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lskatz / mashtree

:deciduous_tree: Create a tree using Mash distances
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EXCEPTION: Bio::Root::Exception #88

Open caizhangbin opened 2 weeks ago

caizhangbin commented 2 weeks ago

I installed the software through CPAN I tried to run the software with: mashtree *.fasta --numcpus 12 --min-depth 0 > mashtree.dnd while I always got this error: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: parse error: expected ; or ) or ,

STACK: Error::throw STACK: Bio::Root::Root::throw /home/zhangbin/bin/../lib/perl5/Bio/Root/Root.pm:449 STACK: Bio::TreeIO::NewickParser::parse_newick /home/zhangbin/bin/../lib/perl5/Mashtree/../Bio/TreeIO/NewickParser.pm:204 STACK: Bio::TreeIO::newick::next_tree /home/zhangbin/bin/../lib/perl5/Mashtree/../Bio/TreeIO/newick.pm:144 STACK: Mashtree::createTreeFromPhylip /home/zhangbin/bin/../lib/perl5/Mashtree.pm:337 STACK: main::main /home/zhangbin/bin/mashtree:149 STACK: /home/zhangbin/bin/mashtree:37 thoughts?

lskatz commented 2 weeks ago

Hi, can I see the output of these commands?

caizhangbin commented 2 weeks ago

mashtree --version: Mashtree 1.4.6 ls -lhS *.fasta: -rw-r-----. 1 zhangbin zhangbin 68K Aug 30 21:39 '50002216A_PHAGE_Staphy_CNPx_NC_031241(43).fasta' -rw-r-----. 1 zhangbin zhangbin 68K Aug 30 21:39 '50003327B_PHAGE_Staphy_CNPx_NC_031241(43).fasta' -rw-r-----. 1 zhangbin zhangbin 59K Aug 30 21:39 '40002844A_PHAGE_Staphy_vB_SauS_phi2_NC_028862(51).fasta' -rw-r-----. 1 zhangbin zhangbin 58K Aug 30 21:39 '10002115B_PHAGE_Staphy_2638A_NC_007051(9).fasta' -rw-r-----. 1 zhangbin zhangbin 58K Aug 30 21:39 '10002115A_PHAGE_Staphy_2638A_NC_007051(9).fasta' -rw-r-----. 1 zhangbin zhangbin 58K Aug 30 21:39 '50000089B_PHAGE_Staphy_SA7_NC_048658(15).fasta' -rw-r-----. 1 zhangbin zhangbin 58K Aug 30 21:39 '50000925_PHAGE_Staphy_SA7_NC_048658(15).fasta' -rw-r-----. 1 zhangbin zhangbin 58K Aug 30 21:39 '50002399_PHAGE_Staphy_SA7_NC_048658(15).fasta' -rw-r-----. 1 zhangbin zhangbin 58K Aug 30 21:39 '50003458A_PHAGE_Staphy_SA7_NC_048658(15).fasta' -rw-r-----. 1 zhangbin zhangbin 58K Aug 30 21:39 '50003458B_PHAGE_Staphy_SA7_NC_048658(15).fasta' -rw-r-----. 1 zhangbin zhangbin 58K Aug 30 21:39 '50001121_PHAGE_Staphy_SA7_NC_048658(15).fasta' -rw-r-----. 1 zhangbin zhangbin 58K Aug 30 21:39 '50001708A_PHAGE_Staphy_SA7_NC_048658(15).fasta' -rw-r-----. 1 zhangbin zhangbin 58K Aug 30 21:39 '50005521A_PHAGE_Staphy_SA7_NC_048658(15).fasta' -rw-r-----. 1 zhangbin zhangbin 58K Aug 30 21:39 '50006919_PHAGE_Staphy_SA7_NC_048658(15).fasta' -rw-r-----. 1 zhangbin zhangbin 58K Aug 30 21:39 '50005521B_PHAGE_Staphy_SA7_NC_048658(15).fasta' -rw-r-----. 1 zhangbin zhangbin 56K Aug 30 21:39 '50001943_PHAGE_Staphy_2638A_NC_007051(18).fasta' -rw-r-----. 1 zhangbin zhangbin 56K Aug 30 21:39 '50003349_PHAGE_Staphy_2638A_NC_007051(18).fasta' -rw-r-----. 1 zhangbin zhangbin 56K Aug 30 21:39 '50001801A_PHAGE_Staphy_2638A_NC_007051(18).fasta' -rw-r-----. 1 zhangbin zhangbin 56K Aug 30 21:39 '50001801B_PHAGE_Staphy_2638A_NC_007051(18).fasta' -rw-r-----. 1 zhangbin zhangbin 56K Aug 30 21:39 '50003674_PHAGE_Staphy_2638A_NC_007051(18).fasta' -rw-r-----. 