[2023-06-13 17:33:02,572] [INFO] DFAST_QC pipeline started.
[2023-06-13 17:33:02,577] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 17:33:02,577] [INFO] DQC Reference Directory: /var/lib/cwl/stg10404c0a-ce00-4df1-a81a-c19a5ca3fec8/dqc_reference
[2023-06-13 17:33:03,936] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 17:33:03,937] [INFO] Task started: Prodigal
[2023-06-13 17:33:03,937] [INFO] Running command: gunzip -c /var/lib/cwl/stg8aec2f5d-7de0-43b8-91f5-8e92598421dc/GCA_938033265.1_ERR414453_bin.81_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938033265.1_ERR414453_bin.81_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938033265.1_ERR414453_bin.81_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 17:33:13,423] [INFO] Task succeeded: Prodigal
[2023-06-13 17:33:13,423] [INFO] Task started: HMMsearch
[2023-06-13 17:33:13,423] [INFO] Running command: hmmsearch --tblout GCA_938033265.1_ERR414453_bin.81_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10404c0a-ce00-4df1-a81a-c19a5ca3fec8/dqc_reference/reference_markers.hmm GCA_938033265.1_ERR414453_bin.81_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 17:33:13,681] [INFO] Task succeeded: HMMsearch
[2023-06-13 17:33:13,682] [INFO] Found 6/6 markers.
[2023-06-13 17:33:13,716] [INFO] Query marker FASTA was written to GCA_938033265.1_ERR414453_bin.81_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 17:33:13,716] [INFO] Task started: Blastn
[2023-06-13 17:33:13,717] [INFO] Running command: blastn -query GCA_938033265.1_ERR414453_bin.81_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg10404c0a-ce00-4df1-a81a-c19a5ca3fec8/dqc_reference/reference_markers.fasta -out GCA_938033265.1_ERR414453_bin.81_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:33:14,276] [INFO] Task succeeded: Blastn
[2023-06-13 17:33:14,282] [INFO] Selected 19 target genomes.
[2023-06-13 17:33:14,282] [INFO] Target genome list was writen to GCA_938033265.1_ERR414453_bin.81_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 17:33:14,285] [INFO] Task started: fastANI
[2023-06-13 17:33:14,285] [INFO] Running command: fastANI --query /var/lib/cwl/stg8aec2f5d-7de0-43b8-91f5-8e92598421dc/GCA_938033265.1_ERR414453_bin.81_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938033265.1_ERR414453_bin.81_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938033265.1_ERR414453_bin.81_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 17:33:25,878] [INFO] Task succeeded: fastANI
[2023-06-13 17:33:25,878] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10404c0a-ce00-4df1-a81a-c19a5ca3fec8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 17:33:25,879] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10404c0a-ce00-4df1-a81a-c19a5ca3fec8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 17:33:25,889] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 17:33:25,889] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 17:33:25,889] [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
Mailhella massiliensis	strain=Marseille-P3199	GCA_900155525.1	1903261	1903261	type	True	79.4159	224	1170	95	below_threshold
Desulfovibrio porci	strain=PG-178-WT-4	GCA_009696265.1	2605782	2605782	type	True	77.3905	147	1170	95	below_threshold
Desulfovibrio vulgaris	strain=Hildenborough	GCA_902167245.1	881	881	type	True	77.2046	64	1170	95	below_threshold
Bilophila wadsworthia	strain=ATCC 49260	GCA_000701705.1	35833	35833	type	True	77.1861	137	1170	95	below_threshold
Desulfovibrio piger	strain=ATCC 29098	GCA_000156375.1	901	901	suspected-type	True	77.0622	129	1170	95	below_threshold
Desulfovibrio vulgaris	strain=Hildenborough	GCA_000195755.1	881	881	type	True	77.0274	66	1170	95	below_threshold
Cupidesulfovibrio termitidis	strain=HI1	GCA_000504305.1	42252	42252	type	True	76.9276	115	1170	95	below_threshold
Cupidesulfovibrio oxamicus	strain=NCIMB 9442	GCA_015731765.1	32016	32016	type	True	76.8847	95	1170	95	below_threshold
Desulfovibrio intestinalis	strain=DSM 11275	GCA_014202345.1	58621	58621	type	True	76.6297	78	1170	95	below_threshold
Desulfovibrio legallii	strain=H1T	GCA_004309735.1	571438	571438	type	True	76.5573	96	1170	95	below_threshold
Pseudodesulfovibrio aespoeensis	strain=Aspo-2	GCA_000176915.2	182210	182210	type	True	76.2423	53	1170	95	below_threshold
Pseudodesulfovibrio alkaliphilus	strain=F-1	GCA_009729555.1	2661613	2661613	type	True	76.1654	51	1170	95	below_threshold
Oleidesulfovibrio alaskensis	strain=DSM 16109	GCA_000482745.1	58180	58180	type	True	75.9933	68	1170	95	below_threshold
Desulfovibrio sulfodismutans	strain=DSM 3696	GCA_013376455.1	63561	63561	type	True	75.6352	53	1170	95	below_threshold
