[2023-06-08 11:16:17,504] [INFO] DFAST_QC pipeline started.
[2023-06-08 11:16:17,506] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 11:16:17,506] [INFO] DQC Reference Directory: /var/lib/cwl/stgc60a3098-7b2b-41d6-aaa6-efdbc24f501b/dqc_reference
[2023-06-08 11:16:18,860] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 11:16:18,864] [INFO] Task started: Prodigal
[2023-06-08 11:16:18,864] [INFO] Running command: gunzip -c /var/lib/cwl/stga1dcefcd-396c-4e3e-a91c-ddb9f8c6ada6/GCA_947643555.1_SRR15633994_bin.7_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947643555.1_SRR15633994_bin.7_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947643555.1_SRR15633994_bin.7_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 11:16:32,010] [INFO] Task succeeded: Prodigal
[2023-06-08 11:16:32,010] [INFO] Task started: HMMsearch
[2023-06-08 11:16:32,011] [INFO] Running command: hmmsearch --tblout GCA_947643555.1_SRR15633994_bin.7_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc60a3098-7b2b-41d6-aaa6-efdbc24f501b/dqc_reference/reference_markers.hmm GCA_947643555.1_SRR15633994_bin.7_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 11:16:32,265] [INFO] Task succeeded: HMMsearch
[2023-06-08 11:16:32,266] [INFO] Found 6/6 markers.
[2023-06-08 11:16:32,291] [INFO] Query marker FASTA was written to GCA_947643555.1_SRR15633994_bin.7_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 11:16:32,292] [INFO] Task started: Blastn
[2023-06-08 11:16:32,292] [INFO] Running command: blastn -query GCA_947643555.1_SRR15633994_bin.7_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc60a3098-7b2b-41d6-aaa6-efdbc24f501b/dqc_reference/reference_markers.fasta -out GCA_947643555.1_SRR15633994_bin.7_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:16:32,957] [INFO] Task succeeded: Blastn
[2023-06-08 11:16:32,961] [INFO] Selected 24 target genomes.
[2023-06-08 11:16:32,962] [INFO] Target genome list was writen to GCA_947643555.1_SRR15633994_bin.7_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 11:16:32,964] [INFO] Task started: fastANI
[2023-06-08 11:16:32,964] [INFO] Running command: fastANI --query /var/lib/cwl/stga1dcefcd-396c-4e3e-a91c-ddb9f8c6ada6/GCA_947643555.1_SRR15633994_bin.7_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947643555.1_SRR15633994_bin.7_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947643555.1_SRR15633994_bin.7_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 11:16:48,180] [INFO] Task succeeded: fastANI
[2023-06-08 11:16:48,181] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc60a3098-7b2b-41d6-aaa6-efdbc24f501b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 11:16:48,181] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc60a3098-7b2b-41d6-aaa6-efdbc24f501b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 11:16:48,182] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 11:16:48,183] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 11:16:48,183] [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
--------------------------------------------------------------------------------
[2023-06-08 11:16:48,185] [INFO] DFAST Taxonomy check result was written to GCA_947643555.1_SRR15633994_bin.7_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 11:16:48,186] [INFO] ===== Taxonomy check completed =====
[2023-06-08 11:16:48,186] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 11:16:48,186] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc60a3098-7b2b-41d6-aaa6-efdbc24f501b/dqc_reference/checkm_data
[2023-06-08 11:16:48,189] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 11:16:48,220] [INFO] Task started: CheckM
[2023-06-08 11:16:48,220] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947643555.1_SRR15633994_bin.7_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947643555.1_SRR15633994_bin.7_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947643555.1_SRR15633994_bin.7_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 11:17:28,892] [INFO] Task succeeded: CheckM
[2023-06-08 11:17:28,893] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.89%
Contamintation: 1.85%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-08 11:17:28,916] [INFO] ===== Completeness check finished =====
[2023-06-08 11:17:28,916] [INFO] ===== Start GTDB Search =====
[2023-06-08 11:17:28,916] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947643555.1_SRR15633994_bin.7_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 11:17:28,917] [INFO] Task started: Blastn
[2023-06-08 11:17:28,917] [INFO] Running command: blastn -query GCA_947643555.1_SRR15633994_bin.7_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc60a3098-7b2b-41d6-aaa6-efdbc24f501b/dqc_reference/reference_markers_gtdb.fasta -out GCA_947643555.1_SRR15633994_bin.7_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:17:29,748] [INFO] Task succeeded: Blastn
[2023-06-08 11:17:29,751] [INFO] Selected 23 target genomes.