1 zhangbin zhangbin 56K Aug 30 21:39 '40005021_PHAGE_Staphy_vB_SpsS_QT1_NC_048192(17).fasta' -rw-r-----. 1 zhangbin zhangbin 56K Aug 30 21:39 '40004097A_PHAGE_Staphy_2638A_NC_007051(17).fasta' -rw-r-----. 1 zhangbin zhangbin 56K Aug 30 21:39 '40004097B_PHAGE_Staphy_2638A_NC_007051(17).fasta' -rw-r-----. 1 zhangbin zhangbin 51K Aug 30 21:39 '10000467_PHAGE_Staphy_P1105_NC_048636(5).fasta' -rw-r-----. 1 zhangbin zhangbin 51K Aug 30 21:39 '40002212A_PHAGE_Staphy_EW_NC_007056(32).fasta' -rw-r-----. 1 zhangbin zhangbin 51K Aug 30 21:39 '40002212B_PHAGE_Staphy_EW_NC_007056(32).fasta' -rw-r-----. 1 zhangbin zhangbin 51K Aug 30 21:39 '40006071_PHAGE_Staphy_EW_NC_007056(32).fasta' -rw-r-----. 1 zhangbin zhangbin 51K Aug 30 21:39 '40006570A_PHAGE_Staphy_EW_NC_007056(32).fasta' -rw-r-----. 1 zhangbin zhangbin 51K Aug 30 21:39 '40006570B_PHAGE_Staphy_EW_NC_007056(32).fasta' -rw-r-----. 1 zhangbin zhangbin 50K Aug 30 21:39 '20000877A_PHAGE_Staphy_phiPV83_NC_002486(27).fasta' -rw-r-----. 1 zhangbin zhangbin 50K Aug 30 21:39 '20000877B_PHAGE_Staphy_phiPV83_NC_002486(27).fasta' -rw-r-----. 1 zhangbin zhangbin 50K Aug 30 21:39 '20001409A_PHAGE_Staphy_phiPV83_NC_002486(27).fasta' -rw-r-----. 1 zhangbin zhangbin 50K Aug 30 21:39 '20001409B_PHAGE_Staphy_phiPV83_NC_002486(27).fasta' -rw-r-----. 1 zhangbin zhangbin 48K Aug 30 21:39 '40005018_PHAGE_Staphy_StB20_NC_019915(28).fasta' -rw-r-----. 1 zhangbin zhangbin 48K Aug 30 21:39 '50000171_PHAGE_Staphy_vB_SpsS_QT1_NC_048192(19).fasta' -rw-r-----. 1 zhangbin zhangbin 48K Aug 30 21:39 '50000844_PHAGE_Staphy_vB_SpsS_QT1_NC_048192(19).fasta' -rw-r-----. 1 zhangbin zhangbin 48K Aug 30 21:39 '10003548A_PHAGE_Staphy_EW_NC_007056(12).fasta' -rw-r-----. 1 zhangbin zhangbin 46K Aug 30 21:39 '10003548B_PHAGE_Staphy_EW_NC_007056(18).fasta' -rw-r-----. 1 zhangbin zhangbin 46K Aug 30 21:39 '10002115B_PHAGE_Staphy_EW_NC_007056(14).fasta' -rw-r-----. 1 zhangbin zhangbin 46K Aug 30 21:39 '10002115A_PHAGE_Staphy_EW_NC_007056(14).fasta' -rw-r-----. 1 zhangbin zhangbin 45K Aug 30 21:39 '50002401_PHAGE_Staphy_AJ_2017_NC_048644(15).fasta' -rw-r-----. 1 zhangbin zhangbin 45K Aug 30 21:39 '50001123_PHAGE_Staphy_tp310_1_NC_009761(15).fasta' -rw-r-----. 1 zhangbin zhangbin 45K Aug 30 21:39 '50000449_PHAGE_Staphy_SA7_NC_048658(17).fasta' -rw-r-----. 1 zhangbin zhangbin 45K Aug 30 21:39 '50001533_PHAGE_Staphy_SA7_NC_048658(17).fasta' -rw-r-----. 1 zhangbin zhangbin 45K Aug 30 21:39 '40002212A_PHAGE_Staphy_AJ_2017_NC_048644(15).fasta' -rw-r-----. 1 zhangbin zhangbin 45K Aug 30 21:39 '40002212B_PHAGE_Staphy_AJ_2017_NC_048644(15).fasta' -rw-r-----. 1 zhangbin zhangbin 45K Aug 30 21:39 '30001473_PHAGE_Staphy_AJ_2017_NC_048644(15).fasta' -rw-r-----. 1 zhangbin zhangbin 45K Aug 30 21:39 '30003362B_PHAGE_Staphy_AJ_2017_NC_048644(15).fasta' -rw-r-----. 1 zhangbin zhangbin 45K Aug 30 21:39 '40006071_PHAGE_Staphy_AJ_2017_NC_048644(15).fasta' -rw-r-----. 1 zhangbin zhangbin 45K Aug 30 21:39 '40006570A_PHAGE_Staphy_AJ_2017_NC_048644(15).fasta' -rw-r-----. 1 zhangbin zhangbin 45K Aug 30 21:39 '40006570B_PHAGE_Staphy_AJ_2017_NC_048644(15).fasta' -rw-r-----. 1 zhangbin zhangbin 45K Aug 30 21:39 '30003362A_PHAGE_Staphy_AJ_2017_NC_048644(15).fasta' -rw-r-----. 