[2023-06-30 12:04:57,811] [INFO] DFAST_QC pipeline started.
[2023-06-30 12:04:57,813] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 12:04:57,813] [INFO] DQC Reference Directory: /var/lib/cwl/stgd24edc9e-0974-4c02-865d-03be95341615/dqc_reference
[2023-06-30 12:04:59,139] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 12:04:59,140] [INFO] Task started: Prodigal
[2023-06-30 12:04:59,140] [INFO] Running command: gunzip -c /var/lib/cwl/stg60fc7acb-d311-40a1-8bef-1dd3e9b4f242/GCA_946621925.1_SRR873602_bin.131_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_946621925.1_SRR873602_bin.131_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_946621925.1_SRR873602_bin.131_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 12:05:11,173] [INFO] Task succeeded: Prodigal
[2023-06-30 12:05:11,174] [INFO] Task started: HMMsearch
[2023-06-30 12:05:11,174] [INFO] Running command: hmmsearch --tblout GCA_946621925.1_SRR873602_bin.131_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd24edc9e-0974-4c02-865d-03be95341615/dqc_reference/reference_markers.hmm GCA_946621925.1_SRR873602_bin.131_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-30 12:05:11,441] [INFO] Task succeeded: HMMsearch
[2023-06-30 12:05:11,443] [INFO] Found 6/6 markers.
[2023-06-30 12:05:11,468] [INFO] Query marker FASTA was written to GCA_946621925.1_SRR873602_bin.131_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-30 12:05:11,469] [INFO] Task started: Blastn
[2023-06-30 12:05:11,469] [INFO] Running command: blastn -query GCA_946621925.1_SRR873602_bin.131_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgd24edc9e-0974-4c02-865d-03be95341615/dqc_reference/reference_markers.fasta -out GCA_946621925.1_SRR873602_bin.131_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:05:12,070] [INFO] Task succeeded: Blastn
[2023-06-30 12:05:12,075] [INFO] Selected 28 target genomes.
[2023-06-30 12:05:12,076] [INFO] Target genome list was writen to GCA_946621925.1_SRR873602_bin.131_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-30 12:05:12,085] [INFO] Task started: fastANI
[2023-06-30 12:05:12,085] [INFO] Running command: fastANI --query /var/lib/cwl/stg60fc7acb-d311-40a1-8bef-1dd3e9b4f242/GCA_946621925.1_SRR873602_bin.131_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_946621925.1_SRR873602_bin.131_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_946621925.1_SRR873602_bin.131_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 12:05:27,870] [INFO] Task succeeded: fastANI
[2023-06-30 12:05:27,870] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd24edc9e-0974-4c02-865d-03be95341615/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 12:05:27,871] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd24edc9e-0974-4c02-865d-03be95341615/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 12:05:27,880] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 12:05:27,880] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 12:05:27,881] [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
Phocaeicola barnesiae	strain=JCM 13652	GCA_000613645.1	376804	376804	type	True	77.5587	74	713	95	below_threshold
Phocaeicola barnesiae	strain=DSM 18169	GCA_000374585.1	376804	376804	type	True	77.5416	75	713	95	below_threshold
Phocaeicola plebeius	strain=DSM 17135	GCA_000187895.1	310297	310297	suspected-type	True	77.4928	66	713	95	below_threshold
Phocaeicola coprocola	strain=DSM 17136	GCA_000154845.1	310298	310298	suspected-type	True	77.3318	60	713	95	below_threshold
Bacteroides thetaiotaomicron	strain=NCTC10582	GCA_900445595.1	818	818	type	True	77.2798	51	713	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI-5482	GCA_000011065.1	818	818	type	True	77.2065	54	713	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI-5482	GCA_020179495.1	818	818	type	True	77.2065	53	713	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	77.206	54	713	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI-5482	GCA_002959695.1	818	818	type	True	77.206	54	713	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	76.33	51	713	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 12:05:27,883] [INFO] DFAST Taxonomy check result was written to GCA_946621925.1_SRR873602_bin.131_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-30 12:05:27,883] [INFO] ===== Taxonomy check completed =====
