce628f4205db149fe2c1599e7e6d1_b883afe64ed288dec54afe2c1657569c into 500bp segments 2018/11/20 22:02:16 INFO | FastaFileSplitter.pm:127> Splitting t/sha1/pangenome_fragments.fasta into 1 files 2018/11/20 22:02:17 INFO | PanGenome.pm:210> Analyzing the pan-genome 2018/11/20 22:02:17 INFO | PanGenome.pm:215> Processing Blast output files 2018/11/20 22:02:29 INFO | PanGenome.pm:543> Total results: 897 2018/11/20 22:02:29 INFO | PanGenome.pm:303> Processing blast output files complete 2018/11/20 22:02:29 INFO | PanGenome.pm:304> Pan-genome generation complete 2018/11/20 22:02:29 INFO | Panseq.pm:524> Creating zip file not ok 1 - plasmidsCoreSnps generated correctly

Failed test 'plasmidsCoreSnps generated correctly'

at t/output.t line 222.

+-----------+----------------------------------+----+----------------------------------+

| PATH | GOT | OP | CHECK |

+-----------+----------------------------------+----+----------------------------------+

| <Check 0> | a2237420aab789be32b2fb4a360ba7d2 | eq | a7d2902d80543446a6701e8f8770301b |

| <Check 1> | a2237420aab789be32b2fb4a360ba7d2 | eq | 1a7a78da13820f54bb619a4df0f2df2f |

| <Check 2> | a2237420aab789be32b2fb4a360ba7d2 | eq | 1133816b845a5391f552e8e60b0eed8b |

| <Check 3> | a2237420aab789be32b2fb4a360ba7d2 | eq | 388ad37fe11273ece738664fd00ae121 |

| <Check 4> | a2237420aab789be32b2fb4a360ba7d2 | eq | 943a1cf71152037cb1543b0cacec2fff |

| <Check 5> | a2237420aab789be32b2fb4a360ba7d2 | eq | 4c34b6ea16f000281413a51e7f1a96cc |

+-----------+----------------------------------+----+----------------------------------+

not ok 2 - plasmidsPanGenome generated correctly

Failed test 'plasmidsPanGenome generated correctly'

at t/output.t line 223.

+-----------+----------------------------------+----+----------------------------------+

| PATH | GOT | OP | CHECK |

+-----------+----------------------------------+----+----------------------------------+

| <Check 0> | f57d67e93c0e79973994b9c57fc1dc8f | eq | 168d75b59dbe825cd91222906a4f5645 |

| <Check 1> | f57d67e93c0e79973994b9c57fc1dc8f | eq | de611f27d9691d4f2e798007ab49583a |

| <Check 2> | f57d67e93c0e79973994b9c57fc1dc8f | eq | e60ab1fb4adaf0e13ac342a482cc4a96 |

| <Check 3> | f57d67e93c0e79973994b9c57fc1dc8f | eq | 35c7ee30137ccf2737b6e1717149620c |

| <Check 4> | f57d67e93c0e79973994b9c57fc1dc8f | eq | 18b07b36e448492ac162624e36628444 |

| <Check 5> | f57d67e93c0e79973994b9c57fc1dc8f | eq | 6674c78f04dcbe10b569e247990e27b5 |

| <Check 6> | f57d67e93c0e79973994b9c57fc1dc8f | eq | a5c4a6fefc6977063c136e0126a6e2c9 |

+-----------+----------------------------------+----+----------------------------------+

not ok 3 - plasmidsBinaryTable generated correctly

Failed test 'plasmidsBinaryTable generated correctly'

at t/output.t line 224.

+-----------+----------------------------------+----+----------------------------------+

| PATH | GOT | OP | CHECK |

+-----------+----------------------------------+----+----------------------------------+

| <Check 0> | 8fe32d6033793cbfbe08f968b6a35ab8 | eq | fbfffe4e58a1dfc1cd04cb29b5146c0d |

| <Check 1> | 8fe32d6033793cbfbe08f968b6a35ab8 | eq | 387d3415808e3ed9ef0ffa60c6b7fd67 |

| <Check 2> | 8fe32d6033793cbfbe08f968b6a35ab8 | eq | 9524c956d024e323de747623b67871e1 |

| <Check 3> | 8fe32d6033793cbfbe08f968b6a35ab8 | eq | facdac694c0f7f8603f74151cdefd7a6 |

+-----------+----------------------------------+----+----------------------------------+

not ok 4 - plasmidsSnpTable generated correctly

Failed test 'plasmidsSnpTable generated correctly'

at t/output.t line 225.