1 zhangbin zhangbin 45K Aug 30 21:39 '50000788A_PHAGE_Staphy_EW_NC_007056(26).fasta' -rw-r-----. 1 zhangbin zhangbin 45K Aug 30 21:39 '50002248_PHAGE_Staphy_EW_NC_007056(26).fasta' -rw-r-----. 1 zhangbin zhangbin 44K Aug 30 21:39 '50000788A_PHAGE_Staphy_EW_NC_007056(16).fasta' -rw-r-----. 1 zhangbin zhangbin 44K Aug 30 21:39 '50002248_PHAGE_Staphy_EW_NC_007056(16).fasta' -rw-r-----. 1 zhangbin zhangbin 43K Aug 30 21:39 '50000366_PHAGE_Staphy_SA7_NC_048658(17).fasta' -rw-r-----. 1 zhangbin zhangbin 43K Aug 30 21:39 '50001520B_PHAGE_Staphy_SA7_NC_048658(17).fasta' -rw-r-----. 1 zhangbin zhangbin 42K Aug 30 21:39 '40002844A_PHAGE_Staphy_X2_NC_007065(20).fasta' -rw-r-----. 1 zhangbin zhangbin 41K Aug 30 21:39 '40002434B_PHAGE_Staphy_EW_NC_007056(11).fasta' -rw-r-----. 1 zhangbin zhangbin 40K Aug 30 21:39 '40000850_PHAGE_Staphy_AJ_2017_NC_048644(13).fasta' -rw-r-----. 1 zhangbin zhangbin 35K Aug 30 21:39 '10001261_PHAGE_Staphy_StB20_like_NC_028821(8).fasta' -rw-r-----. 1 zhangbin zhangbin 35K Aug 30 21:39 '40004558_PHAGE_Staphy_X2_NC_007065(18).fasta' -rw-r-----. 1 zhangbin zhangbin 34K Aug 30 21:39 '10001261_PHAGE_Staphy_StB20_NC_019915(23).fasta' -rw-r-----. 1 zhangbin zhangbin 34K Aug 30 21:39 '40004558_PHAGE_Staphy_vB_SauS_phi2_NC_028862(40).fasta' -rw-r-----. 1 zhangbin zhangbin 34K Aug 30 21:39 '10001261_PHAGE_Staphy_Ipla7_NC_018284(29).fasta' -rw-r-----. 1 zhangbin zhangbin 34K Aug 30 21:39 '40002844B_PHAGE_Staphy_X2_NC_007065(18).fasta' -rw-r-----. 1 zhangbin zhangbin 33K Aug 30 21:39 '40002844B_PHAGE_Staphy_vB_SauS_phi2_NC_028862(39).fasta' -rw-r-----. 1 zhangbin zhangbin 28K Aug 30 21:39 '50002118A_PHAGE_Staphy_vB_SauS_phi2_NC_028862(31).fasta' -rw-r-----. 1 zhangbin zhangbin 28K Aug 30 21:39 '50005684_PHAGE_Staphy_vB_SauS_phi2_NC_028862(28).fasta' -rw-r-----. 1 zhangbin zhangbin 27K Aug 30 21:39 '40003147A_PHAGE_Staphy_StB12_NC_020490(12).fasta' -rw-r-----. 1 zhangbin zhangbin 27K Aug 30 21:39 '50002221A_PHAGE_Staphy_Ipla88_NC_011614(20).fasta' -rw-r-----. 1 zhangbin zhangbin 27K Aug 30 21:39 '50002221B_PHAGE_Staphy_Ipla88_NC_011614(20).fasta' -rw-r-----. 1 zhangbin zhangbin 27K Aug 30 21:39 '50003869_PHAGE_Staphy_Ipla88_NC_011614(20).fasta' -rw-r-----. 1 zhangbin zhangbin 27K Aug 30 21:39 '50005684_PHAGE_Staphy_Ipla88_NC_011614(20).fasta' -rw-r-----. 1 zhangbin zhangbin 27K Aug 30 21:39 '50006538B_PHAGE_Staphy_Ipla88_NC_011614(20).fasta' -rw-r-----. 1 zhangbin zhangbin 27K Aug 30 21:39 '50002221A_PHAGE_Staphy_vB_SauS_phi2_NC_028862(27).fasta' -rw-r-----. 1 zhangbin zhangbin 27K Aug 30 21:39 '50002221B_PHAGE_Staphy_vB_SauS_phi2_NC_028862(27).fasta' -rw-r-----. 1 zhangbin zhangbin 27K Aug 30 21:39 '50003869_PHAGE_Staphy_vB_SauS_phi2_NC_028862(27).fasta' -rw-r-----. 1 zhangbin zhangbin 27K Aug 30 21:39 '50006538A_PHAGE_Staphy_vB_SauS_phi2_NC_028862(27).fasta' -rw-r-----. 1 zhangbin zhangbin 27K Aug 30 21:39 '50006538B_PHAGE_Staphy_vB_SauS_phi2_NC_028862(27).fasta' -rw-r-----. 1 zhangbin zhangbin 27K Aug 30 21:39 '50006538A_PHAGE_Staphy_Ipla88_NC_011614(20).fasta' -rw-r-----. 1 zhangbin zhangbin 26K Aug 30 21:39 '40003147A_PHAGE_Staphy_StB20_NC_019915(21).fasta' head -n 2 *.fasta: ==> 10000467_PHAGE_Staphy_P1105_NC_048636(5).fasta <==

