========= Execution of SEPP failed with exit code 1 ================= temporary working directories are NOT deleted for further inspection: $tmp = /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tmp-T4enK $tmpssd = /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3 --------- Content of STDOUT ----------------------------------------- --------- Content of STDERR ----------------------------------------- [08:35:36] config.py (line 272): DEBUG: Main configuration file at /data/users/nscales/miniconda3/envs/qiime2-2019.1/share/fragment-insertion/sepp/.sepp/main.config [08:35:36] config.py (line 303): INFO: Seed number: 297834 [08:35:36] algorithm.py (line 231): INFO: Reading input alignment: <_io.TextIOWrapper name='/scratch/6534112.1.mic/qiime2-archive-rnx1clux/b199d679-1701-4100-a352-21e0e74790ec/data/aligned-dna-sequences.fasta' mode='r' encoding='ISO-8859-15'> [08:35:36] algorithm.py (line 237): INFO: Reading input tree: <_io.TextIOWrapper name='/scratch/6534112.1.mic/qiime2-archive-p301d7jr/333eb21f-35bf-41c3-aaa8-f70d5645c0a0/data/tree.nwk' mode='r' encoding='ISO-8859-15'> [08:35:36] algorithm.py (line 212): WARNING: Input placement size larger than total number of sequences! Setting placement size to 65 [08:35:36] algorithm.py (line 215): WARNING: Input alignment size larger than total number of sequences! Setting alignment size to 65 [08:35:36] algorithm.py (line 218): INFO: Decomposition Sizes are set to alignment: 65 placement: 65 [08:35:36] exhaustive.py (line 313): INFO: Breaking into 1 placement subsets. [08:35:36] exhaustive.py (line 321): DEBUG: Placement subset P_0 has 65 nodes [08:35:36] exhaustive.py (line 336): DEBUG: Placement subset P_0 has 1 alignment subsets: [0] [08:35:36] exhaustive.py (line 337): DEBUG: Placement subset P_0 has 65 taxa: [08:35:36] exhaustive.py (line 346): INFO: Breaking into 1 alignment subsets. [08:35:36] algorithm.py (line 246): DEBUG: start reading fragment files and breaking to at least 1 chunks but at most 20000 sequences [08:35:36] filemgr.py (line 114): INFO: Root temp directory built: /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc [08:35:36] alignment.py (line 195): DEBUG: Writing alignment of type with length 10820 to file /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/fragment_chunks/fragment_chunk_0yocyaheb.fasta [08:35:36] algorithm.py (line 272): DEBUG: fragment files read and divided. [08:35:36] exhaustive.py (line 359): INFO: Breaking each alignment subset into 1 fragment chunks. [08:35:36] exhaustive.py (line 360): DEBUG: Subproblem structure: (((FC_0_0_0)A_0_0)P_0)root [08:35:36] alignment.py (line 333): DEBUG: Alignment length reduced to 1623 [08:35:36] alignment.py (line 195): DEBUG: Writing alignment of type with length 65 to file /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/hmmbuild.input.xsgfob5_.fasta [08:35:36] problem.py (line 207): DEBUG: subalignment without allgap columns written to /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/hmmbuild.input.xsgfob5_.fasta; 1623 columns remaining. [08:35:36] jobs.py (line 353): DEBUG: HmmSearch: Piped?: False and keep on temp?: True [08:35:36] jobs.py (line 75): DEBUG: Starting hmmbuild Job with input: /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/hmmbuild.input.xsgfob5_.fasta [08:35:36] jobs.py (line 250): DEBUG: Running HMMBUILD command: /data/users/nscales/miniconda3/envs/qiime2-2019.1/share/fragment-insertion/sepp/.sepp/bundled-v4.3.5/hmmbuild --ere 0.59 --cpu 1 --dna --symfrac 0.0 --informat afa /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/hmmbuild.model.pflri0rd /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/hmmbuild.input.xsgfob5_.fasta [08:35:36] jobs.py (line 250): DEBUG: Running HMMBUILD command: /data/users/nscales/miniconda3/envs/qiime2-2019.1/share/fragment-insertion/sepp/.sepp/bundled-v4.3.5/hmmbuild --ere 0.59 --cpu 1 --dna --symfrac 0.0 --informat afa /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/hmmbuild.model.pflri0rd /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/hmmbuild.input.xsgfob5_.fasta [08:35:36] jobs.py (line 250): DEBUG: Running HMMBUILD command: /data/users/nscales/miniconda3/envs/qiime2-2019.1/share/fragment-insertion/sepp/.sepp/bundled-v4.3.5/hmmbuild --ere 0.59 --cpu 1 --dna --symfrac 0.0 --informat afa /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/hmmbuild.model.pflri0rd /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/hmmbuild.input.xsgfob5_.fasta [08:35:36] jobs.py (line 97): DEBUG: Invocation of /data/users/nscales/miniconda3/envs/qiime2-2019.1/share/fragment-insertion/sepp/.sepp/bundled-v4.3.5/hmmbuild --ere 0.59 --cpu 1 --dna --symfrac 0.0 --informat afa /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/hmmbuild.model.pflri0rd /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/hmmbuild.input.xsgfob5_.fasta [08:35:36] jobs.py (line 250): DEBUG: Running HMMBUILD command: /data/users/nscales/miniconda3/envs/qiime2-2019.1/share/fragment-insertion/sepp/.sepp/bundled-v4.3.5/hmmbuild --ere 0.59 --cpu 1 --dna --symfrac 0.0 --informat afa /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/hmmbuild.model.pflri0rd /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/hmmbuild.input.xsgfob5_.fasta [08:35:37] jobs.py (line 117): INFO: Finished hmmbuild Job with input: /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/hmmbuild.input.xsgfob5_.fasta [08:35:37] jobs.py (line 122): DEBUG: Finished hmmbuild Job with input: /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/hmmbuild.input.xsgfob5_.fasta with: return code: 0 output: # hmmbuild :: profile HMM construction from multiple sequence alignments # HMMER 3.1b2 (February 201 ... (continued: 1179 ) ... [08:35:37] jobs.py (line 75): DEBUG: Starting hmmsearch Job with input: model:/scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/hmmbuild.model.pflri0rd, fragments:/scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/fragment_chunks/fragment_chunk_0yocyaheb.fasta, elim:99999999, filter:False, output:/scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/FC_0_0_0/hmmsearch.results.6_fzgt5h [08:35:37] jobs.py (line 97): DEBUG: Invocation of /data/users/nscales/miniconda3/envs/qiime2-2019.1/share/fragment-insertion/sepp/.sepp/bundled-v4.3.5/hmmsearch --noali --cpu 1 -o /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/FC_0_0_0/hmmsearch.results.6_fzgt5h -E 99999999 --max /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/hmmbuild.model.pflri0rd /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/fragment_chunks/fragment_chunk_0yocyaheb.fasta [08:37:12] jobs.py (line 117): INFO: Finished hmmsearch Job with input: model:/scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/hmmbuild.model.pflri0rd, fragments:/scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/fragment_chunks/fragment_chunk_0yocyaheb.fasta, elim:99999999, filter:False, output:/scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/FC_0_0_0/hmmsearch.results.6_fzgt5h [08:37:12] jobs.py (line 122): DEBUG: Finished hmmsearch Job with input: model:/scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/hmmbuild.model.pflri0rd, fragments:/scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/fragment_chunks/fragment_chunk_0yocyaheb.fasta, elim:99999999, filter:False, output:/scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/FC_0_0_0/hmmsearch.results.6_fzgt5h with: return code: 0 output: [08:37:12] exhaustive.py (line 72): WARNING: Fragments ['38c93b6cfe768997b24607a70e2c60da', 'a45a6dbcb908636222f165d6c5fa5380', '49217afcadfb38e3a449fda04e999917', 'dfe6a508119ecfbb4d86d6cbda325490', '7ec0fe3bb0be08dd173929fbef565a24', '3f723c02306ffd32a6c78b44865cbe75', '129985799e519a70447085517127b6c8', 'dd2e777622de03665d0873fa0646bc16', '9588a08d7d0879d1f05a2962bbdb46f2', 'f043748d17f6b8a0e2063819fc23ca7f', 'c96d10e52a7d2f6d11e8a52db57bbcff', 'a1035ebbbf3afb7ba4f1a8a68d8039ea', '0e4267287a0262c4d018ca39d3fcb2c2', '5a986773c05d7a7b5cc15cbc294993a4', '9f0d12bd1e843802b97ae696a7fd576d', '91ba3ad2c428956e6a58d90c47d3151e', 'ccc907d4264812618ede733d083b70ae', 'f4f5a690da4cde272f6c757b026da16a', 'ca174962f9340544b1c0679021b6e206', '818e9ce590b7028fa5e2b19af7615de9', '5c2c4537ecfa7b5cf40e1cc4d54592e3', 'f4df71c071c8bb75812aa5e2231754c1', 'bd5584b5b65d5dc45a2a60228d26dc85', 'ca9912e63a8be97dc1ca72d6ce977131', '363ade1212e0cd1d58ea44ec9974a4de', '175dce4b2abade42f6793503a106ce2e', '43b5b052fc8aadad28ee4d5510c8c0e8', '8819ada4b6ffe1cad02fb715bff94199', '71ab8162f061d228412adbb0b0e190aa', 'b8388dad240cfbcedf77e1f81ce02828', '4d62f9aed2a8220f8b7aaecb5d8a8ce0', '672a18a90116465146854b9833969469', '13471862ada3b4bdafe66e23379555fa', 'de3cb70f6d35a19802078da5d7b57c4d', '23e168799b311fb9de3c311d64af679f', '13333ded586d7231b9393e9cc2d7ea76', 'b546caa05f613ac485e0b0e537de72b5', 'e9e9d198eedfab348641e02a2868fbae', 'bddba4dbd25f316fdabf47a836584404', '2c1b1259aa5362fa92649e3f6decec84', 'c6077e934073f9142f2c63b58327cd59', 'd86c81c1de05ddee034691e3ba961495', 'dfe67b16b6b3d4d3aa3fdcb3132edaae', '70b59ef18f8233cb3736415c6039c091', 'b906e25f750a36ba0e29c3f23baf9304', 'f82170f2800f24c3cc3554546a6d2ccc', '6db439294e70f188e52013f6da9b7554', '879bea636612a483d9f30f6100603d5e', '7c06150d19163c802d5c6dbf8b3aea3d', '3984e9b96b9dfd532dd1ca081ea15ff3', '64256e00969d97d05380ff541fae4150', '74a6e4151818c7245d4efb94938efce8', 'd476678e64c6599e7dd2c5049cac7b9a', '017081949d6860e40fd1ce225a328f74', '4c3b46a812af7e5c25cf014a3ac5b096', 'f229f3a3a7d3ef7b15a2ddbf47908ab2', 'c16da7eddb7d5e2209ad3d168d3dbcd6', 'd4777c93a9cf2c3e4eb319acb4874ad4', 'e26cec55dde1fe83c74c05c01ba1c967', 'a7b6e88fd1818970325ce5f8080a7154', '8089e69eef7e19d7cf874bed699b494d', '4663956cfc8039412f918c3bf7253dca', 'e26b5b245c95a3a1212b57556ea8b2fe', 'ef94808f268a80c9e1e9df35772db838', '2b3efdbce0d8b1a0b9efb74604da5a9f', '9971d9759eb3d73a665fcebb31f95ef6', '06d9438b5c368a3a47bf205e24c58aba', '724b8b8e2b352b510779f061525cbf83', 'c9e152c005a365a0ba966cba4c092599', 'd1c597decc196e14a87ea67533ab8400', 'b80efb3cef5965b6d16c4f1f9a7edec8', '97b68f18612c1e0ebd5114bd4b2ea559', 'ac96bcd2d92c96dc1cf8a5ab3f017716', '1768a06b94cbf19a6956eee06dbcaeb6', '154b184ac1774b0485b65a7dcb224a21', 'aceb0c39c5e491f4f3e0090e2514e78d', '14c90d0a4053857f2e5085b00735fbce', 