+-----------+----------------------------------+----+----------------------------------+

| PATH | GOT | OP | CHECK |

+-----------+----------------------------------+----+----------------------------------+

| <Check 0> | 07038ffb3f4ce431780e052817de606e | eq | 188356ccf7f73066c333e82dd18e531d |

| <Check 1> | 07038ffb3f4ce431780e052817de606e | eq | 2e69ced50fb7d1f13e84e00dfdbd2b5a |

| <Check 2> | 07038ffb3f4ce431780e052817de606e | eq | b8624a47c1edc7193d01a8b07c039e27 |

| <Check 3> | 07038ffb3f4ce431780e052817de606e | eq | 5e03e2cdc49d4d4d1a33cf124f192ee2 |

| <Check 4> | 07038ffb3f4ce431780e052817de606e | eq | 883396f6d5f8d5d5918777a0a4ee6e97 |

| <Check 5> | 07038ffb3f4ce431780e052817de606e | eq | 92a15888a3beee351cebc43302457824 |

+-----------+----------------------------------+----+----------------------------------+

not ok 5 - plasmidsSnpPhylip generated correctly

Failed test 'plasmidsSnpPhylip generated correctly'

at t/output.t line 226.

+-----------+----------------------------------+----+----------------------------------+

| PATH | GOT | OP | CHECK |

+-----------+----------------------------------+----+----------------------------------+

| <Check 0> | 6e451ad99b50e40ea187c13789c244d4 | eq | 6c8f15448b0f19be9efbb79e16256350 |

| <Check 1> | 6e451ad99b50e40ea187c13789c244d4 | eq | 4ae7de5409064454c0b8c17d47cd10c8 |

| <Check 2> | 6e451ad99b50e40ea187c13789c244d4 | eq | 52b8a7b0e45e8e0ccdcddebd47e4c3a4 |

| <Check 3> | 6e451ad99b50e40ea187c13789c244d4 | eq | 922767f0f9205ea242303ee766014624 |

| <Check 4> | 6e451ad99b50e40ea187c13789c244d4 | eq | 2ca6ba039d01c1ca0cf4bae11bd07cfc |

| <Check 5> | 6e451ad99b50e40ea187c13789c244d4 | eq | d490e061720aa36303cb3acbf55b4bb3 |

+-----------+----------------------------------+----+----------------------------------+

not ok 6 - plasmidsBinaryPhylip generated correctly

Failed test 'plasmidsBinaryPhylip generated correctly'

at t/output.t line 227.

+-----------+----------------------------------+----+----------------------------------+

| PATH | GOT | OP | CHECK |

+-----------+----------------------------------+----+----------------------------------+

| <Check 0> | b0cc82027ad54d5c7a022ae6d62c40b9 | eq | db5e15a38d9b7b7be53811df302d7558 |

| <Check 1> | b0cc82027ad54d5c7a022ae6d62c40b9 | eq | b418d9d4a7c404ba859a40b2540a30ec |

| <Check 2> | b0cc82027ad54d5c7a022ae6d62c40b9 | eq | 210104cefd498b805d040ae789e81f52 |

| <Check 3> | b0cc82027ad54d5c7a022ae6d62c40b9 | eq | fd0779e2c1cacef90fbf5594a52cf8a6 |

+-----------+----------------------------------+----+----------------------------------+

ok 7 - plasmidsNameConversion generated correctly not ok 8 - plasmidsAccessoryFragments generated correctly

Failed test 'plasmidsAccessoryFragments generated correctly'

at t/output.t line 234.

+-----------+----------------------------------+----+----------------------------------+

| PATH | GOT | OP | CHECK |

+-----------+----------------------------------+----+----------------------------------+

| <Check 0> | 5ead69d2346a17df1723542564bd8d9d | eq | f17e29fd8ca3dbaac3033ce188018465 |

| <Check 1> | 5ead69d2346a17df1723542564bd8d9d | eq | 3c853ac88d7ea51c757b60fc9edda08f |

| <Check 2> | 5ead69d2346a17df1723542564bd8d9d | eq | 203f613ce413cc2e97f15134ae3fe627 |

| <Check 3> | 5ead69d2346a17df1723542564bd8d9d | eq | 399c70234d36995e7660261494255098 |

+-----------+----------------------------------+----+----------------------------------+

not ok 9 - plasmidsCoreFragments generated correctly

Failed test 'plasmidsCoreFragments generated correctly'

at t/output.t line 235.