PHAGE_Staphy_P1105_NC_048636(5) Contig_8_77.9353_pilon:7814-58888 ATAAATAAAAAAAGACAATTTCTATTGAAATAATATAGAAATTGTCTTTTTTTATTATTT

==> 10001261_PHAGE_Staphy_Ipla7_NC_018284(29).fasta <==

PHAGE_Staphy_Ipla7_NC_018284(29) Contig_5_63.7916_pilon:1-33214 AAAAAATATATTAGAGAAAGTCGTTATAAACCTACGATTGCACAAATCATTGATCGTAAA

==> 10001261_PHAGE_Staphy_StB20_like_NC_028821(8).fasta <==

PHAGE_Staphy_StB20_like_NC_028821(8) Contig_3_86.6431_Circ_pilon:1603-36063 AAAAAGAATTTAAATTAAAAACAATTTACTAAGTAATGAATCCGAACAAGTTATTAAAGG

==> 10001261_PHAGE_Staphy_StB20_NC_019915(23).fasta <==

PHAGE_Staphy_StB20_NC_019915(23) Contig_9_66.1651_pilon:1-33784 AAGAAATATGTTAGAGAAAGTCGTTATAAACCTACGATTGCACAAATTATTGATCGCAAA

==> 10002115A_PHAGE_Staphy_2638A_NC_007051(9).fasta <==

PHAGE_Staphy_2638A_NC_007051(9) Contig_13_28.0159_pilon:66437-124419 CCTTATTATTTTTGCGAACAGGCACGACCATCGCACTGTTAATTTCGTCAAGGCGATTTA

==> 10002115A_PHAGE_Staphy_EW_NC_007056(14).fasta <==

PHAGE_Staphy_EW_NC_007056(14) Contig_13_28.0159_pilon:162975-209003 ATGATTTATAAAGGAGGCTTTACTATGCAAGTTAACAAGCTCGCTTATGTATTATTAGCA

==> 10002115B_PHAGE_Staphy_2638A_NC_007051(9).fasta <==

PHAGE_Staphy_2638A_NC_007051(9) Contig_15_45.3195_pilon:872174-930156 CCTTATTATTTTTGCGAACAGGCACGACCATCGCACTGTTAATTTCGTCAAGGCGATTTA

==> 10002115B_PHAGE_Staphy_EW_NC_007056(14).fasta <==

PHAGE_Staphy_EW_NC_007056(14) Contig_15_45.3195_pilon:968712-1014740 ATGATTTATAAAGGAGGCTTTACTATGCAAGTTAACAAGCTCGCTTATGTATTATTAGCA

==> 10003548A_PHAGE_Staphy_EW_NC_007056(12).fasta <==

PHAGE_Staphy_EW_NC_007056(12) Contig_12_85.1395_pilon:886232-933711 TTAGCGGACTTTCTCAACCATTTCACTTTCTACTTTGTCCATTTCATCCTCAATTTCCAT

==> 10003548B_PHAGE_Staphy_EW_NC_007056(18).fasta <==

PHAGE_Staphy_EW_NC_007056(18) Contig_8_135.349_pilon:281306-327408 ATGGATCATTATAAAAACCCACGTAATAAAGGTGTTATCGAAGATGGTACGATGACTGTT

==> 20000877A_PHAGE_Staphy_phiPV83_NC_002486(27).fasta <==

PHAGE_Staphy_phiPV83_NC_002486(27) Contig_1_61.6377_pilon:128474-178485 TTAAAATTGTATAATTTGTGGTTGTTTGTGCATATGACGCTCATTATCTTTAAAATCCAT

==> 20000877B_PHAGE_Staphy_phiPV83_NC_002486(27).fasta <==

PHAGE_Staphy_phiPV83_NC_002486(27) Contig_4_120.675_pilon:128471-178482 TTAAAATTGTATAATTTGTGGTTGTTTGTGCATATGACGCTCATTATCTTTAAAATCCAT

==> 20001409A_PHAGE_Staphy_phiPV83_NC_002486(27).fasta <==

PHAGE_Staphy_phiPV83_NC_002486(27) Contig_1_31.7852_pilon:128474-178485 TTAAAATTGTATAATTTGTGGTTGTTTGTGCATATGACGCTCATTATCTTTAAAATCCAT

==> 20001409B_PHAGE_Staphy_phiPV83_NC_002486(27).fasta <==

PHAGE_Staphy_phiPV83_NC_002486(27) Contig_2_118.051_pilon:128474-178485 TTAAAATTGTATAATTTGTGGTTGTTTGTGCATATGACGCTCATTATCTTTAAAATCCAT

==> 30001473_PHAGE_Staphy_AJ_2017_NC_048644(15).fasta <==

PHAGE_Staphy_AJ_2017_NC_048644(15) Contig_4_74.8446_pilon:781625-826434 TCATGCGTGCGCCCCCTTCTCTATTTCACCATTGCGAACCGTGATAACACGATGAAAATG

==> 30003362A_PHAGE_Staphy_AJ_2017_NC_048644(15).fasta <==

PHAGE_Staphy_AJ_2017_NC_048644(15) Contig_3_35.599_pilon:781615-826424 TCATGCGTGCGCCCCCTTCTCTATTTCACCATTGCGAACCGTGATAACACGATGAAAATG

==> 30003362B_PHAGE_Staphy_AJ_2017_NC_048644(15).fasta <==

PHAGE_Staphy_AJ_2017_NC_048644(15) Contig_3_144.556_pilon:781625-826434 TCATGCGTGCGCCCCCTTCTCTATTTCACCATTGCGAACCGTGATAACACGATGAAAATG

==> 40000850_PHAGE_Staphy_AJ_2017_NC_048644(13).fasta <==

PHAGE_Staphy_AJ_2017_NC_048644(13) Contig_10_64.5453_pilon:46275-85572 ATCCCTCACTCTCCGTACTAAAACCTTGATATGACAGGGTTTGAGAGTAGCAAGTGTCAA

