[2023-06-17 14:32:39,895] [INFO] DFAST_QC pipeline started.
[2023-06-17 14:32:39,899] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 14:32:39,899] [INFO] DQC Reference Directory: /var/lib/cwl/stg802758b7-89f0-48f5-84b5-b4d994e9c2be/dqc_reference
[2023-06-17 14:32:41,210] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 14:32:41,211] [INFO] Task started: Prodigal
[2023-06-17 14:32:41,211] [INFO] Running command: gunzip -c /var/lib/cwl/stgd6bed5de-c672-4094-b03a-a63f77e2070e/GCA_905211085.1_ERR414333-mag-bin.20_genomic.fna.gz | prodigal -d GCA_905211085.1_ERR414333-mag-bin.20_genomic.fna/cds.fna -a GCA_905211085.1_ERR414333-mag-bin.20_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 14:33:04,289] [INFO] Task succeeded: Prodigal
[2023-06-17 14:33:04,290] [INFO] Task started: HMMsearch
[2023-06-17 14:33:04,290] [INFO] Running command: hmmsearch --tblout GCA_905211085.1_ERR414333-mag-bin.20_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg802758b7-89f0-48f5-84b5-b4d994e9c2be/dqc_reference/reference_markers.hmm GCA_905211085.1_ERR414333-mag-bin.20_genomic.fna/protein.faa > /dev/null
[2023-06-17 14:33:04,635] [INFO] Task succeeded: HMMsearch
[2023-06-17 14:33:04,636] [INFO] Found 6/6 markers.
[2023-06-17 14:33:04,688] [INFO] Query marker FASTA was written to GCA_905211085.1_ERR414333-mag-bin.20_genomic.fna/markers.fasta
[2023-06-17 14:33:04,689] [INFO] Task started: Blastn
[2023-06-17 14:33:04,689] [INFO] Running command: blastn -query GCA_905211085.1_ERR414333-mag-bin.20_genomic.fna/markers.fasta -db /var/lib/cwl/stg802758b7-89f0-48f5-84b5-b4d994e9c2be/dqc_reference/reference_markers.fasta -out GCA_905211085.1_ERR414333-mag-bin.20_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 14:33:05,430] [INFO] Task succeeded: Blastn
[2023-06-17 14:33:05,437] [INFO] Selected 16 target genomes.
[2023-06-17 14:33:05,438] [INFO] Target genome list was writen to GCA_905211085.1_ERR414333-mag-bin.20_genomic.fna/target_genomes.txt
[2023-06-17 14:33:05,439] [INFO] Task started: fastANI
[2023-06-17 14:33:05,440] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6bed5de-c672-4094-b03a-a63f77e2070e/GCA_905211085.1_ERR414333-mag-bin.20_genomic.fna.gz --refList GCA_905211085.1_ERR414333-mag-bin.20_genomic.fna/target_genomes.txt --output GCA_905211085.1_ERR414333-mag-bin.20_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 14:33:16,536] [INFO] Task succeeded: fastANI
[2023-06-17 14:33:16,537] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg802758b7-89f0-48f5-84b5-b4d994e9c2be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 14:33:16,537] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg802758b7-89f0-48f5-84b5-b4d994e9c2be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 14:33:16,558] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 14:33:16,559] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 14:33:16,559] [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 plebeius	strain=DSM 17135	GCA_000187895.1	310297	310297	suspected-type	True	83.9026	761	1274	95	below_threshold
Phocaeicola faecicola	strain=AGMB03916	GCA_013618865.1	2739389	2739389	type	True	81.2573	375	1274	95	below_threshold
Phocaeicola coprophilus	strain=JCM 13818	GCA_001315785.1	387090	387090	type	True	80.5329	358	1274	95	below_threshold
Phocaeicola coprophilus	strain=DSM 18228	GCA_000157915.1	387090	387090	type	True	80.5044	362	1274	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	79.9413	164	1274	95	below_threshold
Phocaeicola barnesiae	strain=JCM 13652	GCA_000613645.1	376804	376804	type	True	79.8215	376	1274	95	below_threshold
Phocaeicola barnesiae	strain=DSM 18169	GCA_000374585.1	376804	376804	type	True	79.7945	375	1274	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	78.9091	162	1274	95	below_threshold
Phocaeicola intestinalis	strain=Sa1CVN1	GCA_014837065.1	2762212	2762212	type	True	78.7982	262	1274	95	below_threshold
Phocaeicola salanitronis	strain=DSM 18170	GCA_000190575.1	376805	376805	type	True	78.6083	277	1274	95	below_threshold
Phocaeicola faecium	strain=Sa1YUN3	GCA_014837055.1	2762213	2762213	type	True	78.4877	262	1274	95	below_threshold
Phocaeicola faecalis	strain=FXJYN30E22	GCA_021730445.1	2786956	2786956	type	True	78.4506	164	1274	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	78.3399	138	1274	95	below_threshold
