Hi, I'm having an urgent issue with Galaxy GEMINI Load tool.
It kept giving me following error but I've followed the tutorial to make the vcf file using SnpEff tool...
sorry I'm really new here and don't know what did I do wrong..
Dataset Error Report
An error occurred while running the tool toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2.
Details
Execution resulted in the following messages:
Fatal error: Exit code 1 ()
Fatal error: Matched on Error:
Tool generated the following standard error:
Hi, I'm having an urgent issue with Galaxy GEMINI Load tool. It kept giving me following error but I've followed the tutorial to make the vcf file using SnpEff tool... sorry I'm really new here and don't know what did I do wrong..
Dataset Error Report An error occurred while running the tool toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2.
Details Execution resulted in the following messages:
Fatal error: Exit code 1 () Fatal error: Matched on Error: Tool generated the following standard error:
CADD scores are being loaded (to skip use:--skip-cadd). GERP per bp is being loaded (to skip use:--skip-gerp-bp). pid 4112999: 9999 variants processed. pid 4112996: 9999 variants processed. pid 4113002: 9999 variants processed. pid 4112999: 19999 variants processed. pid 4112996: 19999 variants processed. pid 4113002: 19999 variants processed. pid 4112996: 29999 variants processed. pid 4113002: 29999 variants processed. pid 4112999: 29999 variants processed. pid 4113002: 39999 variants processed. pid 4112999: 39999 variants processed. pid 4112996: 39999 variants processed. pid 4113002: 49999 variants processed. pid 4112999: 49999 variants processed. pid 4112996: 49999 variants processed. pid 4113002: 59999 variants processed. pid 4112999: 59999 variants processed. pid 4112996: 59999 variants processed. pid 4113002: 69999 variants processed. pid 4112999: 69999 variants processed. pid 4112996: 69999 variants processed. pid 4112999: 79999 variants processed. pid 4113002: 79999 variants processed. pid 4112996: 79999 variants processed. pid 4112999: 89999 variants processed. pid 4113002: 89999 variants processed. pid 4112996: 89999 variants processed. pid 4112999: 99999 variants processed. pid 4113002: 99999 variants processed. insert error trying 1 at a time: Traceback (most recent call last): File "/mnt/tools-indices/tool_dependencies/_conda/envs/gemini@0.20.1/bin/gemini", line 7, in
gemini_main.main()
File "/mnt/tools-indices/tool_dependencies/_conda/envs/__gemini@0.20.1/lib/python2.7/site-packages/gemini/gemini_main.py", line 1248, in main
args.func(parser, args)
File "/mnt/tools-indices/tool_dependencies/_conda/envs/ gemini@0.20.1/lib/python2.7/site-packages/gemini/gemini_main.py", line 311, in loadchunk_fn
gemini_load_chunk.load(parser, args)
File "/mnt/tools-indices/tool_dependencies/_conda/envs/gemini@0.20.1/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 914, in load
gemini_loader.populate_from_vcf()
File "/mnt/tools-indices/tool_dependencies/_conda/envs/gemini@0.20.1/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 228, in populate_from_vcf