'bd5a25ad93a68758b0783f15597ee626', '073167b6dba67e0656a50f5a301c4de6', '96e2e2ddb0c3697c3d59b8f65207ca3a', '5b37b85ebf0d205f4010ccea834e590b', '712104a422ba4baa74b973b1766703e8', '9413c635ac5f3e3b7b1c9640949cac90', '783d70d0c9487cb32d10f3a70459bc1a', 'bf5fe982d79591ec98a8bec0f393bf01', 'f5daf470a84a0693526c5697e68064c8', 'f60dcc4d01073bcb8839aa1df9b81901', '9865cb500491ed6dec3ac0e4ada2d0ee', '7ea2e17259296ca51f758c25476f4ebe', '6bebdc33eac4f6207f3152ccbf6b892b', '1b35bd0f313c5edbaeeda85fc0b734fd', 'f4be5cc0f7983a409880735264f187e3', '9aaadb1282ead7b7d5c60788a84d4721', 'ca1723592adca84fa63b60e871ba3f89', 'ee71508f0baa2b6c60f3302cb5a5136b', 'c1a18223b665816bc6b723a58256d25f', '4f6e6e481297362844e7f28c92e2042a', 'a88fb5a9d51b032ad674793d83ca0959', '1f0b819a486832c999cbd8556e6b215c', '255da8672944ce7652bad0206ccc2917', '5f5d6818be42f84daccf67643a2bc738', '30148d793037c63be07300cd7d26b94a', 'cfd6b7dcb0a4874626e324e1b9608ba6', 'c89880fd20a182b194cd680f1319c725', '9e7430e5514c6b4c4e99be50d96386c6', 'e713399829e859763c9bee7cf78dca6d', '6f209e7162684169970796c4244845cd', 'e4196db539a2097204837a0e042c263d', '1ffe1bd63fcfd64167435e8133596551', '0731952ef55c2e2fe158ffa17ad07a82', 'fc6551168799b246e6390a8c09c486a4', '8d27774014c660e1b2cb072b56c8e983', '06c056daf7c2aba3c847b0ead3c318a8', '3a362634ac1276d77603db47b0307cb6', '1a771eb4364d8a051ca5b5c831a8abda', 'a107008314e43f7e132482039d50754f', '31888993d4aea2467a295b1aeac198a1', '77a4478f2e980ee9f261074f4242157f', 'b469156cf7eea2d892a9998cceda3fa3', '33c51ad23de65d05aa8d7ce66c86bd7c', '24a5dd98d18f87956c373f3944451d1c', '44f8d6fb381813e4ff2b5c76cf63a3d6', '4c6736bb1c83d26b1851c6b547eb0a59', '83d87b16349c90e4b924446c91e78e81', '80bc05c680c10d5f53e8873e85bf3d03', '6407a058b0b9cb18fa0bbbfbd55a2ff5', '6ada78c78e1c5bdf1c080b7688a4ffdb', '6ce5c9a647c73a20e8b64131805c01a3', '5a65d9b479d556509e11f588405844c9', '0af7f1991b549feb7e04bcc62c4a6495', '47b0323f503fda3d0e3895d64df0dc56', 'fe3db5fcd9b3f7aca527396323b69ff2', '85fdc70a3355cdd1fc051b3f34d106cf', '9e9bec385ec2b1dccce5606531798d09', '652b937d987581f44901c59780c9c377', '625d7f40949d8068306890bbe62cfa79', '123c2ab385748b4ccb0b87e418920893', 'dc545ab14080b058d3535797c9fce64d', '74b82b5b91cbc7abef7e22f658bc1baa', '4f3f1a79cbe15f92ad1ab5aa0d83aafe', 'e367792cfce57f5a11df81b595c551f5', 'bf13b61ee58add09cc98795ce126a72a', 'ed37de9ad0fb0ad9e41f000ebf2f4f14', '940848716ee7684a028d26b33bea26d0', 'f82581b30b3a39f3bc2a5c1d66a6e64c', 'ae3dbc8f101c48086c1acdbb30fee2e2', '11737a22b8b634a72273b58e9070e53d', '2d1edc1cb4afae136320fa7c8960ebb9', '17349c38f1927d0b841225b93f7e0685', '91b13d0c11da908a0ccf5f4c041e6078', '069b39fcbe582c8f0126b91594303372', 'f1e672b42a4c5c322f4fde09a190deaf', 'e97f8ea13776fd2e88f239a43651d8d3', '5787453fe6933957d47893a4f253e39a', '6ae8fc92f691071d2f9f9f5f34448cc3', 'cac79cc721fe0e35e7d12a7c0d281359', 'b2cef5fbffb26aa3ba327c7edcecab3e', '05c619d694728aaf38d76de333fa7287', '471b1628c8a15b9701430247a20edf7b', '0b04ab69a613e3a6c7d4e3f1fe2f19e6', 'be82e11f309e147814adafdee87befe7', 'c02e4603ff736feefae6640aa620990a', '04fe6fb1691cf36bc3ae2124d0634c66', 'c59751650d049e2aa75e39a5cf646107', '98c51e1dfa192d0d68bf4ea06d4ee843', '0d9f6214ab7960cc23406e221c7e5361', '80baaa6465f77e31c2c02f5b820ea6f5', 'd7ba41bd15f3cc425f762e19abb9518c', 'bf42f4f1dbab1f36e633242eb65934a4', '32f8ad8ae51ea26f7973074ad9a3c104', '156a62516be0e31d0afa7e2b7925245f', 