[2023-03-16 04:24:46,332] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:24:46,332] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:24:46,332] [INFO] DQC Reference Directory: /var/lib/cwl/stg4441cbad-8716-4a57-b389-50d66bfd8323/dqc_reference
[2023-03-16 04:24:48,117] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:24:48,117] [INFO] Task started: Prodigal
[2023-03-16 04:24:48,117] [INFO] Running command: cat /var/lib/cwl/stg68a430ef-5161-4ca8-b45e-1b8439e7e2c4/OceanDNA-b21002.fa | prodigal -d OceanDNA-b21002/cds.fna -a OceanDNA-b21002/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:25:33,665] [INFO] Task succeeded: Prodigal
[2023-03-16 04:25:33,665] [INFO] Task started: HMMsearch
[2023-03-16 04:25:33,666] [INFO] Running command: hmmsearch --tblout OceanDNA-b21002/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4441cbad-8716-4a57-b389-50d66bfd8323/dqc_reference/reference_markers.hmm OceanDNA-b21002/protein.faa > /dev/null
[2023-03-16 04:25:33,967] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:25:33,968] [INFO] Found 6/6 markers.
[2023-03-16 04:25:34,006] [INFO] Query marker FASTA was written to OceanDNA-b21002/markers.fasta
[2023-03-16 04:25:34,008] [INFO] Task started: Blastn
[2023-03-16 04:25:34,008] [INFO] Running command: blastn -query OceanDNA-b21002/markers.fasta -db /var/lib/cwl/stg4441cbad-8716-4a57-b389-50d66bfd8323/dqc_reference/reference_markers.fasta -out OceanDNA-b21002/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:25:34,629] [INFO] Task succeeded: Blastn
[2023-03-16 04:25:34,630] [INFO] Selected 35 target genomes.
[2023-03-16 04:25:34,630] [INFO] Target genome list was writen to OceanDNA-b21002/target_genomes.txt
[2023-03-16 04:25:34,653] [INFO] Task started: fastANI
[2023-03-16 04:25:34,654] [INFO] Running command: fastANI --query /var/lib/cwl/stg68a430ef-5161-4ca8-b45e-1b8439e7e2c4/OceanDNA-b21002.fa --refList OceanDNA-b21002/target_genomes.txt --output OceanDNA-b21002/fastani_result.tsv --threads 1
[2023-03-16 04:26:00,561] [INFO] Task succeeded: fastANI
[2023-03-16 04:26:00,562] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4441cbad-8716-4a57-b389-50d66bfd8323/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:26:00,562] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4441cbad-8716-4a57-b389-50d66bfd8323/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:26:00,579] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:26:00,579] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:26:00,579] [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
Thermomonas haemolytica	strain=LMG 19653	GCA_006352395.1	141949	141949	type	True	75.042	54	2216	95	below_threshold
Thermomonas haemolytica	strain=DSM 13605	GCA_004346265.1	141949	141949	type	True	75.0049	58	2216	95	below_threshold
Solimonas variicoloris	strain=DSM 15731	GCA_000382285.1	254408	254408	type	True	74.9064	111	2216	95	below_threshold
Luteimonas huabeiensis	strain=HB2	GCA_000559025.1	1244513	1244513	type	True	74.8941	104	2216	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	74.8873	77	2216	95	below_threshold
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	74.8856	78	2216	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	74.8776	79	2216	95	below_threshold
Pseudoxanthomonas composti	strain=GSS15	GCA_004122095.1	2137479	2137479	type	True	74.8563	53	2216	95	below_threshold
Lujinxingia sediminis	strain=SEH01	GCA_004005565.1	2480984	2480984	type	True	74.8478	55	2216	95	below_threshold
Myxococcus virescens	strain=NBRC 100334	GCA_007989405.1	83456	83456	type	True	74.8318	102	2216	95	below_threshold
Rubrimonas cliftonensis	strain=DSM 15345	GCA_900107585.1	89524	89524	type	True	74.8317	134	2216	95	below_threshold
Myxococcus virescens	strain=DSM 2260	GCA_900101905.1	83456	83456	type	True	74.8282	103	2216	95	below_threshold
Thiorhodococcus minor	strain=DSM 11518	GCA_010820565.1	57489	57489	type	True	74.828	52	2216	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	74.8148	117	2216	95	below_threshold
Solimonas flava	strain=DSM 18980	GCA_000426685.1	415849	415849	type	True	74.7953	117	2216	95	below_threshold