+-----------+----------------------------------+----+----------------------------------+

| PATH | GOT | OP | CHECK |

+-----------+----------------------------------+----+----------------------------------+

| <Check 0> | 95b4a2283940c89138b4bb57ac386445 | eq | 2fa21523c2c0e9abde0836f2a754640e |

| <Check 1> | 95b4a2283940c89138b4bb57ac386445 | eq | ba16baa4bf8786d2d6ab961f6bff4c54 |

| <Check 2> | 95b4a2283940c89138b4bb57ac386445 | eq | bd5e19b696e6ef5602c3456e2792b493 |

| <Check 3> | 95b4a2283940c89138b4bb57ac386445 | eq | a277c0f894016404a5570adb5236c35f |

+-----------+----------------------------------+----+----------------------------------+

ok 10 - queryCoreSnps generated correctly ok 11 - queryPanGenome generated correctly ok 12 - queryBinaryTable generated correctly ok 13 - querySnpTable generated correctly ok 14 - querySnpPhylip generated correctly ok 15 - queryBinaryPhylip generated correctly ok 16 - queryNameConversion generated correctly ok 17 - queryAlleles generated correctly not ok 18 - genomesCoreSnps generated correctly

Failed test 'genomesCoreSnps generated correctly'

at t/output.t line 222.

+-----------+----------------------------------+----+----------------------------------+

| PATH | GOT | OP | CHECK |

+-----------+----------------------------------+----+----------------------------------+

| <Check 0> | 4ac46e9e16ccf2aaaa6a8279c46530f4 | eq | 83beb7f1fbdcf2f6cb38cb5604b8385b |

| <Check 1> | 4ac46e9e16ccf2aaaa6a8279c46530f4 | eq | 445a61d3f5cda294630fe24806d5c33b |

| <Check 2> | 4ac46e9e16ccf2aaaa6a8279c46530f4 | eq | 2441e0d01b5be5a44260173b112685e3 |

| <Check 3> | 4ac46e9e16ccf2aaaa6a8279c46530f4 | eq | eb253c8ac7a465053cac92e3dac44f5e |

| <Check 4> | 4ac46e9e16ccf2aaaa6a8279c46530f4 | eq | 844eea70caa520d625c98b94898d3497 |

+-----------+----------------------------------+----+----------------------------------+

not ok 19 - genomesPanGenome generated correctly

Failed test 'genomesPanGenome generated correctly'

at t/output.t line 223.

+-----------+----------------------------------+----+----------------------------------+

| PATH | GOT | OP | CHECK |

+-----------+----------------------------------+----+----------------------------------+

| <Check 0> | 23456b22fce3b9926d68b68518bc6fb8 | eq | 3e00bb9e7d7fa9b02b34052fd005fa00 |

| <Check 1> | 23456b22fce3b9926d68b68518bc6fb8 | eq | 865f831d6255fa110c13a2309ba1aeb9 |

| <Check 2> | 23456b22fce3b9926d68b68518bc6fb8 | eq | 46fa77ff7c402d76a954698862fb55c7 |

| <Check 3> | 23456b22fce3b9926d68b68518bc6fb8 | eq | d201ccaec94cf11214b54fdfebd4091c |

| <Check 4> | 23456b22fce3b9926d68b68518bc6fb8 | eq | 9a4a0f910743f764634dd23ac7dba7f0 |

+-----------+----------------------------------+----+----------------------------------+

not ok 20 - genomesBinaryTable generated correctly

Failed test 'genomesBinaryTable generated correctly'

at t/output.t line 224.

+-----------+----------------------------------+----+----------------------------------+

| PATH | GOT | OP | CHECK |

+-----------+----------------------------------+----+----------------------------------+

| <Check 0> | 7b88bf23f3ed6eaaac186db4abc8a799 | eq | 1f1aaef9c674a5e847cae718964b0385 |

| <Check 1> | 7b88bf23f3ed6eaaac186db4abc8a799 | eq | b1f08ef0b7abc7e24a1f4691654723e8 |

| <Check 2> | 7b88bf23f3ed6eaaac186db4abc8a799 | eq | d4c1edc8e846f24b7ac2c5a4e35b3779 |

+-----------+----------------------------------+----+----------------------------------+

not ok 21 - genomesSnpTable generated correctly

Failed test 'genomesSnpTable generated correctly'

at t/output.t line 225.