==> 40002212A_PHAGE_Staphy_AJ_2017_NC_048644(15).fasta <==

PHAGE_Staphy_AJ_2017_NC_048644(15) Contig_2_112.854_pilon:781560-826371 TCATGCGTGCGCCCCCTTCTCTATTTCACCATTGCGAACCGTGATAACACGATGAAAATG

==> 40002212A_PHAGE_Staphy_EW_NC_007056(32).fasta <==

PHAGE_Staphy_EW_NC_007056(32) Contig_2_112.854_pilon:958821-1009355 TACCCTTATTATATAAACACAAACATAACAAAAACGCATTTAGACCAATCGTTTTAAGAA

==> 40002212B_PHAGE_Staphy_AJ_2017_NC_048644(15).fasta <==

PHAGE_Staphy_AJ_2017_NC_048644(15) Contig_2_129.504_pilon:781626-826437 TCATGCGTGCGCCCCCTTCTCTATTTCACCATTGCGAACCGTGATAACACGATGAAAATG

==> 40002212B_PHAGE_Staphy_EW_NC_007056(32).fasta <==

PHAGE_Staphy_EW_NC_007056(32) Contig_2_129.504_pilon:958887-1009421 TACCCTTATTATATAAACACAAACATAACAAAAACGCATTTAGACCAATCGTTTTAAGAA

==> 40002434B_PHAGE_Staphy_EW_NC_007056(11).fasta <==

PHAGE_Staphy_EW_NC_007056(11) Contig_20_155.953_pilon:88817-129050 TTGATATGACGGGATTTCGGAGTAGCAAGTGTCAAATATGTGTCAAGAGAATAATTCTCT

==> 40002844A_PHAGE_Staphy_vB_SauS_phi2_NC_028862(51).fasta <==

PHAGE_Staphy_vB_SauS_phi2_NC_028862(51) Contig_4_50.014_pilon:232-59279 TTAGTTAGTTTTGCTTGCATTGTCGCCACCTCCATAATGATATTCGTTCACGTCAAAACC

==> 40002844A_PHAGE_Staphy_X2_NC_007065(20).fasta <==

PHAGE_Staphy_X2_NC_007065(20) Contig_20_60.0896_pilon:34723-76299 TATGATAAAAGGGAATAAGAAGCGTTTTTTACACAAAAAACTTTGAAAATGAGGTTGACG

==> 40002844B_PHAGE_Staphy_vB_SauS_phi2_NC_028862(39).fasta <==

PHAGE_Staphy_vB_SauS_phi2_NC_028862(39) Contig_9_98.9161_pilon:21-33160 ATGGCAGTATTAGAAGATATTTTTGAAGAATTAAAACTATTAAATAAGAATTTACGCGTG

==> 40002844B_PHAGE_Staphy_X2_NC_007065(18).fasta <==

PHAGE_Staphy_X2_NC_007065(18) Contig_10_123.265_pilon:17-33210 ATGAAGCAGACTGTAACTTATATCATTCGTCATAGGGATATGCCAATTTATATAACTAAC

==> 40003147A_PHAGE_Staphy_StB12_NC_020490(12).fasta <==

PHAGE_Staphy_StB12_NC_020490(12) Contig_43_159.351_pilon:3-26914 GGGAAAGCACAAAATACAAATGCAGCTGAAACGATAAAGAAATACGGTAAATTTCTAAAG

==> 40003147A_PHAGE_Staphy_StB20_NC_019915(21).fasta <==

PHAGE_Staphy_StB20_NC_019915(21) Contig_18_155.8_pilon:26-26060 ATGATTAAACGCATATTAAAGATTTGGTTCACTATCGCCATTTACGAGGTAGGTAAATGG

==> 40004097A_PHAGE_Staphy_2638A_NC_007051(17).fasta <==

PHAGE_Staphy_2638A_NC_007051(17) Contig_22_142.204_pilon:61819-117502 CCTTATTATTTTTGCGAACAGGCACGACCATCGCACTGTTAATTTCGTCAAGGCGATTTA

==> 40004097B_PHAGE_Staphy_2638A_NC_007051(17).fasta <==

PHAGE_Staphy_2638A_NC_007051(17) Contig_21_154.365_pilon:61819-117502 CCTTATTATTTTTGCGAACAGGCACGACCATCGCACTGTTAATTTCGTCAAGGCGATTTA

==> 40004558_PHAGE_Staphy_vB_SauS_phi2_NC_028862(40).fasta <==

PHAGE_Staphy_vB_SauS_phi2_NC_028862(40) Contig_23_64.9056_pilon:3-33401 GGCGAAATCATACGCAAAAATATTCATGTTAACGGATTCGATTTTAAGCTATTCATTTTA

==> 40004558_PHAGE_Staphy_X2_NC_007065(18).fasta <==

PHAGE_Staphy_X2_NC_007065(18) Contig_21_80.2649_pilon:8-34245 ATGACGCAGGAAGAAATAAAAGACTTATTATCTGAAAAAACCGCAGAATTATATGAATTA

==> 40005018_PHAGE_Staphy_StB20_NC_019915(28).fasta <==

PHAGE_Staphy_StB20_NC_019915(28) Contig_14_30.4186_pilon:76835-124742 TGCATTGATTTTAGGTGGTCTGGGCGTGCATAAATTTTATGCCGACCAAGTTGGACAAGG

==> 40005021_PHAGE_Staphy_vB_SpsS_QT1_NC_048192(17).fasta <==

PHAGE_Staphy_vB_SpsS_QT1_NC_048192(17) Contig_23_86.6284_pilon:61820-117503 CCTTATTATTTTTGCGAACAGGCACGACCATCGCACTGTTAATTTCGTCAAGGCGATTTA