database.insert_variation(self.c, self.metadata, self.var_buffer)
File "/mnt/tools-indices/tool_dependencies/_conda/envs/gemini@0.20.1/lib/python2.7/site-packages/gemini/database.py", line 452, in insert_variation
trans.execute(stmt, b)
File "/mnt/tools-indices/tool_dependencies/_conda/envs/gemini@0.20.1/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 984, in execute
return meth(self, multiparams, params)
File "/mnt/tools-indices/tool_dependencies/_conda/envs/gemini@0.20.1/lib/python2.7/site-packages/sqlalchemy/sql/elements.py", line 293, in _execute_on_connection
return connection._execute_clauseelement(self, multiparams, params)
File "/mnt/tools-indices/tool_dependencies/_conda/envs/__gemini@0.20.1/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1103, in _execute_clauseelement
distilled_params,
File "/mnt/tools-indices/tool_dependencies/_conda/envs/gemini@0.20.1/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1288, in _execute_context
e, statement, parameters, cursor, context
File "/mnt/tools-indices/tool_dependencies/_conda/envs/gemini@0.20.1/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1482, in _handle_dbapi_exception
sqlalchemy_exception, with_traceback=excinfo[2], from=e
File "/mnt/tools-indices/tool_dependencies/_conda/envs/gemini@0.20.1/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1248, in _execute_context
cursor, statement, parameters, context
File "/mnt/tools-indices/tool_dependencies/_conda/envs/gemini@0.20.1/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 588, in do_execute
cursor.execute(statement, parameters)
sqlalchemy.exc.IntegrityError: (sqlite3.IntegrityError) UNIQUE constraint failed: variants.variant_id
[SQL: INSERT INTO variants (chrom, start, "end", vcf_id, variant_id, anno_id, ref, alt, qual, filter, type, sub_type, gts, gt_types, gt_phases, gt_depths, gt_ref_depths, gt_alt_depths, gt_alt_freqs, gt_quals, gt_copy_numbers, call_rate, max_aaf_all, in_dbsnp, rs_ids, sv_cipos_start_left, sv_cipos_end_left, sv_cipos_start_right, sv_cipos_end_right, sv_length, sv_is_precise, sv_tool, sv_evidence_type, sv_event_id, sv_mate_id, sv_strand, in_omim, clinvar_sig, clinvar_disease_name, clinvar_dbsource, clinvar_dbsource_id, clinvar_origin, clinvar_dsdb, clinvar_dsdbid, clinvar_disease_acc, clinvar_in_locus_spec_db, clinvar_on_diag_assay, clinvar_causal_allele, clinvar_gene_phenotype, geno2mp_hpo_ct, pfam_domain, cyto_band, rmsk, in_cpg_island, in_segdup, is_conserved, gerp_bp_score, gerp_element_pval, num_hom_ref, num_het, num_hom_alt, num_unknown, aaf, hwe, inbreeding_coeff, pi, recomb_rate, gene, transcript, is_exonic, is_coding, is_splicing, is_lof, exon, codon_change, aa_change, aa_length, biotype, impact, impact_so, impact_severity, polyphen_pred, polyphen_score, sift_pred, sift_score, anc_allele, rms_bq, cigar, depth, strand_bias, rms_map_qual, in_hom_run, num_mapq_zero, num_alleles, num_reads_w_dels, haplotype_score, qual_depth, allele_count, allele_bal, in_hm2, in_hm3, is_somatic, somatic_score, in_esp, aaf_esp_ea, aaf_esp_aa, aaf_esp_all, exome_chip, in_1kg, aaf_1kg_amr, aaf_1kg_eas, aaf_1kg_sas, aaf_1kg_afr, aaf_1kg_eur, aaf_1kg_all, grc, gms_illumina, gms_solid, gms_iontorrent, in_cse, encode_tfbs, "encode_dnaseI_cell_count", "encode_dnaseI_cell_list", encode_consensus_gm12878, encode_consensus_h1hesc, encode_consensus_helas3, encode_consensus_hepg2, encode_consensus_huvec, encode_consensus_k562, vista_enhancers, cosmic_ids, info, cadd_raw, cadd_scaled, fitcons, in_exac, aaf_exac_all, aaf_adj_exac_all, aaf_adj_exac_afr, aaf_adj_exac_amr, aaf_adj_exac_eas, aaf_adj_exac_fin, aaf_adj_exac_nfe, aaf_adj_exac_oth, aaf_adj_exac_sas, exac_num_het, exac_num_hom_alt, exac_num_chroms, aaf_gnomad_all, aaf_gnomad_afr, aaf_gnomad_amr, aaf_gnomad_asj, aaf_gnomad_eas, aaf_gnomad_fin, aaf_gnomad_nfe, aaf_gnomad_oth, aaf_gnomad_sas, gnomad_num_het, gnomad_num_hom_alt, gnomad_num_chroms) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)]
[parameters: (u'chr11', 3061779, 3061780, None, 90001, 1, u'C', u'T', 560.64697265625, None, u'snp', u'ts', <read-only buffer for 0x55d49d10ee20, size -1, offset 0 at 0x14da502ee0b0>, <read-only buffer for 0x55d49dee61c0, size -1, offset 0 at 0x14da502ee0f0>, <read-only buffer for 0x55d4ad33e540, size -1, offset 0 at 0x14da502ee130>, <read-only buffer for 0x55d4b65d1d70, size -1, offset 0 at 0x14da502ee170>, <read-only buffer for 0x55d4b8428cf0, size -1, offset 0 at 0x14da502ee1b0>, <read-only buffer for 0x55d4b9fedca0, size -1, offset 0 at 0x14da502ee1f0>, <read-only buffer for 0x55d4b801da10, size -1, offset 0 at 0x14da502ee230>, <read-only buffer for 0x55d4b81a1150, size -1, offset 0 at 0x14da502ee270>, <read-only buffer for 0x55d4b7e3af10, size -1, offset 0 at 0x14da502ee2b0>, 1.0, 0.6911764705882353, 1, 'rs399565', None, None, None, None, None, 1, None, None, None, None, None, 0, None, None, None, None, None, None, None, None, 0, 0, None, None, -1, None, 'chr11p15.4', None, 0, 0, 0, -2.3299999237060547, None, 0, 1, 0, 0, 0.5, 0.31731050767247415, -1.0, 1.0, 0.190533, u'CARS', u'NM_001014437.2', 0, 0, 0, 0, u'4/22', u'c.455+346G>A', u'', None, u'protein_coding', u'intron_variant', u'intron_variant', 'LOW', None, None, None, None, None, None, u'1M1X', 36, None, None, None, None, 2, None, None, None, 1, 0.5833330154418945, None, None, None, None, 0, -1.0, -1.0, -1.0, 0, 1, 0.5317, 0.6845, 0.4387, 0.034, 0.3956, 0.385583, None, None, None, None, 0, None, '1', '8988t', 'T', 'T', 'T', 'T', 'T', 'T', None, None, <read-only buffer for 0x55d4b7e3af50, size -1, offset 0 at 0x14da502ee2f0>, -0.11, 1.63, 0.088506, 1, 0.316, 0.40455893254262415, 0.12105263157894737, 0.4782608695652174, 0.6911764705882353, 0.0, 0.4007272727272727, 0.4406779661016949, 0.4064748201438849, 2506, 930, 10792, 0.443146, 0.07415036045314109, 0.5932842140921409, 0.41499109188088573, 0.6655830963023162, 0.31648434552998866, 0.40059465696281177, 0.4202524383247275, 0.4121579463410286, 28285, 13208, 123438)]
(Background on this error at: http://sqlalche.me/e/gkpj)
pid 4112999: 109999 variants processed.
pid 4113002: 109999 variants processed.
pid 4112999: 119999 variants processed.
pid 4113002: 119999 variants processed.
pid 4112999: 129999 variants processed.
pid 4113002: 129999 variants processed.