Myxococcus vastator	strain=AM301	GCA_010894475.1	2709664	2709664	type	True	74.7879	106	2216	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	74.7495	66	2216	95	below_threshold
Burkholderia oklahomensis	strain=C6786	GCA_000170375.1	342113	342113	type	True	74.7447	113	2216	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	74.742	84	2216	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	74.7263	125	2216	95	below_threshold
Stigmatella aurantiaca	strain=DSM 17044	GCA_900109545.1	41	41	type	True	74.7136	93	2216	95	below_threshold
Burkholderia oklahomensis	strain=LMG 23618	GCA_900608545.1	342113	342113	type	True	74.7127	132	2216	95	below_threshold
Burkholderia oklahomensis	strain=C6786	GCA_001522135.2	342113	342113	type	True	74.7101	133	2216	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	74.7088	160	2216	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	74.7072	102	2216	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	74.705	109	2216	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	74.6968	108	2216	95	below_threshold
Alcanivorax profundimaris	strain=ST75FaO-1	GCA_015265435.1	2735259	2735259	type	True	74.6943	52	2216	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	74.6833	91	2216	95	below_threshold
Pleomorphomonas carboxyditropha	strain=SVCO-16	GCA_002770725.1	2023338	2023338	type	True	74.6816	100	2216	95	below_threshold
Glycomyces buryatensis	strain=18	GCA_004912275.1	2570927	2570927	type	True	74.5679	61	2216	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:26:00,579] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21002/tc_result.tsv
[2023-03-16 04:26:00,579] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:26:00,579] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:26:00,579] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4441cbad-8716-4a57-b389-50d66bfd8323/dqc_reference/checkm_data
[2023-03-16 04:26:00,580] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:26:00,588] [INFO] Task started: CheckM
[2023-03-16 04:26:00,588] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21002/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21002/checkm_input OceanDNA-b21002/checkm_result
[2023-03-16 04:27:50,463] [INFO] Task succeeded: CheckM
[2023-03-16 04:27:50,463] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:27:50,467] [INFO] ===== Completeness check finished =====
[2023-03-16 04:27:50,467] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:27:50,467] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21002/markers.fasta)
[2023-03-16 04:27:50,468] [INFO] Task started: Blastn
[2023-03-16 04:27:50,469] [INFO] Running command: blastn -query OceanDNA-b21002/markers.fasta -db /var/lib/cwl/stg4441cbad-8716-4a57-b389-50d66bfd8323/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21002/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:27:51,351] [INFO] Task succeeded: Blastn
[2023-03-16 04:27:51,352] [INFO] Selected 32 target genomes.
[2023-03-16 04:27:51,352] [INFO] Target genome list was writen to OceanDNA-b21002/target_genomes_gtdb.txt
[2023-03-16 04:27:51,377] [INFO] Task started: fastANI
[2023-03-16 04:27:51,377] [INFO] Running command: fastANI --query /var/lib/cwl/stg68a430ef-5161-4ca8-b45e-1b8439e7e2c4/OceanDNA-b21002.fa --refList OceanDNA-b21002/target_genomes_gtdb.txt --output OceanDNA-b21002/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:28:20,010] [INFO] Task succeeded: fastANI
[2023-03-16 04:28:20,025] [INFO] Found 28 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:28:20,026] [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
GCA_002726535.1	s__UBA9042 sp002726535	76.215	73	2216	d__Bacteria;p__Myxococcota;c__UBA9042;o__UBA9042;f__UBA9042;g__UBA9042	95.0	99.84	99.84	0.69	0.69	2	-
GCA_903896545.1	s__CAIYBN01 sp903896545	75.931	167	2216	d__Bacteria;p__Myxococcota;c__UBA9042;o__UBA9042;f__UBA9042;g__CAIYBN01	95.0	99.47	98.78	0.94	0.88	6	-
GCA_903917305.1	s__CAIXAA01 sp903917305	75.8002	184	2216	d__Bacteria;p__Myxococcota;c__UBA9042;o__UBA9042;f__UBA9042;g__CAIXAA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903955385.1	s__CAJBNH01 sp903955385	75.7825	171	2216	d__Bacteria;p__Myxococcota;c__UBA9042;o__UBA9042;f__UBA9042;g__CAJBNH01	95.0	99.88	99.77	0.96	0.95	7	-