==> 40006071_PHAGE_Staphy_AJ_2017_NC_048644(15).fasta <==

PHAGE_Staphy_AJ_2017_NC_048644(15) Contig_1_111.388_pilon:781625-826434 TCATGCGTGCGCCCCCTTCTCTATTTCACCATTGCGAACCGTGATAACACGATGAAAATG

==> 40006071_PHAGE_Staphy_EW_NC_007056(32).fasta <==

PHAGE_Staphy_EW_NC_007056(32) Contig_1_111.388_pilon:958884-1009418 TACCCTTATTATATAAACACAAACATAACAAAAACGCATTTAGACCAATCGTTTTAAGAA

==> 40006570A_PHAGE_Staphy_AJ_2017_NC_048644(15).fasta <==

PHAGE_Staphy_AJ_2017_NC_048644(15) Contig_3_112.481_pilon:781626-826435 TCATGCGTGCGCCCCCTTCTCTATTTCACCATTGCGAACCGTGATAACACGATGAAAATG

==> 40006570A_PHAGE_Staphy_EW_NC_007056(32).fasta <==

PHAGE_Staphy_EW_NC_007056(32) Contig_3_112.481_pilon:958885-1009419 TACCCTTATTATATAAACACAAACATAACAAAAACGCATTTAGACCAATCGTTTTAAGAA

==> 40006570B_PHAGE_Staphy_AJ_2017_NC_048644(15).fasta <==

PHAGE_Staphy_AJ_2017_NC_048644(15) Contig_3_124.453_pilon:781560-826369 TCATGCGTGCGCCCCCTTCTCTATTTCACCATTGCGAACCGTGATAACACGATGAAAATG

==> 40006570B_PHAGE_Staphy_EW_NC_007056(32).fasta <==

PHAGE_Staphy_EW_NC_007056(32) Contig_3_124.453_pilon:958819-1009353 TACCCTTATTATATAAACACAAACATAACAAAAACGCATTTAGACCAATCGTTTTAAGAA

==> 50000089B_PHAGE_Staphy_SA7_NC_048658(15).fasta <==

PHAGE_Staphy_SA7_NC_048658(15) Contig_8_89.3814_pilon:770844-828428 TCCTAAATATGGCTACCGTAACGGTGTAGGACGTCCTGAAGGAATCGTAGTGCATGATAC

==> 50000171_PHAGE_Staphy_vB_SpsS_QT1_NC_048192(19).fasta <==

PHAGE_Staphy_vB_SpsS_QT1_NC_048192(19) Contig_5_99.7331_pilon:26490-74071 CTCTATAAATAAAGCCCGACTACCGATAATCGAATAGTCGAGCGAGTGATTATTGAATAT

==> 50000366_PHAGE_Staphy_SA7_NC_048658(17).fasta <==

PHAGE_Staphy_SA7_NC_048658(17) Contig_11_60.9639_pilon:297072-339862 ATGGACCATTATAAAAATCCGAGAAACAAAGGTAAATTAGATAACGGCTCTTTAACTGTT

==> 50000449_PHAGE_Staphy_SA7_NC_048658(17).fasta <==

PHAGE_Staphy_SA7_NC_048658(17) Contig_2_35.4246_pilon:193059-238010 AAAATACTTTTAATAAAACAATCCCTCTAGGAGTAATACTGCACTTTAACGTTGGATATC

==> 50000788A_PHAGE_Staphy_EW_NC_007056(16).fasta <==

PHAGE_Staphy_EW_NC_007056(16) Contig_4_148.355_pilon:825489-869296 TTAGCTTTGATAGGTCATATAATGATAGGTGTGACCATACAACGTCTTTTTATTTGTCGG

==> 50000788A_PHAGE_Staphy_EW_NC_007056(26).fasta <==

PHAGE_Staphy_EW_NC_007056(26) Contig_4_148.355_pilon:50620-95060 CCTCACTCTCCGTTATTTTGAAAATATCTGTTAATATTTGAATAAGAAAAACCTTTAGAA

==> 50000844_PHAGE_Staphy_vB_SpsS_QT1_NC_048192(19).fasta <==

PHAGE_Staphy_vB_SpsS_QT1_NC_048192(19) Contig_9_56.5241_pilon:26492-74073 CTCTATAAATAAAGCCCGACTACCGATAATCGAATAGTCGAGCGAGTGATTATTGAATAT

==> 50000925_PHAGE_Staphy_SA7_NC_048658(15).fasta <==

PHAGE_Staphy_SA7_NC_048658(15) Contig_9_53.5598_pilon:770899-828483 TCCTAAATATGGCTACCGTAACGGTGTAGGACGTCCTGAAGGAATCGTAGTGCATGATAC

==> 50001121_PHAGE_Staphy_SA7_NC_048658(15).fasta <==

PHAGE_Staphy_SA7_NC_048658(15) Contig_7_24.752_pilon:770822-828406 TCCTAAATATGGCTACCGTAACGGTGTAGGACGTCCTGAAGGAATCGTAGTGCATGATAC

==> 50001123_PHAGE_Staphy_tp310_1_NC_009761(15).fasta <==

PHAGE_Staphy_tp310_1_NC_009761(15) Contig_10_124.29_pilon:389473-434460 ATGTTTGAACGATTAAAATCTATGATGGAAGCCCCCATGGATCTTTTATTGCTCGCAGAT

