[2023-06-27 15:18:02,729] [INFO] DFAST_QC pipeline started.
[2023-06-27 15:18:02,731] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 15:18:02,732] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c0bff9f-9b68-451a-aea8-9262acac359f/dqc_reference
[2023-06-27 15:18:03,853] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 15:18:03,853] [INFO] Task started: Prodigal
[2023-06-27 15:18:03,854] [INFO] Running command: gunzip -c /var/lib/cwl/stgd6a0aca3-65ee-4d55-bd5f-099d6a3ccb8b/GCA_026984055.1_ASM2698405v1_genomic.fna.gz | prodigal -d GCA_026984055.1_ASM2698405v1_genomic.fna/cds.fna -a GCA_026984055.1_ASM2698405v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 15:18:11,358] [INFO] Task succeeded: Prodigal
[2023-06-27 15:18:11,358] [INFO] Task started: HMMsearch
[2023-06-27 15:18:11,358] [INFO] Running command: hmmsearch --tblout GCA_026984055.1_ASM2698405v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c0bff9f-9b68-451a-aea8-9262acac359f/dqc_reference/reference_markers.hmm GCA_026984055.1_ASM2698405v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 15:18:11,555] [INFO] Task succeeded: HMMsearch
[2023-06-27 15:18:11,556] [INFO] Found 6/6 markers.
[2023-06-27 15:18:11,583] [INFO] Query marker FASTA was written to GCA_026984055.1_ASM2698405v1_genomic.fna/markers.fasta
[2023-06-27 15:18:11,583] [INFO] Task started: Blastn
[2023-06-27 15:18:11,583] [INFO] Running command: blastn -query GCA_026984055.1_ASM2698405v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c0bff9f-9b68-451a-aea8-9262acac359f/dqc_reference/reference_markers.fasta -out GCA_026984055.1_ASM2698405v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 15:18:12,311] [INFO] Task succeeded: Blastn
[2023-06-27 15:18:12,314] [INFO] Selected 31 target genomes.
[2023-06-27 15:18:12,315] [INFO] Target genome list was writen to GCA_026984055.1_ASM2698405v1_genomic.fna/target_genomes.txt
[2023-06-27 15:18:12,320] [INFO] Task started: fastANI
[2023-06-27 15:18:12,320] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6a0aca3-65ee-4d55-bd5f-099d6a3ccb8b/GCA_026984055.1_ASM2698405v1_genomic.fna.gz --refList GCA_026984055.1_ASM2698405v1_genomic.fna/target_genomes.txt --output GCA_026984055.1_ASM2698405v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 15:18:31,170] [INFO] Task succeeded: fastANI
[2023-06-27 15:18:31,171] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c0bff9f-9b68-451a-aea8-9262acac359f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 15:18:31,172] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c0bff9f-9b68-451a-aea8-9262acac359f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 15:18:31,187] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 15:18:31,187] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 15:18:31,187] [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
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	76.7759	98	885	95	below_threshold
Allochromatium vinosum	strain=DSM 180	GCA_000025485.1	1049	1049	type	True	76.5337	98	885	95	below_threshold
Sedimenticola selenatireducens	strain=DSM 17993	GCA_000428045.1	191960	191960	type	True	76.5024	73	885	95	below_threshold
Marichromatium bheemlicum	strain=DSM 18632	GCA_012276755.1	365339	365339	type	True	76.4977	91	885	95	below_threshold
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	76.4708	100	885	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	76.4464	110	885	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	76.423	111	885	95	below_threshold
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	76.3822	97	885	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	76.3746	98	885	95	below_threshold
Halochromatium glycolicum	strain=DSM 11080	GCA_016584085.1	85075	85075	type	True	76.1502	92	885	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	76.1005	82	885	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.0731	77	885	95	below_threshold
Thioalkalivibrio halophilus	strain=HL17	GCA_001995255.1	252474	252474	type	True	76.0169	59	885	95	below_threshold
Thiolapillus brandeum	strain=Hiromi 1	GCA_000828615.1	1076588	1076588	type	True	75.9081	62	885	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	75.7901	57	885	95	below_threshold
Thioalkalivibrio versutus	strain=AL 2	GCA_001999325.1	106634	106634	type	True	75.7878	67	885	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	75.7011	66	885	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	75.6827	98	885	95	below_threshold
Solimonas variicoloris	strain=DSM 15731	GCA_000382285.1	254408	254408	type	True	75.6463	71	885	95	below_threshold
Solimonas flava	strain=DSM 18980	GCA_000426685.1	415849	415849	type	True	75.6173	70	885	95	below_threshold
Halomonas urmiana	strain=TBZ3	GCA_005780185.1	490901	490901	type	True	75.5723	50	885	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	75.5541	63	885	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	75.4625	50	885	95	below_threshold
Pseudoduganella lutea	strain=DSM 17473	GCA_004209755.1	321985	321985	type	True	75.3869	53	885	95	below_threshold
Cupriavidus malaysiensis	strain=USMAA1020	GCA_001854325.1	367825	367825	type	True	75.2299	57	885	95	below_threshold
Pseudoduganella flava	strain=CGMCC 1.10685	GCA_007830495.1	871742	871742	type	True	75.1763	65	885	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 15:18:31,189] [INFO] DFAST Taxonomy check result was written to GCA_026984055.1_ASM2698405v1_genomic.fna/tc_result.tsv
[2023-06-27 15:18:31,189] [INFO] ===== Taxonomy check completed =====
[2023-06-27 15:18:31,190] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 15:18:31,190] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c0bff9f-9b68-451a-aea8-9262acac359f/dqc_reference/checkm_data
[2023-06-27 15:18:31,190] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 15:18:31,222] [INFO] Task started: CheckM
[2023-06-27 15:18:31,223] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026984055.1_ASM2698405v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026984055.1_ASM2698405v1_genomic.fna/checkm_input GCA_026984055.1_ASM2698405v1_genomic.fna/checkm_result
[2023-06-27 15:18:56,452] [INFO] Task succeeded: CheckM
[2023-06-27 15:18:56,453] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 15:18:56,471] [INFO] ===== Completeness check finished =====
[2023-06-27 15:18:56,471] [INFO] ===== Start GTDB Search =====
[2023-06-27 15:18:56,472] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026984055.1_ASM2698405v1_genomic.fna/markers.fasta)
[2023-06-27 15:18:56,472] [INFO] Task started: Blastn
[2023-06-27 15:18:56,472] [INFO] Running command: blastn -query GCA_026984055.1_ASM2698405v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c0bff9f-9b68-451a-aea8-9262acac359f/dqc_reference/reference_markers_gtdb.fasta -out GCA_026984055.1_ASM2698405v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 15:18:57,795] [INFO] Task succeeded: Blastn
[2023-06-27 15:18:57,798] [INFO] Selected 32 target genomes.