'a858bb5b551546a08fd858e3c980dfa2', '7ad9e941f81370e4c742e4d02923cbf9', 'f55c17a57cdf42c3b494bc0e078483ac', 'a9dbb1dbc28256cb9d75a81ee8a45825', 'd5c52b20a27525b3347f318a787d9337', '6840f83accc95bddabb136d91321122f', '26d8b748dd4a72773eff376d55620a70', '15b50ea9457b19393bc1f6d23079b38e', '7a23b84acc681c5cd9ab3d97e2e104d5'] are not scored against any subset [08:37:12] alignment.py (line 195): DEBUG: Writing alignment of type with length 10640 to file /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/FC_0_0_0/hmmalign.frag.e5e0pgq6.fasta [08:37:12] jobs.py (line 75): DEBUG: Starting hmmalign Job with input: model:/scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/hmmbuild.model.pflri0rd, fragments:/scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/FC_0_0_0/hmmalign.frag.e5e0pgq6.fasta, trim:False, base_alignment:/scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/hmmbuild.input.xsgfob5_.fasta [08:37:12] jobs.py (line 97): DEBUG: Invocation of /data/users/nscales/miniconda3/envs/qiime2-2019.1/share/fragment-insertion/sepp/.sepp/bundled-v4.3.5/hmmalign --dna -o /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/FC_0_0_0/hmmalign.results.aea7ufwz /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/hmmbuild.model.pflri0rd /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/FC_0_0_0/hmmalign.frag.e5e0pgq6.fasta [08:38:06] jobs.py (line 117): INFO: Finished hmmalign Job with input: model:/scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/hmmbuild.model.pflri0rd, fragments:/scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/FC_0_0_0/hmmalign.frag.e5e0pgq6.fasta, trim:False, base_alignment:/scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/hmmbuild.input.xsgfob5_.fasta [08:38:06] jobs.py (line 122): DEBUG: Finished hmmalign Job with input: model:/scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/hmmbuild.model.pflri0rd, fragments:/scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/FC_0_0_0/hmmalign.frag.e5e0pgq6.fasta, trim:False, base_alignment:/scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/hmmbuild.input.xsgfob5_.fasta with: return code: 0 output: [08:38:06] exhaustive.py (line 134): INFO: Merging sub-alignments for placement problem : P_0. [08:38:06] problem.py (line 223): DEBUG: Reading /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/hmmbuild.input.xsgfob5_.fasta ['/scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/FC_0_0_0/hmmalign.results.aea7ufwz'] and relabeling it based on 1623 orig column labels. [08:38:06] alignment.py (line 519): DEBUG: Reading base alignment: /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/hmmbuild.input.xsgfob5_.fasta. [08:38:06] alignment.py (line 529): DEBUG: Reading sto extended alignment: /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/FC_0_0_0/hmmalign.results.aea7ufwz. [08:38:10] alignment.py (line 549): DEBUG: /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/FC_0_0_0/hmmalign.results.aea7ufwz insertions: 15584 [08:38:10] alignment.py (line 532): INFO: Merging extension sto file (/scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/FC_0_0_0/hmmalign.results.aea7ufwz) into base alignment (/scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/hmmbuild.input.xsgfob5_.fasta). [08:38:10] alignment.py (line 685): DEBUG: Merging started ... [08:38:11] alignment.py (line 780): DEBUG: Merging finished ... [08:38:11] alignment.py (line 