chadlaing/Panseq

Cannot open settings.txt

rupesh-sinha opened this issue · 14 comments

rupesh-sinha commented

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

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

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

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

rupesh-sinha commented

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

Hi,

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

rupesh-sinha commented

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 <inputfile> -out <outputfile>

Common options (for a complete list please see the User Guide):

-in <inputfile>    Input file in FASTA format (default stdin)
-out <outputfile>  Output alignment in FASTA format (default stdout)
-diags             Find diagonals (faster for similar sequences)
-maxiters <n>      Maximum number of iterations (integer, default 16)
-maxhours <h>      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] <logfile>  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

Hi,

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

rupesh-sinha commented

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
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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

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

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

Hi,

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

rupesh-sinha commented

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

Hi Rupesh,

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

Thanks,
Chad

rupesh-sinha commented