[2023-06-08 11:17:29,751] [INFO] Target genome list was writen to GCA_947643555.1_SRR15633994_bin.7_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 11:17:29,752] [INFO] Task started: fastANI
[2023-06-08 11:17:29,753] [INFO] Running command: fastANI --query /var/lib/cwl/stga1dcefcd-396c-4e3e-a91c-ddb9f8c6ada6/GCA_947643555.1_SRR15633994_bin.7_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947643555.1_SRR15633994_bin.7_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947643555.1_SRR15633994_bin.7_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 11:17:40,494] [INFO] Task succeeded: fastANI
[2023-06-08 11:17:40,522] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 11:17:40,522] [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_910573745.1	s__CAG-485 sp002361215	97.6409	585	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	99.35	98.98	0.93	0.87	9	conclusive
GCA_003833075.1	s__CAG-485 sp002362485	77.846	62	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	98.88	97.97	0.89	0.83	18	-
GCA_910589425.1	s__CAG-485 sp910589425	77.8037	166	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900761855.1	s__CAG-485 sp900761855	77.7367	146	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584125.1	s__CAG-485 sp910584125	77.4643	120	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014802425.1	s__CAG-485 sp014802425	77.2815	106	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554345.1	s__CAG-485 sp900554345	77.277	89	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	99.71	99.71	0.77	0.77	2	-
GCA_014867205.1	s__CAG-485 sp014867205	77.2691	91	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579305.1	s__CAG-485 sp910579305	77.236	57	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900760885.1	s__CAG-485 sp900760885	77.1385	101	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588245.1	s__CAG-485 sp910588245	77.1186	82	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	98.72	98.72	0.89	0.89	2	-
GCA_002491165.1	s__CAG-485 sp002491165	77.1098	94	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	99.22	96.16	0.89	0.85	9	-
GCA_910575615.1	s__UBA7173 sp001689685	77.1025	65	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	99.70	99.58	0.97	0.94	9	-
GCA_002493515.1	s__CAG-485 sp002493515	77.0937	104	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	97.64	97.64	0.78	0.78	2	-
GCA_900549375.1	s__CAG-485 sp900549375	77.0629	64	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	96.66	96.66	0.84	0.84	2	-
GCA_910585275.1	s__CAG-485 sp910585275	76.8577	83	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545955.1	s__UBA7173 sp900545955	76.8245	53	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	97.61	97.55	0.88	0.85	4	-
GCA_900550645.1	s__CAG-485 sp900550645	76.7109	95	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552315.1	s__CAG-485 sp900552315	76.5903	70	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	100.00	100.00	0.98	0.98	2	-
GCA_002404675.1	s__CAG-485 sp002404675	76.579	98	661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	98.43	98.18	0.88	0.86	3	-
--------------------------------------------------------------------------------
[2023-06-08 11:17:40,525] [INFO] GTDB search result was written to GCA_947643555.1_SRR15633994_bin.7_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 11:17:40,525] [INFO] ===== GTDB Search completed =====
[2023-06-08 11:17:40,529] [INFO] DFAST_QC result json was written to GCA_947643555.1_SRR15633994_bin.7_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 11:17:40,529] [INFO] DFAST_QC completed!
[2023-06-08 11:17:40,529] [INFO] Total running time: 0h1m23s