+-----------+----------------------------------+----+----------------------------------+

| PATH | GOT | OP | CHECK |

+-----------+----------------------------------+----+----------------------------------+

| <Check 0> | 01758b973551178cdc6d83348277f0b9 | eq | 63ca2aa391938fb521375f0b2353bb06 |

| <Check 1> | 01758b973551178cdc6d83348277f0b9 | eq | 9353ec59942c3cd3c94165cf8be26dee |

| <Check 2> | 01758b973551178cdc6d83348277f0b9 | eq | a384b00607770e723b013a08d04eeb43 |

| <Check 3> | 01758b973551178cdc6d83348277f0b9 | eq | 00cb15d599ab6ee43a86c7c21b86e4d3 |

| <Check 4> | 01758b973551178cdc6d83348277f0b9 | eq | ba851f5aff6a6a49cc567324cc8c0238 |

+-----------+----------------------------------+----+----------------------------------+

not ok 22 - genomesSnpPhylip generated correctly

Failed test 'genomesSnpPhylip generated correctly'

at t/output.t line 226.

+-----------+----------------------------------+----+----------------------------------+

| PATH | GOT | OP | CHECK |

+-----------+----------------------------------+----+----------------------------------+

| <Check 0> | 5dd90429c01110e5241b63c89f9b8bd4 | eq | f438ce263872f10b36cb3247a3d5dd59 |

| <Check 1> | 5dd90429c01110e5241b63c89f9b8bd4 | eq | 309eb8bce6de7737a4de799131a2b4e3 |

| <Check 2> | 5dd90429c01110e5241b63c89f9b8bd4 | eq | 11966e574aacd819e8e610d3628c3fac |

| <Check 3> | 5dd90429c01110e5241b63c89f9b8bd4 | eq | 9769a69d8ae1958baa59e4b94fcddd2b |

| <Check 4> | 5dd90429c01110e5241b63c89f9b8bd4 | eq | 0e7f68277f8f661435c33ad8fd2c1550 |

+-----------+----------------------------------+----+----------------------------------+

not ok 23 - genomesBinaryPhylip generated correctly

Failed test 'genomesBinaryPhylip generated correctly'

at t/output.t line 227.

+-----------+----------------------------------+----+----------------------------------+

| PATH | GOT | OP | CHECK |

+-----------+----------------------------------+----+----------------------------------+

| <Check 0> | e26c2aa1c754be0d49d3b7a842e7dcbf | eq | 4b341c515a3aa54377b7a7f8a9e71d17 |

| <Check 1> | e26c2aa1c754be0d49d3b7a842e7dcbf | eq | 0109650c91d4b100bcf61c4dd213bbb7 |

| <Check 2> | e26c2aa1c754be0d49d3b7a842e7dcbf | eq | e621cd93f3e89d1bba6c3e32f710c33a |

+-----------+----------------------------------+----+----------------------------------+

ok 24 - genomesNameConversion generated correctly not ok 25 - genomesAccessoryFragments generated correctly

Failed test 'genomesAccessoryFragments generated correctly'

at t/output.t line 234.

+-----------+----------------------------------+----+----------------------------------+

| PATH | GOT | OP | CHECK |

+-----------+----------------------------------+----+----------------------------------+

| <Check 0> | 8c220f224f65ae04d06dc04d54fb6f86 | eq | 6dca4cb62aabfbca4d54279d959fc451 |

| <Check 1> | 8c220f224f65ae04d06dc04d54fb6f86 | eq | 82b63375b744f0352d5c809135b20d51 |

| <Check 2> | 8c220f224f65ae04d06dc04d54fb6f86 | eq | 32c321d798c3ff57ec85e4294c49b145 |

| <Check 3> | 8c220f224f65ae04d06dc04d54fb6f86 | eq | 20ed6e5b514f8291327cf70011f0923f |

+-----------+----------------------------------+----+----------------------------------+

not ok 26 - genomesCoreFragments generated correctly

Failed test 'genomesCoreFragments generated correctly'

at t/output.t line 235.

+-----------+----------------------------------+----+----------------------------------+

| PATH | GOT | OP | CHECK |

+-----------+----------------------------------+----+----------------------------------+

| <Check 0> | fa2f69150376fbd383460f14e94ada3d | eq | 117d52a380e05eddd33a31d07a4f7829 |

| <Check 1> | fa2f69150376fbd383460f14e94ada3d | eq | f4dbb98ee7e952389e4787c31f1ab75a |

| <Check 2> | fa2f69150376fbd383460f14e94ada3d | eq | 786a682d3ee41c6cc6d59640fd657310 |

| <Check 3> | fa2f69150376fbd383460f14e94ada3d | eq | 9a09685130eba1fecaa740517d9921a6 |

+-----------+----------------------------------+----+----------------------------------+

not ok 27 - sha1CoreSnps generated correctly

Failed test 'sha1CoreSnps generated correctly'

at t/output.t line 222.