==> 50001520B_PHAGE_Staphy_SA7_NC_048658(17).fasta <==

PHAGE_Staphy_SA7_NC_048658(17) Contig_12_123.736_pilon:297072-339862 ATGGACCATTATAAAAATCCGAGAAACAAAGGTAAATTAGATAACGGCTCTTTAACTGTT

==> 50001533_PHAGE_Staphy_SA7_NC_048658(17).fasta <==

PHAGE_Staphy_SA7_NC_048658(17) Contig_2_44.1238_pilon:193059-238010 AAAATACTTTTAATAAAACAATCCCTCTAGGAGTAATACTGCACTTTAACGTTGGATATC

==> 50001708A_PHAGE_Staphy_SA7_NC_048658(15).fasta <==

PHAGE_Staphy_SA7_NC_048658(15) Contig_7_57.236_pilon:770823-828407 TCCTAAATATGGCTACCGTAACGGTGTAGGACGTCCTGAAGGAATCGTAGTGCATGATAC

==> 50001801A_PHAGE_Staphy_2638A_NC_007051(18).fasta <==

PHAGE_Staphy_2638A_NC_007051(18) Contig_8_95.3289_pilon:269620-325635 TTGTATCGTTCAGTGATTATGGATCATTATAAAAACCCACGGAATAAAGGTGTTATCGAA

==> 50001801B_PHAGE_Staphy_2638A_NC_007051(18).fasta <==

PHAGE_Staphy_2638A_NC_007051(18) Contig_8_95.3289_pilon:269620-325635 TTGTATCGTTCAGTGATTATGGATCATTATAAAAACCCACGGAATAAAGGTGTTATCGAA

==> 50001943_PHAGE_Staphy_2638A_NC_007051(18).fasta <==

PHAGE_Staphy_2638A_NC_007051(18) Contig_16_85.3673_pilon:269590-325605 TTGTATCGTTCAGTGATTATGGATCATTATAAAAACCCACGGAATAAAGGTGTTATCGAA

==> 50002118A_PHAGE_Staphy_vB_SauS_phi2_NC_028862(31).fasta <==

PHAGE_Staphy_vB_SauS_phi2_NC_028862(31) Contig_20_131.452_pilon:2-28027 ATCGTGCCAGGTTGGCAAGGCGTGAAAAAGACATTTGATACAGCGGAAGAGCTCGAAATA

==> 50002216A_PHAGE_Staphy_CNPx_NC_031241(43).fasta <==

PHAGE_Staphy_CNPx_NC_031241(43) Contig_14_149.133_pilon:74947-142660 TAAAAAAATGTTTACAAAAGCGAAATGGAATTCTGATGAAAAATAACGTATAATTTACTA

==> 50002221A_PHAGE_Staphy_Ipla88_NC_011614(20).fasta <==

PHAGE_Staphy_Ipla88_NC_011614(20) Contig_31_25.6645_pilon:1-26906 TTAGTCACAACATTCAAAGATTCAACAGGACGACCACATGAACATATTACTGTGGCTAGA

==> 50002221A_PHAGE_Staphy_vB_SauS_phi2_NC_028862(27).fasta <==

PHAGE_Staphy_vB_SauS_phi2_NC_028862(27) Contig_30_26.0283_pilon:1-26389 TTAGTCACAACATTCAAAGATTCAACAGGACGACCACATGAACATATTACTGTGGCTAGA

==> 50002221B_PHAGE_Staphy_Ipla88_NC_011614(20).fasta <==

PHAGE_Staphy_Ipla88_NC_011614(20) Contig_26_142.329_pilon:1-26906 TTAGTCACAACATTCAAAGATTCAACAGGACGACCACATGAACATATTACTGTGGCTAGA

==> 50002221B_PHAGE_Staphy_vB_SauS_phi2_NC_028862(27).fasta <==

PHAGE_Staphy_vB_SauS_phi2_NC_028862(27) Contig_25_147.666_pilon:1-26389 TTAGTCACAACATTCAAAGATTCAACAGGACGACCACATGAACATATTACTGTGGCTAGA

==> 50002248_PHAGE_Staphy_EW_NC_007056(16).fasta <==

PHAGE_Staphy_EW_NC_007056(16) Contig_6_66.4806_pilon:799458-843265 TTAGCTTTGATAGGTCATATAATGATAGGTGTGACCATACAACGTCTTTTTATTTGTCGG

==> 50002248_PHAGE_Staphy_EW_NC_007056(26).fasta <==

PHAGE_Staphy_EW_NC_007056(26) Contig_6_66.4806_pilon:24589-69029 CCTCACTCTCCGTTATTTTGAAAATATCTGTTAATATTTGAATAAGAAAAACCTTTAGAA

==> 50002399_PHAGE_Staphy_SA7_NC_048658(15).fasta <==

PHAGE_Staphy_SA7_NC_048658(15) Contig_5_47.3764_pilon:770822-828406 TCCTAAATATGGCTACCGTAACGGTGTAGGACGTCCTGAAGGAATCGTAGTGCATGATAC

==> 50002401_PHAGE_Staphy_AJ_2017_NC_048644(15).fasta <==

PHAGE_Staphy_AJ_2017_NC_048644(15) Contig_10_141.646_pilon:389473-434460 ATGTTTGAACGATTAAAATCTATGATGGAAGCCCCCATGGATCTTTTATTGCTCGCAGAT