534): DEBUG: Finished merging extension sto file (/scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/FC_0_0_0/hmmalign.results.aea7ufwz) into base alignment (/scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/A_0_0/hmmbuild.input.xsgfob5_.fasta). [08:38:11] alignment.py (line 585): DEBUG: Relabeling 17207 (17207) with 1623 labels. [08:38:11] exhaustive.py (line 163): DEBUG: Merging alignment subset into placement subset for chunk 0: A_0_0. [08:38:11] alignment.py (line 685): DEBUG: Merging started ... [08:38:11] alignment.py (line 780): DEBUG: Merging finished ... [08:38:11] alignment.py (line 195): DEBUG: Writing alignment of type with length 10640 to file /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/pplacer.extended.0.q35kv891.fasta [08:38:11] alignment.py (line 195): DEBUG: Writing alignment of type with length 65 to file /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/pplacer.backbone.icku9u8i.fasta [08:38:12] jobs.py (line 75): DEBUG: Starting pplacer Job with input: backbone_alignment_file:/scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/pplacer.backbone.icku9u8i.fasta, tree_file:/scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/pplacer.tree.ld_yvhoc.tre, info_file:/data/users/nscales/miniconda3/envs/qiime2-2019.1/share/fragment-insertion//ref/RAxML_info-reference-gg-raxml-bl.info, extended alignment:/scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/pplacer.extended.0.q35kv891.fasta, output:/scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/pplacer.extended.0.q35kv891.jplace [08:38:12] jobs.py (line 97): DEBUG: Invocation of /data/users/nscales/miniconda3/envs/qiime2-2019.1/share/fragment-insertion/sepp/.sepp/bundled-v4.3.5/pplacer --out-dir /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0 -j 1 -r /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/pplacer.backbone.icku9u8i.fasta -s /data/users/nscales/miniconda3/envs/qiime2-2019.1/share/fragment-insertion//ref/RAxML_info-reference-gg-raxml-bl.info -t /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/pplacer.tree.ld_yvhoc.tre --groups 10 /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/pplacer.extended.0.q35kv891.fasta [08:39:17] jobs.py (line 128): DEBUG: Finished pplacer Job with input: backbone_alignment_file:/scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/pplacer.backbone.icku9u8i.fasta, tree_file:/scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/pplacer.tree.ld_yvhoc.tre, info_file:/data/users/nscales/miniconda3/envs/qiime2-2019.1/share/fragment-insertion//ref/RAxML_info-reference-gg-raxml-bl.info, extended alignment:/scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/pplacer.extended.0.q35kv891.fasta, output:/scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/pplacer.extended.0.q35kv891.jplace with: return code: 2 output: Running pplacer v1.1.alpha13-0-g1ec7786 analysis on /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/pplacer.extended.0.q35kv891.fasta... Didn't find any reference sequences in given alignment file. Using supplied reference alignment. Splitting query alignment into 10 groups... done. Running sequence group 1 of 10. Warning: using a statistics file directly is now deprecated. We suggest using a reference package. If you already are, then please use the latest version of taxtastic. WARNING: your stats file is from RAxML 8.2.12; RAxML has been tested with the following