insert error trying 1 at a time:
sqlalchemy.OperationalError: (sqlite3.OperationalError) no such table: variants
[SQL: INSERT INTO variants (chrom, start, "end", vcf_id, variant_id, anno_id, ref, alt, qual, filter, type, sub_type, gts, gt_types, gt_phases, gt_depths, gt_ref_depths, gt_alt_depths, gt_alt_freqs, gt_quals, gt_copy_numbers, call_rate, max_aaf_all, in_dbsnp, rs_ids, sv_cipos_start_left, sv_cipos_end_left, sv_cipos_start_right, sv_cipos_end_right, sv_length, sv_is_precise, sv_tool, sv_evidence_type, sv_event_id, sv_mate_id, sv_strand, in_omim, clinvar_sig, clinvar_disease_name, clinvar_dbsource, clinvar_dbsource_id, clinvar_origin, clinvar_dsdb, clinvar_dsdbid, clinvar_disease_acc, clinvar_in_locus_spec_db, clinvar_on_diag_assay, clinvar_causal_allele, clinvar_gene_phenotype, geno2mp_hpo_ct, pfam_domain, cyto_band, rmsk, in_cpg_island, in_segdup, is_conserved, gerp_bp_score, gerp_element_pval, num_hom_ref, num_het, num_hom_alt, num_unknown, aaf, hwe, inbreeding_coeff, pi, recomb_rate, gene, transcript, is_exonic, is_coding, is_splicing, is_lof, exon, codon_change, aa_change, aa_length, biotype, impact, impact_so, impact_severity, polyphen_pred, polyphen_score, sift_pred, sift_score, anc_allele, rms_bq, cigar, depth, strand_bias, rms_map_qual, in_hom_run, num_mapq_zero, num_alleles, num_reads_w_dels, haplotype_score, qual_depth, allele_count, allele_bal, in_hm2, in_hm3, is_somatic, somatic_score, in_esp, aaf_esp_ea, aaf_esp_aa, aaf_esp_all, exome_chip, in_1kg, aaf_1kg_amr, aaf_1kg_eas, aaf_1kg_sas, aaf_1kg_afr, aaf_1kg_eur, aaf_1kg_all, grc, gms_illumina, gms_solid, gms_iontorrent, in_cse, encode_tfbs, "encode_dnaseI_cell_count", "encode_dnaseI_cell_list", encode_consensus_gm12878, encode_consensus_h1hesc, encode_consensus_helas3, encode_consensus_hepg2, encode_consensus_huvec, encode_consensus_k562, vista_enhancers, cosmic_ids, info, cadd_raw, cadd_scaled, fitcons, in_exac, aaf_exac_all, aaf_adj_exac_all, aaf_adj_exac_afr, aaf_adj_exac_amr, aaf_adj_exac_eas, aaf_adj_exac_fin, aaf_adj_exac_nfe, aaf_adj_exac_oth, aaf_adj_exac_sas, exac_num_het, exac_num_hom_alt, exac_num_chroms, aaf_gnomad_all, aaf_gnomad_afr, aaf_gnomad_amr, aaf_gnomad_asj, aaf_gnomad_eas, aaf_gnomad_fin, aaf_gnomad_nfe, aaf_gnomad_oth, aaf_gnomad_sas, gnomad_num_het, gnomad_num_hom_alt, gnomad_num_chroms) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)]
[parameters: (u'chr2', 191379267, 191379268, None, 340754, 1, u'G', u'A', 942.4420166015625, None, u'snp', u'ts', <read-only buffer for 0x559ee2dfeb70, size -1, offset 0 at 0x14b5d4756e70>, <read-only buffer for 0x559ee8774c50, size -1, offset 0 at 0x14b5d4756eb0>, <read-only buffer for 0x559ee8a6f560, size -1, offset 0 at 0x14b5d4756ef0>, <read-only buffer for 0x559ee2e1c5a0, size -1, offset 0 at 0x14b5d4756f30>, <read-only buffer for 0x559ee8aa4bc0, size -1, offset 0 at 0x14b5d4756f70>, <read-only buffer for 0x559ee87917a0, size -1, offset 0 at 0x14b5d4756fb0>, <read-only buffer for 0x559ee2edde20, size -1, offset 0 at 0x14b5d475b030>, <read-only buffer for 0x559ee2e94970, size -1, offset 0 at 0x14b5d475b070>, <read-only buffer for 0x559ee4456180, size -1, offset 0 at 0x14b5d475b0b0>, 