Bacteroides propionicigenes	strain=NSJ-90	GCA_018390535.1	2834112	2834112	type	True	78.2923	142	1274	95	below_threshold
Bacteroides clarus	strain=YIT 12056	GCA_900129655.1	626929	626929	type	True	77.0673	135	1274	95	below_threshold
Bacteroides clarus	strain=YIT 12056	GCA_000195615.1	626929	626929	type	True	77.043	132	1274	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 14:33:16,564] [INFO] DFAST Taxonomy check result was written to GCA_905211085.1_ERR414333-mag-bin.20_genomic.fna/tc_result.tsv
[2023-06-17 14:33:16,565] [INFO] ===== Taxonomy check completed =====
[2023-06-17 14:33:16,565] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 14:33:16,565] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg802758b7-89f0-48f5-84b5-b4d994e9c2be/dqc_reference/checkm_data
[2023-06-17 14:33:16,567] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 14:33:16,624] [INFO] Task started: CheckM
[2023-06-17 14:33:16,625] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905211085.1_ERR414333-mag-bin.20_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905211085.1_ERR414333-mag-bin.20_genomic.fna/checkm_input GCA_905211085.1_ERR414333-mag-bin.20_genomic.fna/checkm_result
[2023-06-17 14:34:21,927] [INFO] Task succeeded: CheckM
[2023-06-17 14:34:21,928] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.86%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 14:34:21,953] [INFO] ===== Completeness check finished =====
[2023-06-17 14:34:21,953] [INFO] ===== Start GTDB Search =====
[2023-06-17 14:34:21,953] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905211085.1_ERR414333-mag-bin.20_genomic.fna/markers.fasta)
[2023-06-17 14:34:21,954] [INFO] Task started: Blastn
[2023-06-17 14:34:21,954] [INFO] Running command: blastn -query GCA_905211085.1_ERR414333-mag-bin.20_genomic.fna/markers.fasta -db /var/lib/cwl/stg802758b7-89f0-48f5-84b5-b4d994e9c2be/dqc_reference/reference_markers_gtdb.fasta -out GCA_905211085.1_ERR414333-mag-bin.20_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 14:34:22,879] [INFO] Task succeeded: Blastn
[2023-06-17 14:34:22,884] [INFO] Selected 7 target genomes.
[2023-06-17 14:34:22,885] [INFO] Target genome list was writen to GCA_905211085.1_ERR414333-mag-bin.20_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 14:34:22,890] [INFO] Task started: fastANI
[2023-06-17 14:34:22,890] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6bed5de-c672-4094-b03a-a63f77e2070e/GCA_905211085.1_ERR414333-mag-bin.20_genomic.fna.gz --refList GCA_905211085.1_ERR414333-mag-bin.20_genomic.fna/target_genomes_gtdb.txt --output GCA_905211085.1_ERR414333-mag-bin.20_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 14:34:28,818] [INFO] Task succeeded: fastANI
[2023-06-17 14:34:28,832] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 14:34:28,833] [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_902362595.1	s__Phocaeicola merdigallinarum	98.4856	1022	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.33	96.40	0.87	0.80	6	conclusive
GCF_900128455.1	s__Phocaeicola mediterraneensis	91.7879	880	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.66	98.61	0.84	0.80	3	-
GCA_900551445.1	s__Phocaeicola sp900551445	91.0065	646	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.87	97.79	0.75	0.72	3	-
GCF_016900355.1	s__Phocaeicola sp900551065	89.2668	788	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	96.34	95.04	0.86	0.84	4	-
GCA_900552075.1	s__Phocaeicola sp900552075	89.1823	583	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000187895.1	s__Phocaeicola plebeius	83.9357	759	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.22	96.70	0.79	0.55	12	-
GCF_003437535.1	s__Phocaeicola plebeius_A	83.525	737	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.72	95.85	0.84	0.73	27	-
--------------------------------------------------------------------------------
[2023-06-17 14:34:28,836] [INFO] GTDB search result was written to GCA_905211085.1_ERR414333-mag-bin.20_genomic.fna/result_gtdb.tsv
[2023-06-17 14:34:28,837] [INFO] ===== GTDB Search completed =====
[2023-06-17 14:34:28,842] [INFO] DFAST_QC result json was written to GCA_905211085.1_ERR414333-mag-bin.20_genomic.fna/dqc_result.json
[2023-06-17 14:34:28,843] [INFO] DFAST_QC completed!
[2023-06-17 14:34:28,843] [INFO] Total running time: 0h1m49s