[2023-06-17 14:48:39,562] [INFO] DFAST_QC pipeline started.
[2023-06-17 14:48:39,566] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 14:48:39,567] [INFO] DQC Reference Directory: /var/lib/cwl/stg00908d56-d290-4e57-b26e-931d1170e944/dqc_reference
[2023-06-17 14:48:40,897] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 14:48:40,898] [INFO] Task started: Prodigal
[2023-06-17 14:48:40,899] [INFO] Running command: gunzip -c /var/lib/cwl/stg53890520-0de8-435c-ba5f-aae40b1470b8/GCA_905201065.1_SRR413762-mag-bin.9_genomic.fna.gz | prodigal -d GCA_905201065.1_SRR413762-mag-bin.9_genomic.fna/cds.fna -a GCA_905201065.1_SRR413762-mag-bin.9_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 14:48:59,021] [INFO] Task succeeded: Prodigal
[2023-06-17 14:48:59,021] [INFO] Task started: HMMsearch
[2023-06-17 14:48:59,022] [INFO] Running command: hmmsearch --tblout GCA_905201065.1_SRR413762-mag-bin.9_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg00908d56-d290-4e57-b26e-931d1170e944/dqc_reference/reference_markers.hmm GCA_905201065.1_SRR413762-mag-bin.9_genomic.fna/protein.faa > /dev/null
[2023-06-17 14:48:59,383] [INFO] Task succeeded: HMMsearch
[2023-06-17 14:48:59,384] [INFO] Found 6/6 markers.
[2023-06-17 14:48:59,423] [INFO] Query marker FASTA was written to GCA_905201065.1_SRR413762-mag-bin.9_genomic.fna/markers.fasta
[2023-06-17 14:48:59,423] [INFO] Task started: Blastn
[2023-06-17 14:48:59,423] [INFO] Running command: blastn -query GCA_905201065.1_SRR413762-mag-bin.9_genomic.fna/markers.fasta -db /var/lib/cwl/stg00908d56-d290-4e57-b26e-931d1170e944/dqc_reference/reference_markers.fasta -out GCA_905201065.1_SRR413762-mag-bin.9_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 14:49:00,194] [INFO] Task succeeded: Blastn
[2023-06-17 14:49:00,199] [INFO] Selected 23 target genomes.
[2023-06-17 14:49:00,199] [INFO] Target genome list was writen to GCA_905201065.1_SRR413762-mag-bin.9_genomic.fna/target_genomes.txt
[2023-06-17 14:49:00,203] [INFO] Task started: fastANI
[2023-06-17 14:49:00,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg53890520-0de8-435c-ba5f-aae40b1470b8/GCA_905201065.1_SRR413762-mag-bin.9_genomic.fna.gz --refList GCA_905201065.1_SRR413762-mag-bin.9_genomic.fna/target_genomes.txt --output GCA_905201065.1_SRR413762-mag-bin.9_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 14:49:18,043] [INFO] Task succeeded: fastANI
[2023-06-17 14:49:18,043] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg00908d56-d290-4e57-b26e-931d1170e944/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 14:49:18,044] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg00908d56-d290-4e57-b26e-931d1170e944/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 14:49:18,053] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2023-06-17 14:49:18,053] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-17 14:49:18,053] [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
Culturomica massiliensis	strain=Marseille-P2698	GCA_900091655.1	1841857	1841857	type	True	99.1618	1196	1285	95	conclusive
Odoribacter laneus	strain=YIT 12061	GCA_000243215.1	626933	626933	type	True	77.6672	306	1285	95	below_threshold
Odoribacter splanchnicus	strain=DSM 220712	GCA_000190535.1	28118	28118	type	True	77.2091	213	1285	95	below_threshold
Odoribacter splanchnicus	strain=NCTC10825	GCA_900187175.1	28118	28118	type	True	77.209	213	1285	95	below_threshold
Butyricimonas faecihominis	strain=JCM 18676	GCA_014647335.1	1472416	1472416	type	True	76.9299	95	1285	95	below_threshold
Butyricimonas faecihominis	strain=DSM 105721	GCA_014196975.1	1472416	1472416	type	True	76.8462	93	1285	95	below_threshold
Butyricimonas faecihominis	strain=CCUG 65562	GCA_008830385.1	1472416	1472416	type	True	76.8082	96	1285	95	below_threshold
Butyricimonas virosa	strain=DSM 23226	GCA_000519105.1	544645	544645	type	True	76.7684	87	1285	95	below_threshold
Butyricimonas virosa	strain=DSM 23226	GCA_025148635.1	544645	544645	type	True	76.757	89	1285	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 14:49:18,055] [INFO] DFAST Taxonomy check result was written to GCA_905201065.1_SRR413762-mag-bin.9_genomic.fna/tc_result.tsv
[2023-06-17 14:49:18,055] [INFO] ===== Taxonomy check completed =====
[2023-06-17 14:49:18,056] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 14:49:18,056] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg00908d56-d290-4e57-b26e-931d1170e944/dqc_reference/checkm_data
[2023-06-17 14:49:18,057] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 14:49:18,100] [INFO] Task started: CheckM