1.0, 0.7552613996993486, 1, 'rs4586658', None, None, None, None, None, 1, None, None, None, None, None, 0, None, None, None, None, None, None, None, None, 0, 0, None, None, -1, None, 'chr2q32.2', None, 0, 0, 1, -0.4729999899864197, None, 0, 1, 0, 0, 0.5, 0.31731050767247415, -1.0, 1.0, 0.06186, u'NEMP2', u'NM_001142645.1', 1, 1, 0, 0, u'7/9', u'c.864C>T', u'p.Ala288Ala', 417, u'protein_coding', u'synonymous_variant', u'synonymous_variant', 'LOW', None, None, None, None, None, None, u'1X', 62, None, None, None, None, 2, None, None, None, 1, 0.5483869910240173, None, None, None, None, 1, 0.5725958516656191, 0.3417630057803468, 0.5026281208935611, 0, 1, 0.696, 0.5833, 0.59, 0.3321, 0.5765, 0.532548, None, None, None, None, 0, None, None, None, 'T', 'R', 'T', 'T', 'R', 'T', None, None, <read-only buffer for 0x559ee44561c0, size -1, offset 0 at 0x14b5d475b0f0>, 1.81, 15.03, 0.706548, 1, 0.51, 0.5525758969641215, 0.34281716417910446, 0.6519607843137255, 0.5967741935483871, 0.775990099009901, 0.5586630286493861, 0.5491803278688525, 0.5485338725985844, 5155, 3429, 21740, 0.602428, 0.3560725552050473, 0.7552613996993486, 0.47668771248178726, 0.5506934948232076, 0.779171668667467, 0.5669502368848774, 0.573309241094476, 0.5585889570552147, 34026, 28536, 151218)]
(Background on this error at: http://sqlalche.me/e/e3q8)
Traceback (most recent call last):
File "/mnt/tools-indices/tool_dependencies/_conda/envs/__gemini@0.20.1/bin/gemini", line 7, in
gemini_main.main()
File "/mnt/tools-indices/tool_dependencies/_conda/envs/ gemini@0.20.1/lib/python2.7/site-packages/gemini/gemini_main.py", line 1248, in main
args.func(parser, args)
File "/mnt/tools-indices/tool_dependencies/_conda/envs/gemini@0.20.1/lib/python2.7/site-packages/gemini/gemini_main.py", line 311, in loadchunk_fn
gemini_load_chunk.load(parser, args)
File "/mnt/tools-indices/tool_dependencies/_conda/envs/gemini@0.20.1/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 910, in load
gemini_loader = GeminiLoader(args)
File "/mnt/tools-indices/tool_dependencies/_conda/envs/gemini@0.20.1/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 100, in init
self.vcf_reader = self._get_vcf_reader()
File "/mnt/tools-indices/tool_dependencies/_conda/envs/gemini@0.20.1/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 284, in _get_vcf_reader
return vcf.VCFReader(self.args.vcf)
File "cyvcf2/cyvcf2.pyx", line 257, in cyvcf2.cyvcf2.VCF.init
File "cyvcf2/cyvcf2.pyx", line 192, in cyvcf2.cyvcf2.HTSFile._open_htsfile
IOError: - is not valid bcf or vcf (format: 2 mode: r)
insert error trying 1 at a time:
sqlalchemy.OperationalError: (sqlite3.OperationalError) no such table: variants
[SQL: INSERT INTO variants (chrom, start, "end", vcf_id, variant_id, anno_id, ref, alt, qual, filter, type, sub_type, gts, gt_types, gt_phases, gt_depths, gt_ref_depths, gt_alt_depths, gt_alt_freqs, gt_quals, gt_copy_numbers, call_rate, max_aaf_all, in_dbsnp, rs_ids, sv_cipos_start_left, sv_cipos_end_left, sv_cipos_start_right, sv_cipos_end_right, sv_length, sv_is_precise, sv_tool, sv_evidence_type, sv_event_id, sv_mate_id, sv_strand, in_omim, clinvar_sig, clinvar_disease_name, clinvar_dbsource, clinvar_dbsource_id, clinvar_origin, clinvar_dsdb, clinvar_dsdbid, clinvar_disease_acc, clinvar_in_locus_spec_db, clinvar_on_diag_assay, clinvar_causal_allele, clinvar_gene_phenotype, geno2mp_hpo_ct, pfam_domain, cyto_band, rmsk, in_cpg_island, in_segdup, is_conserved, gerp_bp_score, gerp_element_pval, num_hom_ref, num_het, num_hom_alt, num_unknown, aaf, hwe, inbreeding_coeff, pi, recomb_rate, gene, transcript, is_exonic, is_coding, is_splicing, is_lof, exon, codon_change, aa_change, aa_length, biotype, impact, impact_so, impact_severity, polyphen_pred, polyphen_score, sift_pred, sift_score, anc_allele, rms_bq, cigar, depth, strand_bias, rms_map_qual, in_hom_run, num_mapq_zero, num_alleles, num_reads_w_dels, haplotype_score, qual_depth, allele_count, allele_bal, in_hm2, in_hm3, is_somatic, somatic_score, in_esp, aaf_esp_ea, aaf_esp_aa, aaf_esp_all, exome_chip, in_1kg, aaf_1kg_amr, aaf_1kg_eas, aaf_1kg_sas, aaf_1kg_afr, aaf_1kg_eur, aaf_1kg_all, grc, gms_illumina, gms_solid, gms_iontorrent, in_cse, encode_tfbs, "encode_dnaseI_cell_count", "encode_dnaseI_cell_list", encode_consensus_gm12878, encode_consensus_h1hesc, encode_consensus_helas3, encode_consensus_hepg2, encode_consensus_huvec, encode_consensus_k562, vista_enhancers, cosmic_ids, info, cadd_raw, cadd_scaled, fitcons, in_exac, aaf_exac_all, aaf_adj_exac_all, aaf_adj_exac_afr, aaf_adj_exac_amr, aaf_adj_exac_eas, aaf_adj_exac_fin, aaf_adj_exac_nfe, aaf_adj_exac_oth, aaf_adj_exac_sas, exac_num_het, exac_num_hom_alt, exac_num_chroms, aaf_gnomad_all, aaf_gnomad_afr, aaf_gnomad_amr, aaf_gnomad_asj, aaf_gnomad_eas, aaf_gnomad_fin, aaf_gnomad_nfe, aaf_gnomad_oth, aaf_gnomad_sas, gnomad_num_het, gnomad_num_hom_alt, gnomad_num_chroms) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)]
[parameters: (u'chr8', 20190773, 20190774, None, 551507, 1, u'A', u'G', 65.75830078125, None, u'snp', u'ts', <read-only buffer for 0x556d4fc3ca20, size -1, offset 0 at 0x14fa96ba2eb0>, <read-only buffer for 0x556d5ae7f7b0, size -1, offset 0 at 0x14fa96ba2ef0>, <read-only buffer for 0x556d5a7c92d0, size -1, offset 0 at 0x14fa96ba2f30>, <read-only buffer for 0x556d5a93b190, size -1, offset 0 at 0x14fa96ba2f70>, <read-only buffer for 0x556d3c7ea320, size -1, offset 0 at 0x14fa96ba2fb0>, <read-only buffer for 0x556d4f53a1e0, size -1, offset 0 at 0x14fa96ba5030>, <read-only buffer for 0x556d5a613260, size -1, offset 0 at 0x14fa96ba5070>, <read-only buffer for 0x556d5a4b2df0, size -1, offset 0 at 0x14fa96ba50b0>, <read-only buffer for 0x556d5a555510, size -1, offset 0 at 0x14fa96ba50f0>, 1.0, 0.5337, 1, 'rs35115233', None, None, None, None, None, 1, None, None, None, None, None, 0, None, None, None, None, None, None, None, None, 0, 0, None, None, -1, None, 'chr8p21.3', 'DNA_TcMar-Tigger_Tigger3b;SINE_Alu_AluSg;DNA_TcMar-Tigger_Tigger3b', 0, 0, 0, -0.2980000078678131, None, 0, 0, 1, 0, 1.0, 1.0, None, 0.0, 15.45771, u'LZTS1-AS1-LOC102467222', u'LZTS1-AS1-LOC102467222', 0, 0, 0, 0, u'', u'n.20190774A>G', u'', None, u'', u'intergenic_region', u'intergenic_region', 'LOW', None, None, None, None, None, None, u'1X', 2, None, None, None, None, 2, None, None, None, 2, 0.0, None, None, None, None, 0, -1.0, -1.0, -1.0, 0, 1, 0.4395, 0.501, 0.5337, 0.267, 0.3807, 0.412939, None, None, None, None, 0, None, None, None, 'unknown', 'R', 'R', 'T', 'R', 'R', None, None, <read-only buffer for 0x556d5a555550, size -1, offset 0 at 0x14fa96ba5130>, -0.39, 0.41, 0.053691, 0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1, -1, -1, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1, -1, -1)]
