[2023-06-12 23:05:46,086] [INFO] DFAST_QC pipeline started.
[2023-06-12 23:05:46,088] [INFO] DFAST_QC version: 0.5.7
[2023-06-12 23:05:46,089] [INFO] DQC Reference Directory: /var/lib/cwl/stg69578990-1b69-4e51-9101-86383954ae21/dqc_reference
[2023-06-12 23:05:47,872] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-12 23:05:47,873] [INFO] Task started: Prodigal
[2023-06-12 23:05:47,873] [INFO] Running command: gunzip -c /var/lib/cwl/stg079b4a20-8f7a-4574-8c9f-694486a5a76f/GCA_938014115.1_ERR3160563_bin.110_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938014115.1_ERR3160563_bin.110_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938014115.1_ERR3160563_bin.110_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-12 23:06:00,911] [INFO] Task succeeded: Prodigal
[2023-06-12 23:06:00,912] [INFO] Task started: HMMsearch
[2023-06-12 23:06:00,912] [INFO] Running command: hmmsearch --tblout GCA_938014115.1_ERR3160563_bin.110_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69578990-1b69-4e51-9101-86383954ae21/dqc_reference/reference_markers.hmm GCA_938014115.1_ERR3160563_bin.110_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-12 23:06:01,188] [INFO] Task succeeded: HMMsearch
[2023-06-12 23:06:01,190] [INFO] Found 6/6 markers.
[2023-06-12 23:06:01,230] [INFO] Query marker FASTA was written to GCA_938014115.1_ERR3160563_bin.110_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-12 23:06:01,231] [INFO] Task started: Blastn
[2023-06-12 23:06:01,231] [INFO] Running command: blastn -query GCA_938014115.1_ERR3160563_bin.110_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg69578990-1b69-4e51-9101-86383954ae21/dqc_reference/reference_markers.fasta -out GCA_938014115.1_ERR3160563_bin.110_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 23:06:01,895] [INFO] Task succeeded: Blastn
[2023-06-12 23:06:01,900] [INFO] Selected 19 target genomes.
[2023-06-12 23:06:01,900] [INFO] Target genome list was writen to GCA_938014115.1_ERR3160563_bin.110_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-12 23:06:01,904] [INFO] Task started: fastANI
[2023-06-12 23:06:01,904] [INFO] Running command: fastANI --query /var/lib/cwl/stg079b4a20-8f7a-4574-8c9f-694486a5a76f/GCA_938014115.1_ERR3160563_bin.110_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938014115.1_ERR3160563_bin.110_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938014115.1_ERR3160563_bin.110_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-12 23:06:15,624] [INFO] Task succeeded: fastANI
[2023-06-12 23:06:15,625] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69578990-1b69-4e51-9101-86383954ae21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-12 23:06:15,625] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69578990-1b69-4e51-9101-86383954ae21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-12 23:06:15,636] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2023-06-12 23:06:15,636] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-12 23:06:15,636] [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
Bilophila wadsworthia	strain=ATCC 49260	GCA_000701705.1	35833	35833	type	True	98.8472	1177	1370	95	conclusive
Desulfovibrio piger	strain=ATCC 29098	GCA_000156375.1	901	901	suspected-type	True	77.4852	194	1370	95	below_threshold
Mailhella massiliensis	strain=Marseille-P3199	GCA_900155525.1	1903261	1903261	type	True	77.4541	173	1370	95	below_threshold
Cupidesulfovibrio oxamicus	strain=NCIMB 9442	GCA_015731765.1	32016	32016	type	True	77.4477	151	1370	95	below_threshold
Cupidesulfovibrio termitidis	strain=HI1	GCA_000504305.1	42252	42252	type	True	77.3588	176	1370	95	below_threshold
Cupidesulfovibrio liaohensis	strain=XJ01	GCA_011682075.1	2604158	2604158	type	True	77.3587	163	1370	95	below_threshold
Desulfovibrio vulgaris	strain=Hildenborough	GCA_000195755.1	881	881	type	True	77.1556	151	1370	95	below_threshold
Desulfovibrio vulgaris	strain=Hildenborough	GCA_902167245.1	881	881	type	True	77.1422	153	1370	95	below_threshold
Desulfovibrio subterraneus	strain=HN2	GCA_013340285.1	2718620	2718620	type	True	76.7615	84	1370	95	below_threshold