[2023-06-27 15:18:57,798] [INFO] Target genome list was writen to GCA_026984055.1_ASM2698405v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 15:18:57,810] [INFO] Task started: fastANI
[2023-06-27 15:18:57,811] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6a0aca3-65ee-4d55-bd5f-099d6a3ccb8b/GCA_026984055.1_ASM2698405v1_genomic.fna.gz --refList GCA_026984055.1_ASM2698405v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026984055.1_ASM2698405v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 15:19:15,272] [INFO] Task succeeded: fastANI
[2023-06-27 15:19:15,287] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 15:19:15,288] [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_018409545.1	s__Allochromatium tepidum	76.7759	98	885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720725.1	s__Allochromatium palmeri	76.657	83	885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011321775.1	s__Thiogranum sp011321775	76.6055	95	885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-19610;f__DSM-19610;g__Thiogranum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009497875.2	s__JADGBD01 sp009497875	76.5825	108	885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__JADGBD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003696465.1	s__J044 sp003696465	76.5774	52	885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__J044;f__J044;g__J044	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428045.1	s__Sedimenticola selenatireducens	76.5024	73	885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Sedimenticola	95.0	98.15	98.15	0.90	0.90	2	-
GCF_012276755.1	s__Marichromatium bheemlicum	76.4977	91	885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018812525.1	s__YD12-FULL-61-37 sp018812525	76.4762	68	885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__YD12-FULL-61-37	95.0	99.98	99.98	0.97	0.97	3	-
GCF_000224005.2	s__Marichromatium purpuratum	76.4708	100	885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343155.1	s__Marichromatium gracile	76.4418	110	885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	98.88	96.74	0.96	0.94	6	-
GCF_008632335.1	s__Thiohalocapsa marina	76.3746	98	885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiohalocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013385175.1	s__Allochromatium humboldtianum	76.3631	98	885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011374975.1	s__Thiogranum sp011374975	76.3422	61	885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-19610;f__DSM-19610;g__Thiogranum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004001245.1	s__Sulfurivermis fontis	76.1005	82	885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018819175.1	s__JAHJQQ01 sp018819175	76.0767	71	885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__JAHJQQ01;f__JAHJQQ01;g__JAHJQQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018398425.1	s__Pseudomonas_E lalucatii	76.0731	77	885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	99.28	0.97	0.92	4	-
GCF_001995255.1	s__Thioalkalivibrio halophilus	76.0455	58	885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	96.06	95.07	0.84	0.81	11	-
GCA_011051655.1	s__DRKS01 sp011051655	75.972	86	885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__DRKS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003676145.1	s__Thiodiazotropha endolucinida	75.9386	60	885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	97.91	96.39	0.93	0.89	26	-
GCA_018399035.1	s__Thiocapsa sp018399035	75.8367	74	885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	99.92	99.89	0.99	0.99	3	-
GCA_006212015.1	s__28-57-27 sp006212015	75.7992	58	885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Halothiobacillales;f__Halothiobacillaceae;g__28-57-27	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426685.1	s__Solimonas flava	75.6018	71	885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0372	N/A	N/A	N/A	N/A	1	-
GCF_000377785.1	s__Thioalkalivibrio sp000377785	75.5852	69	885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101755.1	s__Pseudomonas_E alcaliphila	75.5287	57	885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.74	97.49	0.95	0.92	3	-
GCF_007665395.1	s__Pseudomonas_B psychrotolerans_C	75.3404	53	885	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 15:19:15,289] [INFO] GTDB search result was written to GCA_026984055.1_ASM2698405v1_genomic.fna/result_gtdb.tsv
[2023-06-27 15:19:15,290] [INFO] ===== GTDB Search completed =====
[2023-06-27 15:19:15,294] [INFO] DFAST_QC result json was written to GCA_026984055.1_ASM2698405v1_genomic.fna/dqc_result.json
[2023-06-27 15:19:15,294] [INFO] DFAST_QC completed!
[2023-06-27 15:19:15,294] [INFO] Total running time: 0h1m13s