(Background on this error at: http://sqlalche.me/e/e3q8)
Traceback (most recent call last):
File "/mnt/tools-indices/tool_dependencies/_conda/envs/gemini@0.20.1/bin/gemini", line 7, in
gemini_main.main()
File "/mnt/tools-indices/tool_dependencies/_conda/envs/__gemini@0.20.1/lib/python2.7/site-packages/gemini/gemini_main.py", line 1248, in main
args.func(parser, args)
File "/mnt/tools-indices/tool_dependencies/_conda/envs/ gemini@0.20.1/lib/python2.7/site-packages/gemini/gemini_main.py", line 311, in loadchunk_fn
gemini_load_chunk.load(parser, args)
File "/mnt/tools-indices/tool_dependencies/_conda/envs/gemini@0.20.1/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 910, in load
gemini_loader = GeminiLoader(args)
File "/mnt/tools-indices/tool_dependencies/_conda/envs/gemini@0.20.1/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 100, in init
self.vcf_reader = self._get_vcf_reader()
File "/mnt/tools-indices/tool_dependencies/_conda/envs/gemini@0.20.1/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 284, in _get_vcf_reader
return vcf.VCFReader(self.args.vcf)
File "cyvcf2/cyvcf2.pyx", line 257, in cyvcf2.cyvcf2.VCF.init
File "cyvcf2/cyvcf2.pyx", line 192, in cyvcf2.cyvcf2.HTSFile._open_htsfile
IOError: - is not valid bcf or vcf (format: 2 mode: r)
Traceback (most recent call last):
File "/mnt/tools-indices/tool_dependencies/_conda/envs/gemini@0.20.1/bin/gemini", line 7, in
gemini_main.main()
File "/mnt/tools-indices/tool_dependencies/_conda/envs/gemini@0.20.1/lib/python2.7/site-packages/gemini/gemini_main.py", line 1248, in main
args.func(parser, args)
File "/mnt/tools-indices/tool_dependencies/_conda/envs/__gemini@0.20.1/lib/python2.7/site-packages/gemini/gemini_main.py", line 204, in load_fn
gemini_load.load(parser, args)
File "/mnt/tools-indices/tool_dependencies/_conda/envs/gemini@0.20.1/lib/python2.7/site-packages/gemini/gemini_load.py", line 49, in load
load_multicore(args)
File "/mnt/tools-indices/tool_dependencies/_conda/envs/gemini@0.20.1/lib/python2.7/site-packages/gemini/gemini_load.py", line 93, in load_multicore
chunks = load_chunks_multicore(grabix_file, args)
File "/mnt/tools-indices/tool_dependencies/_conda/envs/__gemini@0.20.1/lib/python2.7/site-packages/gemini/gemini_load.py", line 264, in load_chunks_multicore
wait_until_finished(procs)
File "/mnt/tools-indices/tool_dependencies/_conda/envs/gemini@0.20.1/lib/python2.7/site-packages/gemini/gemini_load.py", line 359, in wait_until_finished
raise ValueError("Processing failed on GEMINI chunk load")
ValueError: Processing failed on GEMINI chunk load
Galaxy job runner generated the following standard error:
WARNING:galaxy.datatypes.binary:<galaxy.datatypes.binary.GeminiSQLite object at 0x151fc64df250>, set_meta Exception: no such table: version