[2023-06-04 20:24:02,236] [INFO] DFAST_QC pipeline started.
[2023-06-04 20:24:02,244] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 20:24:02,244] [INFO] DQC Reference Directory: /var/lib/cwl/stg747ac564-5dbb-4853-b128-2148a56e3ea3/dqc_reference
[2023-06-04 20:24:03,767] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 20:24:03,768] [INFO] Task started: Prodigal
[2023-06-04 20:24:03,768] [INFO] Running command: gunzip -c /var/lib/cwl/stg4d2b9ce3-979a-492b-b2d2-5ed64a1f3065/GCA_934647185.1_ERR7746411_bin.300_genomic.fna.gz | prodigal -d GCA_934647185.1_ERR7746411_bin.300_genomic.fna/cds.fna -a GCA_934647185.1_ERR7746411_bin.300_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 20:24:08,903] [INFO] Task succeeded: Prodigal
[2023-06-04 20:24:08,904] [INFO] Task started: HMMsearch
[2023-06-04 20:24:08,904] [INFO] Running command: hmmsearch --tblout GCA_934647185.1_ERR7746411_bin.300_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg747ac564-5dbb-4853-b128-2148a56e3ea3/dqc_reference/reference_markers.hmm GCA_934647185.1_ERR7746411_bin.300_genomic.fna/protein.faa > /dev/null
[2023-06-04 20:24:09,087] [INFO] Task succeeded: HMMsearch
[2023-06-04 20:24:09,088] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg4d2b9ce3-979a-492b-b2d2-5ed64a1f3065/GCA_934647185.1_ERR7746411_bin.300_genomic.fna.gz]
[2023-06-04 20:24:09,109] [INFO] Query marker FASTA was written to GCA_934647185.1_ERR7746411_bin.300_genomic.fna/markers.fasta
[2023-06-04 20:24:09,109] [INFO] Task started: Blastn
[2023-06-04 20:24:09,110] [INFO] Running command: blastn -query GCA_934647185.1_ERR7746411_bin.300_genomic.fna/markers.fasta -db /var/lib/cwl/stg747ac564-5dbb-4853-b128-2148a56e3ea3/dqc_reference/reference_markers.fasta -out GCA_934647185.1_ERR7746411_bin.300_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:24:09,743] [INFO] Task succeeded: Blastn
[2023-06-04 20:24:09,747] [INFO] Selected 12 target genomes.
[2023-06-04 20:24:09,748] [INFO] Target genome list was writen to GCA_934647185.1_ERR7746411_bin.300_genomic.fna/target_genomes.txt
[2023-06-04 20:24:09,749] [INFO] Task started: fastANI
[2023-06-04 20:24:09,749] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d2b9ce3-979a-492b-b2d2-5ed64a1f3065/GCA_934647185.1_ERR7746411_bin.300_genomic.fna.gz --refList GCA_934647185.1_ERR7746411_bin.300_genomic.fna/target_genomes.txt --output GCA_934647185.1_ERR7746411_bin.300_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 20:24:14,744] [INFO] Task succeeded: fastANI
[2023-06-04 20:24:14,745] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg747ac564-5dbb-4853-b128-2148a56e3ea3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 20:24:14,745] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg747ac564-5dbb-4853-b128-2148a56e3ea3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 20:24:14,754] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 20:24:14,754] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 20:24:14,754] [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
Collinsella aerofaciens	strain=ATCC 25986	GCA_000169035.1	74426	74426	type	True	90.1621	419	531	95	below_threshold
Collinsella aerofaciens	strain=JCM 10188	GCA_010509075.1	74426	74426	type	True	89.9755	416	531	95	below_threshold
Collinsella aerofaciens	strain=NCTC11838	GCA_900461335.1	74426	74426	type	True	89.965	422	531	95	below_threshold
Collinsella bouchesdurhonensis	strain=Marseille-P3296	GCA_900155365.1	1907654	1907654	type	True	79.6199	164	531	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	79.6043	182	531	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	79.4922	184	531	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	78.9237	166	531	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	78.5652	164	531	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 20:24:14,756] [INFO] DFAST Taxonomy check result was written to GCA_934647185.1_ERR7746411_bin.300_genomic.fna/tc_result.tsv
[2023-06-04 20:24:14,757] [INFO] ===== Taxonomy check completed =====
[2023-06-04 20:24:14,757] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 20:24:14,757] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg747ac564-5dbb-4853-b128-2148a56e3ea3/dqc_reference/checkm_data
[2023-06-04 20:24:14,759] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 20:24:14,783] [INFO] Task started: CheckM
[2023-06-04 20:24:14,784] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934647185.1_ERR7746411_bin.300_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934647185.1_ERR7746411_bin.300_genomic.fna/checkm_input GCA_934647185.1_ERR7746411_bin.300_genomic.fna/checkm_result
[2023-06-04 20:24:36,126] [INFO] Task succeeded: CheckM
[2023-06-04 20:24:36,127] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 20:24:36,150] [INFO] ===== Completeness check finished =====
[2023-06-04 20:24:36,151] [INFO] ===== Start GTDB Search =====
[2023-06-04 20:24:36,151] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934647185.1_ERR7746411_bin.300_genomic.fna/markers.fasta)
[2023-06-04 20:24:36,151] [INFO] Task started: Blastn
[2023-06-04 20:24:36,151] [INFO] Running command: blastn -query GCA_934647185.1_ERR7746411_bin.300_genomic.fna/markers.fasta -db /var/lib/cwl/stg747ac564-5dbb-4853-b128-2148a56e3ea3/dqc_reference/reference_markers_gtdb.fasta -out GCA_934647185.1_ERR7746411_bin.300_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:24:37,081] [INFO] Task succeeded: Blastn
[2023-06-04 20:24:37,086] [INFO] Selected 20 target genomes.