+-----------+----------------------------------+----+----------------------------------+

| PATH | GOT | OP | CHECK |

+-----------+----------------------------------+----+----------------------------------+

| <Check 0> | a2237420aab789be32b2fb4a360ba7d2 | eq | 943a1cf71152037cb1543b0cacec2fff |

| <Check 1> | a2237420aab789be32b2fb4a360ba7d2 | eq | 4c34b6ea16f000281413a51e7f1a96cc |

+-----------+----------------------------------+----+----------------------------------+

not ok 28 - sha1PanGenome generated correctly

Failed test 'sha1PanGenome generated correctly'

at t/output.t line 223.

+-----------+----------------------------------+----+----------------------------------+

| PATH | GOT | OP | CHECK |

+-----------+----------------------------------+----+----------------------------------+

| <Check 0> | f57d67e93c0e79973994b9c57fc1dc8f | eq | 6674c78f04dcbe10b569e247990e27b5 |

| <Check 1> | f57d67e93c0e79973994b9c57fc1dc8f | eq | a5c4a6fefc6977063c136e0126a6e2c9 |

+-----------+----------------------------------+----+----------------------------------+

not ok 29 - sha1BinaryTable generated correctly

Failed test 'sha1BinaryTable generated correctly'

at t/output.t line 224.

+-----------+----------------------------------+----+----------------------------------+

| PATH | GOT | OP | CHECK |

+-----------+----------------------------------+----+----------------------------------+

| <Check 0> | 8fe32d6033793cbfbe08f968b6a35ab8 | eq | 9524c956d024e323de747623b67871e1 |

| <Check 1> | 8fe32d6033793cbfbe08f968b6a35ab8 | eq | facdac694c0f7f8603f74151cdefd7a6 |

+-----------+----------------------------------+----+----------------------------------+

not ok 30 - sha1SnpTable generated correctly

Failed test 'sha1SnpTable generated correctly'

at t/output.t line 225.

+-----------+----------------------------------+----+----------------------------------+

| PATH | GOT | OP | CHECK |

+-----------+----------------------------------+----+----------------------------------+

| <Check 0> | 07038ffb3f4ce431780e052817de606e | eq | 883396f6d5f8d5d5918777a0a4ee6e97 |

| <Check 1> | 07038ffb3f4ce431780e052817de606e | eq | 92a15888a3beee351cebc43302457824 |

+-----------+----------------------------------+----+----------------------------------+

not ok 31 - sha1SnpPhylip generated correctly

Failed test 'sha1SnpPhylip generated correctly'

at t/output.t line 226.

+-----------+----------------------------------+----+----------------------------------+

| PATH | GOT | OP | CHECK |

+-----------+----------------------------------+----+----------------------------------+

| <Check 0> | 6e451ad99b50e40ea187c13789c244d4 | eq | 2ca6ba039d01c1ca0cf4bae11bd07cfc |

| <Check 1> | 6e451ad99b50e40ea187c13789c244d4 | eq | d490e061720aa36303cb3acbf55b4bb3 |

+-----------+----------------------------------+----+----------------------------------+

not ok 32 - sha1BinaryPhylip generated correctly

Failed test 'sha1BinaryPhylip generated correctly'

at t/output.t line 227.

+-----------+----------------------------------+----+----------------------------------+

| PATH | GOT | OP | CHECK |

+-----------+----------------------------------+----+----------------------------------+

| <Check 0> | b0cc82027ad54d5c7a022ae6d62c40b9 | eq | 210104cefd498b805d040ae789e81f52 |

| <Check 1> | b0cc82027ad54d5c7a022ae6d62c40b9 | eq | fd0779e2c1cacef90fbf5594a52cf8a6 |

+-----------+----------------------------------+----+----------------------------------+

ok 33 - sha1NameConversion generated correctly not ok 34 - sha1AccessoryFragments generated correctly

Failed test 'sha1AccessoryFragments generated correctly'

at t/output.t line 234.

+-----------+----------------------------------+----+----------------------------------+

| PATH | GOT | OP | CHECK |

+-----------+----------------------------------+----+----------------------------------+

| <Check 0> | 5ead69d2346a17df1723542564bd8d9d | eq | 203f613ce413cc2e97f15134ae3fe627 |

| <Check 1> | 5ead69d2346a17df1723542564bd8d9d | eq | 399c70234d36995e7660261494255098 |

+-----------+----------------------------------+----+----------------------------------+

not ok 35 - sha1CoreFragments generated correctly

Failed test 'sha1CoreFragments generated correctly'

at t/output.t line 235.

