[2023-03-17 03:50:13,837] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:50:13,837] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:50:13,837] [INFO] DQC Reference Directory: /var/lib/cwl/stg281dc904-dbbf-4630-939e-1fa21b830cf7/dqc_reference
[2023-03-17 03:50:15,101] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:50:15,102] [INFO] Task started: Prodigal
[2023-03-17 03:50:15,102] [INFO] Running command: cat /var/lib/cwl/stgb3977982-6101-4ec8-8873-69d655198cc9/OceanDNA-b35148.fa | prodigal -d OceanDNA-b35148/cds.fna -a OceanDNA-b35148/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:50:42,731] [INFO] Task succeeded: Prodigal
[2023-03-17 03:50:42,731] [INFO] Task started: HMMsearch
[2023-03-17 03:50:42,731] [INFO] Running command: hmmsearch --tblout OceanDNA-b35148/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg281dc904-dbbf-4630-939e-1fa21b830cf7/dqc_reference/reference_markers.hmm OceanDNA-b35148/protein.faa > /dev/null
[2023-03-17 03:50:43,018] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:50:43,018] [INFO] Found 6/6 markers.
[2023-03-17 03:50:43,046] [INFO] Query marker FASTA was written to OceanDNA-b35148/markers.fasta
[2023-03-17 03:50:43,046] [INFO] Task started: Blastn
[2023-03-17 03:50:43,046] [INFO] Running command: blastn -query OceanDNA-b35148/markers.fasta -db /var/lib/cwl/stg281dc904-dbbf-4630-939e-1fa21b830cf7/dqc_reference/reference_markers.fasta -out OceanDNA-b35148/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:50:43,928] [INFO] Task succeeded: Blastn
[2023-03-17 03:50:43,929] [INFO] Selected 11 target genomes.
[2023-03-17 03:50:43,929] [INFO] Target genome list was writen to OceanDNA-b35148/target_genomes.txt
[2023-03-17 03:50:43,934] [INFO] Task started: fastANI
[2023-03-17 03:50:43,934] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3977982-6101-4ec8-8873-69d655198cc9/OceanDNA-b35148.fa --refList OceanDNA-b35148/target_genomes.txt --output OceanDNA-b35148/fastani_result.tsv --threads 1
[2023-03-17 03:50:56,728] [INFO] Task succeeded: fastANI
[2023-03-17 03:50:56,728] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg281dc904-dbbf-4630-939e-1fa21b830cf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:50:56,728] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg281dc904-dbbf-4630-939e-1fa21b830cf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:50:56,735] [INFO] Found 11 fastANI hits (7 hits with ANI > threshold)
[2023-03-17 03:50:56,735] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 03:50:56,735] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Enterobacter hormaechei subsp. steigerwaltii	strain=DSM 16691	GCA_001729725.1	299766	158836	type	True	98.8362	1404	1526	95	conclusive
Enterobacter hormaechei subsp. oharae	strain=DSM 16687	GCA_001729705.1	301102	158836	type	True	97.6995	1385	1526	95	conclusive
Enterobacter hormaechei subsp. oharae	strain=FDAARGOS_1533	GCA_020097195.1	301102	158836	type	True	97.6627	1391	1526	95	conclusive
Enterobacter hormaechei subsp. xiangfangensis	strain=LMG27195	GCA_001729785.1	1296536	158836	type	True	97.0868	1374	1526	95	conclusive
Enterobacter hormaechei subsp. hoffmannii	strain=DSM 14563	GCA_001729745.1	1812934	158836	type	True	95.844	1343	1526	95	conclusive
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	95.0537	1369	1526	95	conclusive
Enterobacter hormaechei subsp. hormaechei	strain=ATCC 49162	GCA_001875655.1	301105	158836	type	True	95.0364	1367	1526	95	conclusive
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	88.3911	1182	1526	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	88.2954	1277	1526	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	87.6242	1203	1526	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	87.5762	1262	1526	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 03:50:56,736] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35148/tc_result.tsv
[2023-03-17 03:50:56,736] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:50:56,736] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:50:56,736] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg281dc904-dbbf-4630-939e-1fa21b830cf7/dqc_reference/checkm_data
[2023-03-17 03:50:56,737] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:50:56,742] [INFO] Task started: CheckM
[2023-03-17 03:50:56,743] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35148/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35148/checkm_input OceanDNA-b35148/checkm_result
[2023-03-17 03:52:03,769] [INFO] Task succeeded: CheckM
[2023-03-17 03:52:03,769] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:52:03,772] [INFO] ===== Completeness check finished =====
[2023-03-17 03:52:03,772] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:52:03,773] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35148/markers.fasta)
[2023-03-17 03:52:03,773] [INFO] Task started: Blastn
[2023-03-17 03:52:03,773] [INFO] Running command: blastn -query OceanDNA-b35148/markers.fasta -db /var/lib/cwl/stg281dc904-dbbf-4630-939e-1fa21b830cf7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35148/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:52:05,106] [INFO] Task succeeded: Blastn
[2023-03-17 03:52:05,107] [INFO] Selected 6 target genomes.
[2023-03-17 03:52:05,107] [INFO] Target genome list was writen to OceanDNA-b35148/target_genomes_gtdb.txt
[2023-03-17 03:52:05,112] [INFO] Task started: fastANI
[2023-03-17 03:52:05,112] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3977982-6101-4ec8-8873-69d655198cc9/OceanDNA-b35148.fa --refList OceanDNA-b35148/target_genomes_gtdb.txt --output OceanDNA-b35148/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:52:12,361] [INFO] Task succeeded: fastANI
[2023-03-17 03:52:12,366] [INFO] Found 6 fastANI hits (3 hits with ANI > circumscription radius)
[2023-03-17 03:52:12,366] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_001729745.1	s__Enterobacter hormaechei_A	95.844	1343	1526	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	96.63	95.22	0.89	0.83	1867	inconclusive
GCF_011078175.1	s__Enterobacter cloacae_Q	95.1571	1303	1526	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	100.00	100.00	1.00	1.00	2	inconclusive
GCF_001875655.1	s__Enterobacter hormaechei	95.0364	1367	1526	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.46	98.52	0.92	0.86	32	inconclusive
GCF_900322725.1	s__Enterobacter quasihormaechei	93.5522	1356	1526	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.46	97.61	0.96	0.89	41	-
GCF_013375935.1	s__Enterobacter cloacae_O	91.336	1320	1526	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.68	98.59	0.94	0.92	6	-
GCF_900324475.1	s__Enterobacter bugandensis	88.8959	1260	1526	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.49	95.52	0.94	0.88	115	-
--------------------------------------------------------------------------------
[2023-03-17 03:52:12,366] [INFO] GTDB search result was written to OceanDNA-b35148/result_gtdb.tsv
[2023-03-17 03:52:12,366] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:52:12,367] [INFO] DFAST_QC result json was written to OceanDNA-b35148/dqc_result.json
[2023-03-17 03:52:12,368] [INFO] DFAST_QC completed!
[2023-03-17 03:52:12,368] [INFO] Total running time: 0h1m59s