[2023-06-04 20:24:37,087] [INFO] Target genome list was writen to GCA_934647185.1_ERR7746411_bin.300_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 20:24:37,099] [INFO] Task started: fastANI
[2023-06-04 20:24:37,100] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d2b9ce3-979a-492b-b2d2-5ed64a1f3065/GCA_934647185.1_ERR7746411_bin.300_genomic.fna.gz --refList GCA_934647185.1_ERR7746411_bin.300_genomic.fna/target_genomes_gtdb.txt --output GCA_934647185.1_ERR7746411_bin.300_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 20:24:44,744] [INFO] Task succeeded: fastANI
[2023-06-04 20:24:44,768] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-04 20:24:44,769] [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_900544065.1	s__Collinsella sp900544065	90.5936	372	531	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546455.1	s__Collinsella sp900546455	90.3143	356	531	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900542125.1	s__Collinsella sp900542125	90.2412	393	531	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015553355.1	s__Collinsella aerofaciens_V	90.1638	401	531	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.92	96.92	0.91	0.91	2	-
GCA_900541135.1	s__Collinsella sp900541135	90.1541	384	531	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541715.1	s__Collinsella sp900541715	90.0462	351	531	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0922	N/A	N/A	N/A	N/A	1	-
GCA_900548255.1	s__Collinsella sp900548255	90.0104	348	531	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_019041915.1	s__Collinsella sp019041915	90.0041	405	531	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.145	96.63	95.48	0.93	0.87	6	-
GCF_003436275.1	s__Collinsella sp003436275	89.9505	394	531	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.89	95.08	0.88	0.83	16	-
GCA_900546105.1	s__Collinsella sp900546105	89.9254	356	531	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900765185.1	s__Collinsella sp900765185	89.8896	300	531	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550415.1	s__Collinsella sp900550415	89.8263	358	531	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900756725.1	s__Collinsella sp900756725	89.8095	324	531	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.39	95.39	0.81	0.81	2	-
GCA_900551605.1	s__Collinsella sp900551605	89.7981	268	531	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.27	95.27	0.92	0.92	2	-
GCA_900550205.1	s__Collinsella sp900550205	89.7472	306	531	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.03	95.54	0.85	0.78	4	-
GCF_003466125.1	s__Collinsella sp003466125	89.5117	407	531	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.79	97.08	0.91	0.86	19	-
GCA_900556515.1	s__Collinsella sp900556515	89.5062	260	531	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541695.1	s__Collinsella sp900541695	89.4114	395	531	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.64	95.64	0.91	0.91	2	-
GCA_900552395.1	s__Collinsella sp900552395	89.3509	289	531	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.15	N/A	N/A	N/A	N/A	1	-
GCA_900553345.1	s__Collinsella sp900553345	88.8864	271	531	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 20:24:44,771] [INFO] GTDB search result was written to GCA_934647185.1_ERR7746411_bin.300_genomic.fna/result_gtdb.tsv
[2023-06-04 20:24:44,772] [INFO] ===== GTDB Search completed =====
[2023-06-04 20:24:44,778] [INFO] DFAST_QC result json was written to GCA_934647185.1_ERR7746411_bin.300_genomic.fna/dqc_result.json
[2023-06-04 20:24:44,778] [INFO] DFAST_QC completed!
[2023-06-04 20:24:44,778] [INFO] Total running time: 0h0m43s