Desulfomicrobium escambiense	strain=DSM 10707	GCA_000428825.1	29503	29503	type	True	76.3482	95	1370	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-12 23:06:15,639] [INFO] DFAST Taxonomy check result was written to GCA_938014115.1_ERR3160563_bin.110_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-12 23:06:15,645] [INFO] ===== Taxonomy check completed =====
[2023-06-12 23:06:15,646] [INFO] ===== Start completeness check using CheckM =====
[2023-06-12 23:06:15,647] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69578990-1b69-4e51-9101-86383954ae21/dqc_reference/checkm_data
[2023-06-12 23:06:15,652] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-12 23:06:15,695] [INFO] Task started: CheckM
[2023-06-12 23:06:15,696] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938014115.1_ERR3160563_bin.110_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938014115.1_ERR3160563_bin.110_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938014115.1_ERR3160563_bin.110_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-12 23:06:55,925] [INFO] Task succeeded: CheckM
[2023-06-12 23:06:55,926] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-12 23:06:55,948] [INFO] ===== Completeness check finished =====
[2023-06-12 23:06:55,949] [INFO] ===== Start GTDB Search =====
[2023-06-12 23:06:55,949] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938014115.1_ERR3160563_bin.110_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-12 23:06:55,950] [INFO] Task started: Blastn
[2023-06-12 23:06:55,950] [INFO] Running command: blastn -query GCA_938014115.1_ERR3160563_bin.110_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg69578990-1b69-4e51-9101-86383954ae21/dqc_reference/reference_markers_gtdb.fasta -out GCA_938014115.1_ERR3160563_bin.110_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 23:06:56,847] [INFO] Task succeeded: Blastn
[2023-06-12 23:06:56,852] [INFO] Selected 6 target genomes.
[2023-06-12 23:06:56,852] [INFO] Target genome list was writen to GCA_938014115.1_ERR3160563_bin.110_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-12 23:06:56,854] [INFO] Task started: fastANI
[2023-06-12 23:06:56,854] [INFO] Running command: fastANI --query /var/lib/cwl/stg079b4a20-8f7a-4574-8c9f-694486a5a76f/GCA_938014115.1_ERR3160563_bin.110_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938014115.1_ERR3160563_bin.110_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938014115.1_ERR3160563_bin.110_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-12 23:07:01,630] [INFO] Task succeeded: fastANI
[2023-06-12 23:07:01,644] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-12 23:07:01,645] [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_000701705.1	s__Bilophila wadsworthia	98.8472	1177	1370	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Bilophila	95.0	98.41	97.08	0.87	0.83	9	conclusive
GCA_900550745.1	s__Bilophila sp900550745	92.7067	515	1370	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Bilophila	95.0	97.48	97.27	0.74	0.71	3	-
GCA_900553145.1	s__Bilophila sp900553145	89.9759	842	1370	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Bilophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902373525.1	s__Bilophila sp902373525	84.7527	732	1370	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Bilophila	95.0	98.79	98.79	0.94	0.94	2	-
GCA_019114025.1	s__Bilophila faecipullorum	82.4312	458	1370	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Bilophila	95.0	99.16	98.64	0.81	0.70	3	-
GCA_900555975.1	s__Mailhella sp900555975	78.5929	55	1370	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Mailhella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-12 23:07:01,647] [INFO] GTDB search result was written to GCA_938014115.1_ERR3160563_bin.110_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-12 23:07:01,648] [INFO] ===== GTDB Search completed =====
[2023-06-12 23:07:01,652] [INFO] DFAST_QC result json was written to GCA_938014115.1_ERR3160563_bin.110_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-12 23:07:01,652] [INFO] DFAST_QC completed!
[2023-06-12 23:07:01,652] [INFO] Total running time: 0h1m16s