==> 50003327B_PHAGE_Staphy_CNPx_NC_031241(43).fasta <==

PHAGE_Staphy_CNPx_NC_031241(43) Contig_15_133.435_pilon:74948-142638 TAAAAAAATGTTTACAAAAGCGAAATGGAATTCTGATGAAAAATAACGTATAATTTACTA

==> 50003349_PHAGE_Staphy_2638A_NC_007051(18).fasta <==

PHAGE_Staphy_2638A_NC_007051(18) Contig_16_52.2592_pilon:269672-325687 TTGTATCGTTCAGTGATTATGGATCATTATAAAAACCCACGGAATAAAGGTGTTATCGAA

==> 50003458A_PHAGE_Staphy_SA7_NC_048658(15).fasta <==

PHAGE_Staphy_SA7_NC_048658(15) Contig_3_36.0362_pilon:770823-828407 TCCTAAATATGGCTACCGTAACGGTGTAGGACGTCCTGAAGGAATCGTAGTGCATGATAC

==> 50003458B_PHAGE_Staphy_SA7_NC_048658(15).fasta <==

PHAGE_Staphy_SA7_NC_048658(15) Contig_5_119.211_pilon:770823-828407 TCCTAAATATGGCTACCGTAACGGTGTAGGACGTCCTGAAGGAATCGTAGTGCATGATAC

==> 50003674_PHAGE_Staphy_2638A_NC_007051(18).fasta <==

PHAGE_Staphy_2638A_NC_007051(18) Contig_9_190.794_pilon:269620-325635 TTGTATCGTTCAGTGATTATGGATCATTATAAAAACCCACGGAATAAAGGTGTTATCGAA

==> 50003869_PHAGE_Staphy_Ipla88_NC_011614(20).fasta <==

PHAGE_Staphy_Ipla88_NC_011614(20) Contig_27_94.3363_pilon:1-26906 TTAGTCACAACATTCAAAGATTCAACAGGACGACCACATGAACATATTACTGTGGCTAGA

==> 50003869_PHAGE_Staphy_vB_SauS_phi2_NC_028862(27).fasta <==

PHAGE_Staphy_vB_SauS_phi2_NC_028862(27) Contig_26_92.9198_pilon:1-26389 TTAGTCACAACATTCAAAGATTCAACAGGACGACCACATGAACATATTACTGTGGCTAGA

==> 50005521A_PHAGE_Staphy_SA7_NC_048658(15).fasta <==

PHAGE_Staphy_SA7_NC_048658(15) Contig_7_109.766_pilon:770820-828403 TCCTAAATATGGCTACCGTAACGGTGTAGGACGTCCTGAAGGAATCGTAGTGCATGATAC

==> 50005521B_PHAGE_Staphy_SA7_NC_048658(15).fasta <==

PHAGE_Staphy_SA7_NC_048658(15) Contig_8_115.21_pilon:770820-828403 TCCTAAATATGGCTACCGTAACGGTGTAGGACGTCCTGAAGGAATCGTAGTGCATGATAC

==> 50005684_PHAGE_Staphy_Ipla88_NC_011614(20).fasta <==

PHAGE_Staphy_Ipla88_NC_011614(20) Contig_29_45.0416_pilon:1-26906 TTAGTCACAACATTCAAAGATTCAACAGGACGACCACATGAACATATTACTGTGGCTAGA

==> 50005684_PHAGE_Staphy_vB_SauS_phi2_NC_028862(28).fasta <==

PHAGE_Staphy_vB_SauS_phi2_NC_028862(28) Contig_28_50.7379_pilon:1-27855 TTAGTCACAACATTCAAAGATTCAACAGGACGACCACATGAACATATTACTGTGGCTAGA

==> 50006538A_PHAGE_Staphy_Ipla88_NC_011614(20).fasta <==

PHAGE_Staphy_Ipla88_NC_011614(20) Contig_40_111.321_pilon:1-26257 TTAGTCACAACATTCAAAGATTCAACAGGACGACCACATGAACATATTACTGTGGCTAGA

==> 50006538A_PHAGE_Staphy_vB_SauS_phi2_NC_028862(27).fasta <==

PHAGE_Staphy_vB_SauS_phi2_NC_028862(27) Contig_39_117.232_pilon:1-26389 TTAGTCACAACATTCAAAGATTCAACAGGACGACCACATGAACATATTACTGTGGCTAGA

==> 50006538B_PHAGE_Staphy_Ipla88_NC_011614(20).fasta <==

PHAGE_Staphy_Ipla88_NC_011614(20) Contig_30_129.568_pilon:1-26906 TTAGTCACAACATTCAAAGATTCAACAGGACGACCACATGAACATATTACTGTGGCTAGA

==> 50006538B_PHAGE_Staphy_vB_SauS_phi2_NC_028862(27).fasta <==

PHAGE_Staphy_vB_SauS_phi2_NC_028862(27) Contig_29_126.84_pilon:1-26389 TTAGTCACAACATTCAAAGATTCAACAGGACGACCACATGAACATATTACTGTGGCTAGA

==> 50006919_PHAGE_Staphy_SA7_NC_048658(15).fasta <==

PHAGE_Staphy_SA7_NC_048658(15) Contig_9_185.164_pilon:770820-828403 TCCTAAATATGGCTACCGTAACGGTGTAGGACGTCCTGAAGGAATCGTAGTGCATGATAC

lskatz commented 1 week ago

You might be running into an issue that ( and ) are reserved characters in the newick format. Could you rename your files to remove those characters?