[2023-06-04 21:45:23,260] [INFO] DFAST_QC pipeline started.
[2023-06-04 21:45:23,262] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 21:45:23,262] [INFO] DQC Reference Directory: /var/lib/cwl/stga1d51d3e-75a2-417c-b937-65ec42c67c77/dqc_reference
[2023-06-04 21:45:26,510] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 21:45:26,511] [INFO] Task started: Prodigal
[2023-06-04 21:45:26,511] [INFO] Running command: gunzip -c /var/lib/cwl/stg5add60d4-06c5-4056-9661-4f7f4f1b8ea1/GCA_934539255.1_ERR7738597_bin.71_genomic.fna.gz | prodigal -d GCA_934539255.1_ERR7738597_bin.71_genomic.fna/cds.fna -a GCA_934539255.1_ERR7738597_bin.71_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 21:45:32,705] [INFO] Task succeeded: Prodigal
[2023-06-04 21:45:32,706] [INFO] Task started: HMMsearch
[2023-06-04 21:45:32,706] [INFO] Running command: hmmsearch --tblout GCA_934539255.1_ERR7738597_bin.71_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1d51d3e-75a2-417c-b937-65ec42c67c77/dqc_reference/reference_markers.hmm GCA_934539255.1_ERR7738597_bin.71_genomic.fna/protein.faa > /dev/null
[2023-06-04 21:45:32,970] [INFO] Task succeeded: HMMsearch
[2023-06-04 21:45:32,971] [INFO] Found 6/6 markers.
[2023-06-04 21:45:33,005] [INFO] Query marker FASTA was written to GCA_934539255.1_ERR7738597_bin.71_genomic.fna/markers.fasta
[2023-06-04 21:45:33,005] [INFO] Task started: Blastn
[2023-06-04 21:45:33,005] [INFO] Running command: blastn -query GCA_934539255.1_ERR7738597_bin.71_genomic.fna/markers.fasta -db /var/lib/cwl/stga1d51d3e-75a2-417c-b937-65ec42c67c77/dqc_reference/reference_markers.fasta -out GCA_934539255.1_ERR7738597_bin.71_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 21:45:33,660] [INFO] Task succeeded: Blastn
[2023-06-04 21:45:33,664] [INFO] Selected 13 target genomes.
[2023-06-04 21:45:33,664] [INFO] Target genome list was writen to GCA_934539255.1_ERR7738597_bin.71_genomic.fna/target_genomes.txt
[2023-06-04 21:45:33,667] [INFO] Task started: fastANI
[2023-06-04 21:45:33,667] [INFO] Running command: fastANI --query /var/lib/cwl/stg5add60d4-06c5-4056-9661-4f7f4f1b8ea1/GCA_934539255.1_ERR7738597_bin.71_genomic.fna.gz --refList GCA_934539255.1_ERR7738597_bin.71_genomic.fna/target_genomes.txt --output GCA_934539255.1_ERR7738597_bin.71_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 21:45:41,825] [INFO] Task succeeded: fastANI
[2023-06-04 21:45:41,825] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1d51d3e-75a2-417c-b937-65ec42c67c77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 21:45:41,826] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1d51d3e-75a2-417c-b937-65ec42c67c77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 21:45:41,834] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 21:45:41,835] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 21:45:41,835] [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	77.9708	121	610	95	below_threshold
Bilophila wadsworthia	strain=ATCC 49260	GCA_000701705.1	35833	35833	type	True	77.3111	83	610	95	below_threshold
Desulfovibrio porci	strain=PG-178-WT-4	GCA_009696265.1	2605782	2605782	type	True	77.119	104	610	95	below_threshold
Cupidesulfovibrio liaohensis	strain=XJ01	GCA_011682075.1	2604158	2604158	type	True	77.0221	98	610	95	below_threshold
Desulfovibrio legallii	strain=H1T	GCA_004309735.1	571438	571438	type	True	76.9985	75	610	95	below_threshold
Cupidesulfovibrio termitidis	strain=HI1	GCA_000504305.1	42252	42252	type	True	76.9843	113	610	95	below_threshold
Desulfovibrio piger	strain=ATCC 29098	GCA_000156375.1	901	901	suspected-type	True	76.9628	84	610	95	below_threshold
Fundidesulfovibrio putealis	strain=DSM 16056	GCA_000429325.1	270496	270496	type	True	76.1054	70	610	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 21:45:41,837] [INFO] DFAST Taxonomy check result was written to GCA_934539255.1_ERR7738597_bin.71_genomic.fna/tc_result.tsv
[2023-06-04 21:45:41,838] [INFO] ===== Taxonomy check completed =====