versions: 7.0.4; 7.2.3; 7.2.5; 7.2.6; 7.2.7 I'm going to try parsing as if this was version 7.2.3Problem parsing info or stats file/data/users/nscales/miniconda3/envs/qiime2-2019.1/share/fragment-insertion//ref/RAxML_info-reference-gg-raxml-bl.info error:Uncaught exception: Parse_stats.Stats_parsing_error("too many partitions. Only one is allowed.") Fatal error: exception Parse_stats.Stats_parsing_error("too many partitions. Only one is allowed.") multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/data/users/nscales/miniconda3/envs/qiime2-2019.1/lib/python3.6/multiprocessing/pool.py", line 119, in worker result = (True, func(*args, **kwds)) File "/data/users/nscales/miniconda3/envs/qiime2-2019.1/share/fragment-insertion/sepp/sepp/scheduler.py", line 72, in __call__ return self.run() File "/data/users/nscales/miniconda3/envs/qiime2-2019.1/share/fragment-insertion/sepp/sepp/jobs.py", line 131, in run self.read_stderr() if self.read_stderr() else 'No error messages available'])) sepp.scheduler.JobError: The following execution failed: /data/users/nscales/miniconda3/envs/qiime2-2019.1/share/fragment-insertion/sepp/.sepp/bundled-v4.3.5/pplacer --out-dir /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0 -j 1 -r /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/pplacer.backbone.icku9u8i.fasta -s /data/users/nscales/miniconda3/envs/qiime2-2019.1/share/fragment-insertion//ref/RAxML_info-reference-gg-raxml-bl.info -t /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/pplacer.tree.ld_yvhoc.tre --groups 10 /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/pplacer.extended.0.q35kv891.fasta Uncaught exception: Parse_stats.Stats_parsing_error("too many partitions. Only one is allowed.") Fatal error: exception Parse_stats.Stats_parsing_error("too many partitions. Only one is allowed.") """ The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/data/users/nscales/miniconda3/envs/qiime2-2019.1/share/fragment-insertion//sepp/run_sepp.py", line 25, in ExhaustiveAlgorithm().run() File "/data/users/nscales/miniconda3/envs/qiime2-2019.1/share/fragment-insertion/sepp/sepp/algorithm.py", line 169, in run if (not JobPool().wait_for_all_jobs()): File "/data/users/nscales/miniconda3/envs/qiime2-2019.1/share/fragment-insertion/sepp/sepp/scheduler.py", line 340, in wait_for_all_jobs result.get() File "/data/users/nscales/miniconda3/envs/qiime2-2019.1/lib/python3.6/multiprocessing/pool.py", line 670, in get raise self._value sepp.scheduler.JobError: The following execution failed: /data/users/nscales/miniconda3/envs/qiime2-2019.1/share/fragment-insertion/sepp/.sepp/bundled-v4.3.5/pplacer --out-dir /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0 -j 1 -r /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/pplacer.backbone.icku9u8i.fasta -s /data/users/nscales/miniconda3/envs/qiime2-2019.1/share/fragment-insertion//ref/RAxML_info-reference-gg-raxml-bl.info -t /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/pplacer.tree.ld_yvhoc.tre --groups 10 /scratch/6534112.1.mic/tmp.bE7vXbtSCD/sepp-tempssd-Wzu3/q2-fragment-insertion.xoewjitc/root/P_0/pplacer.extended.0.q35kv891.fasta Uncaught exception: Parse_stats.Stats_parsing_error("too many partitions. Only one is allowed.") Fatal error: exception Parse_stats.Stats_parsing_error("too many partitions. Only one is allowed.") =====================================================================