[2023-06-30 12:05:27,884] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 12:05:27,884] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd24edc9e-0974-4c02-865d-03be95341615/dqc_reference/checkm_data
[2023-06-30 12:05:27,886] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 12:05:27,922] [INFO] Task started: CheckM
[2023-06-30 12:05:27,923] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_946621925.1_SRR873602_bin.131_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_946621925.1_SRR873602_bin.131_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_946621925.1_SRR873602_bin.131_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-30 12:06:07,174] [INFO] Task succeeded: CheckM
[2023-06-30 12:06:07,176] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 12:06:07,199] [INFO] ===== Completeness check finished =====
[2023-06-30 12:06:07,199] [INFO] ===== Start GTDB Search =====
[2023-06-30 12:06:07,199] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_946621925.1_SRR873602_bin.131_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-30 12:06:07,200] [INFO] Task started: Blastn
[2023-06-30 12:06:07,200] [INFO] Running command: blastn -query GCA_946621925.1_SRR873602_bin.131_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgd24edc9e-0974-4c02-865d-03be95341615/dqc_reference/reference_markers_gtdb.fasta -out GCA_946621925.1_SRR873602_bin.131_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:06:07,987] [INFO] Task succeeded: Blastn
[2023-06-30 12:06:07,993] [INFO] Selected 27 target genomes.
[2023-06-30 12:06:07,993] [INFO] Target genome list was writen to GCA_946621925.1_SRR873602_bin.131_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 12:06:08,023] [INFO] Task started: fastANI
[2023-06-30 12:06:08,024] [INFO] Running command: fastANI --query /var/lib/cwl/stg60fc7acb-d311-40a1-8bef-1dd3e9b4f242/GCA_946621925.1_SRR873602_bin.131_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_946621925.1_SRR873602_bin.131_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_946621925.1_SRR873602_bin.131_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 12:06:23,390] [INFO] Task succeeded: fastANI
[2023-06-30 12:06:23,402] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 12:06:23,402] [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_902779535.1	s__Phocaeicola sp902779535	98.3526	618	713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.97	97.63	0.83	0.71	5	conclusive
GCF_016902295.1	s__Phocaeicola caecigallinarum_A	77.6658	55	713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.48	97.48	0.83	0.83	2	-
GCF_016900355.1	s__Phocaeicola sp900551065	77.4283	66	713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	96.34	95.04	0.86	0.84	4	-
GCF_900128455.1	s__Phocaeicola mediterraneensis	77.426	67	713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.66	98.61	0.84	0.80	3	-
GCA_902362595.1	s__Phocaeicola merdigallinarum	77.3228	65	713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.33	96.40	0.87	0.80	6	-
GCF_000011065.1	s__Bacteroides thetaiotaomicron	77.2573	53	713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.45	97.24	0.84	0.75	121	-
GCA_015060765.1	s__Phocaeicola sp015060765	77.2456	70	713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002161765.1	s__Phocaeicola merdavium	77.2367	52	713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.33	98.22	0.87	0.86	5	-
GCF_003437535.1	s__Phocaeicola plebeius_A	77.1489	63	713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.72	95.85	0.84	0.73	27	-
GCA_900551445.1	s__Phocaeicola sp900551445	76.9831	51	713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.87	97.79	0.75	0.72	3	-
GCF_014750685.1	s__Bacteroides sp014750685	76.8895	53	713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015060735.1	s__Phocaeicola sp015060735	76.5516	53	713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015060705.1	s__Phocaeicola sp015060705	76.3176	56	713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 12:06:23,404] [INFO] GTDB search result was written to GCA_946621925.1_SRR873602_bin.131_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-30 12:06:23,405] [INFO] ===== GTDB Search completed =====
[2023-06-30 12:06:23,410] [INFO] DFAST_QC result json was written to GCA_946621925.1_SRR873602_bin.131_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-30 12:06:23,410] [INFO] DFAST_QC completed!
[2023-06-30 12:06:23,410] [INFO] Total running time: 0h1m26s