[2023-06-04 21:45:41,838] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 21:45:41,838] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1d51d3e-75a2-417c-b937-65ec42c67c77/dqc_reference/checkm_data
[2023-06-04 21:45:41,840] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 21:45:41,872] [INFO] Task started: CheckM
[2023-06-04 21:45:41,872] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934539255.1_ERR7738597_bin.71_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934539255.1_ERR7738597_bin.71_genomic.fna/checkm_input GCA_934539255.1_ERR7738597_bin.71_genomic.fna/checkm_result
[2023-06-04 21:46:06,137] [INFO] Task succeeded: CheckM
[2023-06-04 21:46:06,139] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 21:46:06,164] [INFO] ===== Completeness check finished =====
[2023-06-04 21:46:06,164] [INFO] ===== Start GTDB Search =====
[2023-06-04 21:46:06,165] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934539255.1_ERR7738597_bin.71_genomic.fna/markers.fasta)
[2023-06-04 21:46:06,165] [INFO] Task started: Blastn
[2023-06-04 21:46:06,166] [INFO] Running command: blastn -query GCA_934539255.1_ERR7738597_bin.71_genomic.fna/markers.fasta -db /var/lib/cwl/stga1d51d3e-75a2-417c-b937-65ec42c67c77/dqc_reference/reference_markers_gtdb.fasta -out GCA_934539255.1_ERR7738597_bin.71_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 21:46:06,935] [INFO] Task succeeded: Blastn
[2023-06-04 21:46:06,955] [INFO] Selected 13 target genomes.
[2023-06-04 21:46:06,956] [INFO] Target genome list was writen to GCA_934539255.1_ERR7738597_bin.71_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 21:46:07,103] [INFO] Task started: fastANI
[2023-06-04 21:46:07,104] [INFO] Running command: fastANI --query /var/lib/cwl/stg5add60d4-06c5-4056-9661-4f7f4f1b8ea1/GCA_934539255.1_ERR7738597_bin.71_genomic.fna.gz --refList GCA_934539255.1_ERR7738597_bin.71_genomic.fna/target_genomes_gtdb.txt --output GCA_934539255.1_ERR7738597_bin.71_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 21:46:13,489] [INFO] Task succeeded: fastANI
[2023-06-04 21:46:13,499] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 21:46:13,500] [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_900541395.1	s__Mailhella merdigallinarum	99.2084	551	610	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Mailhella	95.0	99.42	99.13	0.88	0.80	5	conclusive
GCA_003150275.1	s__Mailhella excrementigallinarum	78.3945	176	610	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Mailhella	95.0	99.40	99.36	0.86	0.81	5	-
GCA_017408905.1	s__Mailhella sp017408905	78.0082	68	610	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Mailhella	95.0	97.64	97.64	0.73	0.73	2	-
GCF_900155525.1	s__Mailhella massiliensis	77.9732	121	610	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	77.8403	106	610	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_910579055.1	s__Mailhella sp910579055	77.8111	140	610	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	77.7407	78	610	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	77.7249	96	610	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_900553065.1	s__Mailhella sp900553065	77.4232	61	610	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_011039085.1	s__Desulfovibrio sp011039085	77.0692	67	610	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	96.72	96.72	0.85	0.85	2	-
GCA_015062205.1	s__Desulfovibrio desulfuricans_D	76.466	93	610	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118345.1	s__Desulfovibrio intestinavium	76.445	85	610	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 21:46:13,502] [INFO] GTDB search result was written to GCA_934539255.1_ERR7738597_bin.71_genomic.fna/result_gtdb.tsv
[2023-06-04 21:46:13,502] [INFO] ===== GTDB Search completed =====
[2023-06-04 21:46:13,506] [INFO] DFAST_QC result json was written to GCA_934539255.1_ERR7738597_bin.71_genomic.fna/dqc_result.json
[2023-06-04 21:46:13,506] [INFO] DFAST_QC completed!
[2023-06-04 21:46:13,506] [INFO] Total running time: 0h0m50s