+-----------+----------------------------------+----+----------------------------------+

| PATH | GOT | OP | CHECK |

+-----------+----------------------------------+----+----------------------------------+

| <Check 0> | 95b4a2283940c89138b4bb57ac386445 | eq | bd5e19b696e6ef5602c3456e2792b493 |

| <Check 1> | 95b4a2283940c89138b4bb57ac386445 | eq | a277c0f894016404a5570adb5236c35f |

+-----------+----------------------------------+----+----------------------------------+

Can you tell me if something is going wrong.

chadlaing commented 5 years ago

Hi,

It looks like some dependencies are missing. Do you have BLAST, MUSCLE, and MUMMER installed and functioning correctly?

rupesh-sinha commented 5 years ago

Hi, I checked for these three dependencies. The blast was not found. Can you suggest easy way to install it. Pasting my results of search:

rks@rks-VirtualBox:~/Downloads/Panseq-master$ mummer Usage: mummer [options]

Find and output (to stdout) the positions and length of all sufficiently long maximal matches of a substring in

and Options: -mum compute maximal matches that are unique in both sequences -mumcand same as -mumreference -mumreference compute maximal matches that are unique in the reference- sequence but not necessarily in the query-sequence (default) -maxmatch compute all maximal matches regardless of their uniqueness -n match only the characters a, c, g, or t they can be in upper or in lower case -l set the minimum length of a match if not set, the default value is 20 -b compute forward and reverse complement matches -r only compute reverse complement matches -s show the matching substrings -c report the query-position of a reverse complement match relative to the original query sequence -F force 4 column output format regardless of the number of reference sequence inputs -L show the length of the query sequences on the header line -h show possible options -help show possible options rks@rks-VirtualBox:~/Downloads/Panseq-master$ muscle MUSCLE v3.8.31 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. Basic usage muscle -in -out Common options (for a complete list please see the User Guide): -in Input file in FASTA format (default stdin) -out Output alignment in FASTA format (default stdout) -diags Find diagonals (faster for similar sequences) -maxiters Maximum number of iterations (integer, default 16) -maxhours Maximum time to iterate in hours (default no limit) -html Write output in HTML format (default FASTA) -msf Write output in GCG MSF format (default FASTA) -clw Write output in CLUSTALW format (default FASTA) -clwstrict As -clw, with 'CLUSTAL W (1.81)' header -log[a] Log to file (append if -loga, overwrite if -log) -quiet Do not write progress messages to stderr -version Display version information and exit Without refinement (very fast, avg accuracy similar to T-Coffee): -maxiters 2 Fastest possible (amino acids): -maxiters 1 -diags -sv -distance1 kbit20_3 Fastest possible (nucleotides): -maxiters 1 -diags rks@rks-VirtualBox:~/Downloads/Panseq-master$ blast Command 'blast' not found, did you mean: command 'blastn' from deb ncbi-blast+ command 'plast' from deb plast command 'last' from deb util-linux command 'blastp' from deb ncbi-blast+ command 'blasr' from deb blasr command 'blastx' from deb ncbi-blast+ Try: sudo apt install rks@rks-VirtualBox:~/Downloads/Panseq-master$ blast+ Command 'blast+' not found, did you mean: command 'blastp' from deb ncbi-blast+ command 'blastn' from deb ncbi-blast+ command 'blastx' from deb ncbi-blast+ Try: sudo apt install
chadlaing commented 5 years ago

Hi,

The actual command is blastn, within the blast suite of tools. See if that works.