Desulfovibrio sulfodismutans	strain=DSM 3696	GCA_010499425.1	63561	63561	type	True	75.6204	50	1170	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 17:33:25,891] [INFO] DFAST Taxonomy check result was written to GCA_938033265.1_ERR414453_bin.81_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 17:33:25,892] [INFO] ===== Taxonomy check completed =====
[2023-06-13 17:33:25,892] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 17:33:25,892] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10404c0a-ce00-4df1-a81a-c19a5ca3fec8/dqc_reference/checkm_data
[2023-06-13 17:33:25,893] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 17:33:25,930] [INFO] Task started: CheckM
[2023-06-13 17:33:25,931] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938033265.1_ERR414453_bin.81_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938033265.1_ERR414453_bin.81_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938033265.1_ERR414453_bin.81_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 17:33:57,174] [INFO] Task succeeded: CheckM
[2023-06-13 17:33:57,176] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 17:33:57,198] [INFO] ===== Completeness check finished =====
[2023-06-13 17:33:57,198] [INFO] ===== Start GTDB Search =====
[2023-06-13 17:33:57,198] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938033265.1_ERR414453_bin.81_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 17:33:57,199] [INFO] Task started: Blastn
[2023-06-13 17:33:57,199] [INFO] Running command: blastn -query GCA_938033265.1_ERR414453_bin.81_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg10404c0a-ce00-4df1-a81a-c19a5ca3fec8/dqc_reference/reference_markers_gtdb.fasta -out GCA_938033265.1_ERR414453_bin.81_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:33:58,015] [INFO] Task succeeded: Blastn
[2023-06-13 17:33:58,019] [INFO] Selected 13 target genomes.
[2023-06-13 17:33:58,019] [INFO] Target genome list was writen to GCA_938033265.1_ERR414453_bin.81_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 17:33:58,032] [INFO] Task started: fastANI
[2023-06-13 17:33:58,032] [INFO] Running command: fastANI --query /var/lib/cwl/stg8aec2f5d-7de0-43b8-91f5-8e92598421dc/GCA_938033265.1_ERR414453_bin.81_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938033265.1_ERR414453_bin.81_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938033265.1_ERR414453_bin.81_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 17:34:06,373] [INFO] Task succeeded: fastANI
[2023-06-13 17:34:06,381] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 17:34:06,381] [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_003150275.1	s__Mailhella excrementigallinarum	99.3147	964	1170	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Mailhella	95.0	99.40	99.36	0.86	0.81	5	conclusive
GCA_910579055.1	s__Mailhella sp910579055	84.6288	649	1170	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Mailhella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119045.1	s__Mailhella merdavium	81.2012	513	1170	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Mailhella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155525.1	s__Mailhella massiliensis	79.4382	223	1170	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Mailhella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541395.1	s__Mailhella merdigallinarum	79.0833	261	1170	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Mailhella	95.0	99.42	99.13	0.88	0.80	5	-
GCA_900553065.1	s__Mailhella sp900553065	78.151	130	1170	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Mailhella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905187505.1	s__Mailhella sp905187505	78.1332	169	1170	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Mailhella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905192935.1	s__Mailhella sp905192935	77.8663	122	1170	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Mailhella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009696265.1	s__Desulfovibrio porci	77.3897	147	1170	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	99.64	99.64	0.91	0.91	2	-
GCF_000195755.1	s__Nitratidesulfovibrio vulgaris	77.0931	65	1170	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Nitratidesulfovibrio	95.0	99.25	98.85	0.97	0.94	6	-
GCF_013376455.1	s__Desulfolutivibrio sulfodismutans	75.6368	55	1170	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfolutivibrio	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-13 17:34:06,383] [INFO] GTDB search result was written to GCA_938033265.1_ERR414453_bin.81_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 17:34:06,383] [INFO] ===== GTDB Search completed =====
[2023-06-13 17:34:06,386] [INFO] DFAST_QC result json was written to GCA_938033265.1_ERR414453_bin.81_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 17:34:06,387] [INFO] DFAST_QC completed!
[2023-06-13 17:34:06,387] [INFO] Total running time: 0h1m4s