[2023-06-17 14:49:18,100] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905201065.1_SRR413762-mag-bin.9_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905201065.1_SRR413762-mag-bin.9_genomic.fna/checkm_input GCA_905201065.1_SRR413762-mag-bin.9_genomic.fna/checkm_result
[2023-06-17 14:50:10,232] [INFO] Task succeeded: CheckM
[2023-06-17 14:50:10,234] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 14:50:10,258] [INFO] ===== Completeness check finished =====
[2023-06-17 14:50:10,258] [INFO] ===== Start GTDB Search =====
[2023-06-17 14:50:10,259] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905201065.1_SRR413762-mag-bin.9_genomic.fna/markers.fasta)
[2023-06-17 14:50:10,259] [INFO] Task started: Blastn
[2023-06-17 14:50:10,259] [INFO] Running command: blastn -query GCA_905201065.1_SRR413762-mag-bin.9_genomic.fna/markers.fasta -db /var/lib/cwl/stg00908d56-d290-4e57-b26e-931d1170e944/dqc_reference/reference_markers_gtdb.fasta -out GCA_905201065.1_SRR413762-mag-bin.9_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 14:50:11,065] [INFO] Task succeeded: Blastn
[2023-06-17 14:50:11,070] [INFO] Selected 23 target genomes.
[2023-06-17 14:50:11,070] [INFO] Target genome list was writen to GCA_905201065.1_SRR413762-mag-bin.9_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 14:50:11,079] [INFO] Task started: fastANI
[2023-06-17 14:50:11,079] [INFO] Running command: fastANI --query /var/lib/cwl/stg53890520-0de8-435c-ba5f-aae40b1470b8/GCA_905201065.1_SRR413762-mag-bin.9_genomic.fna.gz --refList GCA_905201065.1_SRR413762-mag-bin.9_genomic.fna/target_genomes_gtdb.txt --output GCA_905201065.1_SRR413762-mag-bin.9_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 14:50:26,067] [INFO] Task succeeded: fastANI
[2023-06-17 14:50:26,090] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 14:50:26,091] [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_900091655.1	s__Odoribacter massiliensis	99.1618	1196	1285	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Odoribacter	95.0	99.35	99.12	0.95	0.91	6	conclusive
GCA_905216195.1	s__Odoribacter sp905216195	78.1453	297	1285	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Odoribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000243215.1	s__Odoribacter laneus	77.6569	307	1285	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Odoribacter	95.0	99.26	98.81	0.94	0.87	6	-
GCA_910588375.1	s__Odoribacter sp910588375	77.5762	199	1285	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Odoribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009935865.1	s__Odoribacter sp009935865	77.3663	157	1285	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Odoribacter	95.0	99.00	98.96	0.93	0.92	3	-
GCA_910589025.1	s__Odoribacter sp910589025	77.3641	183	1285	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Odoribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541415.1	s__Odoribacter sp900541415	77.2735	192	1285	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Odoribacter	95.0	99.97	99.97	0.96	0.96	2	-
GCA_900544025.1	s__Odoribacter sp900544025	77.2373	156	1285	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Odoribacter	95.0	98.76	97.68	0.87	0.80	4	-
GCF_000190535.1	s__Odoribacter splanchnicus	77.2221	212	1285	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Odoribacter	95.0	98.99	98.34	0.85	0.73	51	-
GCA_910578105.1	s__Odoribacter sp910578105	77.159	152	1285	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Odoribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548135.1	s__Odoribacter sp900548135	76.9692	102	1285	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Odoribacter	95.0	100.00	100.00	0.94	0.94	2	-
GCF_014647335.1	s__Butyricimonas faecihominis	76.9034	96	1285	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	99.47	98.30	0.95	0.86	7	-
GCF_000519105.1	s__Butyricimonas virosa	76.7927	86	1285	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	98.30	95.30	0.86	0.78	18	-
GCA_905193145.1	s__Odoribacter sp905193145	76.4549	81	1285	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Odoribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184685.1	s__Butyricimonas sp900184685	76.329	106	1285	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	97.37	96.90	0.86	0.81	4	-
--------------------------------------------------------------------------------
[2023-06-17 14:50:26,093] [INFO] GTDB search result was written to GCA_905201065.1_SRR413762-mag-bin.9_genomic.fna/result_gtdb.tsv
[2023-06-17 14:50:26,093] [INFO] ===== GTDB Search completed =====
[2023-06-17 14:50:26,098] [INFO] DFAST_QC result json was written to GCA_905201065.1_SRR413762-mag-bin.9_genomic.fna/dqc_result.json
[2023-06-17 14:50:26,098] [INFO] DFAST_QC completed!
[2023-06-17 14:50:26,098] [INFO] Total running time: 0h1m47s