GCA_016218865.1	s__SXRM01 sp016218865	75.7748	185	2216	d__Bacteria;p__Myxococcota;c__UBA9042;o__UBA9042;f__UBA9042;g__SXRM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903869075.1	s__CAIYBN01 sp903869075	75.6561	205	2216	d__Bacteria;p__Myxococcota;c__UBA9042;o__UBA9042;f__UBA9042;g__CAIYBN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903924465.1	s__CAIYBN01 sp903924465	75.6506	143	2216	d__Bacteria;p__Myxococcota;c__UBA9042;o__UBA9042;f__UBA9042;g__CAIYBN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903929795.1	s__CAIYBN01 sp903929795	75.468	204	2216	d__Bacteria;p__Myxococcota;c__UBA9042;o__UBA9042;f__UBA9042;g__CAIYBN01	95.0	99.55	99.37	0.95	0.92	7	-
GCA_002343455.1	s__UBA2385 sp002343455	74.9498	126	2216	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__UBA2385	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017644045.1	s__UBA1660 sp017644045	74.9174	144	2216	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__UBA1660	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000559025.1	s__Luteimonas huabeiensis	74.8867	106	2216	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016218825.1	s__JACRCV01 sp016218825	74.8602	148	2216	d__Bacteria;p__Myxococcota;c__XYA12-FULL-58-9;o__XYA12-FULL-58-9;f__XYA12-FULL-58-9;g__JACRCV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903847385.1	s__CAINDO01 sp903847385	74.8568	209	2216	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__UBA7976;f__UBA1532;g__CAINDO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903828235.1	s__Rubrivivax sp903828235	74.8531	108	2216	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.94	99.91	0.96	0.96	5	-
GCF_004005565.1	s__Lujinxingia sediminis	74.8478	55	2216	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Lujinxingia	95.0	98.95	98.95	0.97	0.97	3	-
GCF_010820565.1	s__Thiorhodococcus minor	74.8196	53	2216	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiorhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013385.1	s__Anaeromyxobacter dehalogenans_B	74.784	153	2216	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__Anaeromyxobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872755.1	s__GW928-bin9 sp016872755	74.771	75	2216	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GW928-bin9	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254665.1	s__Halomonas lactosivorans	74.744	67	2216	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902706185.1	s__Roseomonas sp902706185	74.7398	139	2216	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525785.1	s__WYBT01 sp011525785	74.7385	157	2216	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__WYBT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016212965.1	s__JACRDA01 sp016212965	74.7327	198	2216	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JACRDA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007679965.1	s__Bordetella_B sp007679965	74.7261	110	2216	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000022145.1	s__Anaeromyxobacter dehalogenans	74.715	157	2216	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__Anaeromyxobacter	95.0	97.16	97.16	0.92	0.92	2	-
GCA_018240795.1	s__Phenylobacterium sp018240795	74.6714	74	2216	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342605.1	s__Caulobacter sp004342605	74.6389	72	2216	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016214985.1	s__JACRMM01 sp016214985	74.6063	61	2216	d__Bacteria;p__Desulfobacterota_C;c__Deferrisomatia;o__Deferrisomatales;f__JACRMM01;g__JACRMM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213885.1	s__JACQZM01 sp016213885	74.5777	64	2216	d__Bacteria;p__UBP17;c__UBA6191;o__JACPRK01;f__JACQZM01;g__JACQZM01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:28:20,026] [INFO] GTDB search result was written to OceanDNA-b21002/result_gtdb.tsv
[2023-03-16 04:28:20,026] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:28:20,029] [INFO] DFAST_QC result json was written to OceanDNA-b21002/dqc_result.json
[2023-03-16 04:28:20,029] [INFO] DFAST_QC completed!
[2023-03-16 04:28:20,029] [INFO] Total running time: 0h3m34s