rupesh-sinha commented 5 years ago

Hi, I have all the dependencies now. But please suggest solution for this error message while running Build.PL: rks@rks-VirtualBox:~/Downloads/Panseq-master$ perl Build.PL WARNING: the following files are missing in your kit: .idea/.name .idea/compiler.xml .idea/copyright/profiles_settings.xml .idea/encodings.xml .idea/inspectionProfiles/Project_Default.xml .idea/jscsPlugin.xml .idea/jsLinters/jscs.xml .idea/jsLinters/jshint.xml .idea/jsLinters/jslint.xml .idea/misc.xml .idea/modules.xml .idea/perl5local.xml .idea/vcs.xml .idea/workspace.xml _Inline/.lock _Inline/config-x86_64-linux-gnu-thread-multi-5.024001 _Inline/lib/auto/Bio/DB/IndexedBase_168b/IndexedBase_168b.inl _Inline/lib/auto/Bio/DB/IndexedBase_168b/IndexedBase_168b.so lib/Interface/html/output/FriFeb2416182920175586.html lib/Interface/html/output/FriFeb2416182920175586.html.zip lib/Interface/html/output/FriFeb2416184320175772.html lib/Interface/html/output/FriFeb2416184320175772.html.zip lib/Interface/html/output/FriMay2009131020168122.html lib/Interface/html/output/FriMay2009131020168122.html.zip lib/Interface/html/output/FriMay2009185220162483.html lib/Interface/html/output/FriMay2009225920165242.html lib/Interface/html/output/FriMay2009245520168418.html lib/Interface/html/output/FriMay2009245520168418.html.zip lib/Interface/html/output/FriMay2009253720166882.html lib/Interface/html/output/FriMay2009253720166882.html.zip lib/Interface/html/output/FriMay2009261520162048.html lib/Interface/html/output/FriMay2009261520162048.html.zip lib/Interface/html/output/FriMay2009264620167796.html lib/Interface/html/output/FriMay2009304320165893.html lib/Interface/html/output/FriMay2009304320165893.html.zip lib/Interface/html/output/FriMay2009470220162232.html lib/Interface/html/output/FriMay2009470220162232.html.zip lib/Interface/html/output/FriMay2016125320163557.html lib/Interface/html/output/FriMay2016125320163557.html.zip lib/Interface/html/output/FriMay2016134120162239.html lib/Interface/html/output/FriMay2016134120162239.html.zip lib/Interface/html/output/FriMay2016150320163847.html lib/Interface/html/output/FriMay2016150320163847.html.zip lib/Interface/html/output/FriMay2016163520162080.html lib/Interface/html/output/FriMay2016163520162080.html.zip lib/Interface/html/output/FriNov2512130520162945.html lib/Interface/html/output/FriNov2512144520167628.html lib/Interface/html/output/FriNov2512403320166878.html lib/Interface/html/output/FriNov2512460520166867.html lib/Interface/html/output/FriNov2512460520166867.html.zip lib/Interface/html/output/ThuMay1913534820164709.html lib/Interface/html/output/ThuMay1913534820164709.html.zip lib/Interface/html/output/ThuMay1914040420169910.html lib/Interface/html/output/ThuMay1914040420169910.html.zip lib/Interface/html/output/ThuMay1914090720167990.html lib/Interface/html/output/ThuMay1914090720167990.html.zip lib/Interface/html/output/ThuMay1915580220162532.html lib/Interface/html/output/ThuMay1916000020168524.html 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lib/Interface/html/output/ThuMay1916180320161205.html.zip lib/Interface/html/output/ThuMay1916185520161934.html lib/Interface/html/output/ThuMay1916185520161934.html.zip lib/Interface/html/output/ThuMay1916194620169756.html lib/Interface/html/output/ThuMay1916210120162607.html lib/Interface/html/output/ThuMay1916235020168210.html lib/Interface/html/output/ThuMay1916235020168210.html.zip lib/Interface/html/output/ThuMay1916262320161910.html lib/Interface/html/output/ThuMay1916274020161950.html lib/Interface/html/output/ThuMay1916274020161950.html.zip lib/Interface/html/output/ThuMay1916294920168425.html lib/Interface/html/output/ThuMay1916294920168425.html.zip lib/Interface/html/output/ThuMay1916304020163503.html lib/Interface/html/output/ThuMay1916304020163503.html.zip lib/Interface/html/output/ThuMay1916305220166327.html lib/Interface/html/output/ThuMay1916305220166327.html.zip lib/Interface/html/output/ThuMay1916310120167487.html 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lib/Interface/html/output/TueFeb2815062720178415.html lib/Interface/html/output/TueFeb2815112220177455.html lib/Interface/html/output/TueFeb2815152420178022.html lib/Interface/html/output/TueFeb2815152420178022.html.zip lib/Interface/html/output/TueFeb2815351020178870.html lib/Interface/html/output/TueFeb2815374920174972.html lib/Interface/html/output/TueFeb2815385920172911.html lib/Interface/html/output/TueFeb2815402020177632.html lib/Interface/html/output/TueFeb2815404920176227.html lib/Interface/html/output/TueFeb2815434020176717.html lib/Interface/html/output/TueFeb2815434020176717.html.zip lib/Interface/html/output/TueFeb2815493820179580.html lib/Interface/html/output/TueFeb2815493820179580.html.zip lib/Interface/html/output/TueMay2414050720162420.html lib/Interface/html/output/TueMay2414050720162420.html.zip lib/Interface/html/output/WedFeb2208501520177043.html lib/Interface/html/output/WedFeb2208522720174969.html lib/Interface/html/output/WedFeb2209132120175101.html lib/Interface/html/output/WedFeb2209220420176049.html lib/Interface/html/output/WedFeb2209281120172709.html lib/Interface/html/output/WedFeb2211190220174524.html lib/Interface/html/output/WedFeb2211254720179829.html lib/Interface/html/output/WedFeb2211304320173311.html lib/Interface/html/output/WedFeb2211314820174619.html lib/Interface/html/output/WedFeb2211333020172440.html lib/Interface/html/output/WedFeb2211383120174320.html lib/Interface/html/output/WedFeb2211383120174320.html.zip lib/Interface/html/output/WedFeb2211483720175082.html lib/Interface/html/output/WedFeb2211483720175082.html.zip lib/Interface/html/output/WedMay2515145020162381.html lib/Interface/html/output/WedMay2516051820167448.html lib/Interface/html/output/WedMay2516051820167448.html.zip lib/Interface/html/output/WedMay2516065620161126.html lib/Interface/html/output/WedMay2516065620161126.html.zip lib/Interface/html/output/WedMay2516085420166409.html lib/Interface/html/output/WedMay2516103620166082.html lib/Interface/html/output/WedMay2516113820168636.html lib/Interface/html/output/WedMay2516212620163783.html lib/Interface/html/output/WedMay2516261120165773.html lib/Interface/html/output/WedMay2516270120161803.html lib/Interface/index.html lib/Interface/scripts/assembly_summary.txt lib/Interface/scripts/server.conf panseq.batch Panseq.iml t/plasmids.batch t/plasmids/accessoryGenomeFragments.fasta t/plasmids/binary.phylip t/plasmids/binary_table.txt t/plasmids/cdhit.fasta.clstr t/plasmids/core_snps.txt t/plasmids/coreGenomeFragments.fasta t/plasmids/locus_alleles.fasta t/plasmids/Master.log t/plasmids/pan_genome.txt t/plasmids/panGenome.fasta t/plasmids/panseq_results.zip t/plasmids/phylip_name_conversion.txt t/plasmids/snp.phylip t/plasmids/snp_table.txt t/query.batch t/query/accessoryGenomeFragments.fasta t/query/binary.phylip t/query/binary_table.txt t/query/core_snps.txt t/query/coreGenomeFragments.fasta t/query/locus_alleles.fasta t/query/Master.log t/query/pan_genome.txt t/query/panseq_results.zip t/query/phylip_name_conversion.txt t/query/snp.phylip t/query/snp_table.txt Please inform the author.

Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'Panseq' version '3.1.1'

chadlaing commented 5 years ago

Hi,

Have you done the following? Panseq requires Perl 5.10 or greater, and the following CPAN package to be installed:

Module::Build

This package can be installed from the command-line using cpan -i Module::Build. Following this, to install, and automatically retrieve the required CPAN packages for Panseq, do the following:

perl Build.PL ./Build installdeps

rupesh-sinha commented 5 years ago

Hi, Yes I have checked all the prerequisites including perl, muscle, mummer, blastn, cd-hit. But when I am running the test script perl t/Ioutput.t am getting error following message:

[rks-cent@localhost Panseq-master]$ perl t/output.t

Seeded srand with seed '20181122' from local date.

1..35 SCRIPT_LOCATION: t Could not create test batch file plasmids.batch at t/output.t line 379.

No tests run!

Looks like your test exited with 13 after test #0.

Did not follow plan: expected 35, ran 0.

Please suggest where is plasmid.batch?

chadlaing commented 5 years ago

Hi,

This looks like a permissions issue. Can you check to ensure write permission?

rupesh-sinha commented 5 years ago

Hi Chadlaing, I have sorted out the above issue. Now my test perl t/output.t generated all OK result. All dependencies are also installed correctly. But when I run the panseq.pl command I get precedence issue as follow: rks@rks-VirtualBox:~/Downloads/downloads_ubuntu1/downloads1/Panseq-master$ perl lib/panseq.pl settings.txt Possible precedence issue with control flow operator at /usr/local/share/perl/5.26.1/Bio/DB/IndexedBase.pm line 845. Settings file: settings.txt

Kindly suggest the solution. Thanks, Rupesh

chadlaing commented 5 years ago

Hi Rupesh,

I hope you figured things out, as I am unable to debug this on my end.

Thanks, Chad

rupesh-sinha commented 5 years ago

Hi, Yes I could figure out. It was issue with perl. Nevertheless, I am grateful for your support.

Many thanks Rupesh

On Tue, Dec 11, 2018, 12:32 AM Chad Laing <notifications@github.com wrote:

Hi Rupesh,

I hope you figured things out, as I am unable to debug this on my end.

Thanks, Chad

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/chadlaing/Panseq/issues/24#issuecomment-445931928, or mute the thread https://github.com/notifications/unsubscribe-auth/AlGmKK88_64bTO4UDRjLQfuYZYIXtCAtks5u3q-9gaJpZM4YrUvO .