[2023-06-13 00:23:48,452] [INFO] DFAST_QC pipeline started.
[2023-06-13 00:23:48,455] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 00:23:48,455] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d3c82fd-ffaf-4ae0-8f24-371638d03d85/dqc_reference
[2023-06-13 00:23:49,750] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 00:23:49,751] [INFO] Task started: Prodigal
[2023-06-13 00:23:49,751] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ed62fab-179b-4c6f-a4ea-54c527554453/GCA_022009975.1_ASM2200997v1_genomic.fna.gz | prodigal -d GCA_022009975.1_ASM2200997v1_genomic.fna/cds.fna -a GCA_022009975.1_ASM2200997v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 00:24:05,655] [INFO] Task succeeded: Prodigal
[2023-06-13 00:24:05,656] [INFO] Task started: HMMsearch
[2023-06-13 00:24:05,656] [INFO] Running command: hmmsearch --tblout GCA_022009975.1_ASM2200997v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d3c82fd-ffaf-4ae0-8f24-371638d03d85/dqc_reference/reference_markers.hmm GCA_022009975.1_ASM2200997v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 00:24:05,881] [INFO] Task succeeded: HMMsearch
[2023-06-13 00:24:05,883] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg0ed62fab-179b-4c6f-a4ea-54c527554453/GCA_022009975.1_ASM2200997v1_genomic.fna.gz]
[2023-06-13 00:24:05,919] [INFO] Query marker FASTA was written to GCA_022009975.1_ASM2200997v1_genomic.fna/markers.fasta
[2023-06-13 00:24:05,919] [INFO] Task started: Blastn
[2023-06-13 00:24:05,920] [INFO] Running command: blastn -query GCA_022009975.1_ASM2200997v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d3c82fd-ffaf-4ae0-8f24-371638d03d85/dqc_reference/reference_markers.fasta -out GCA_022009975.1_ASM2200997v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:24:06,421] [INFO] Task succeeded: Blastn
[2023-06-13 00:24:06,426] [INFO] Selected 20 target genomes.
[2023-06-13 00:24:06,426] [INFO] Target genome list was writen to GCA_022009975.1_ASM2200997v1_genomic.fna/target_genomes.txt
[2023-06-13 00:24:06,429] [INFO] Task started: fastANI
[2023-06-13 00:24:06,430] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ed62fab-179b-4c6f-a4ea-54c527554453/GCA_022009975.1_ASM2200997v1_genomic.fna.gz --refList GCA_022009975.1_ASM2200997v1_genomic.fna/target_genomes.txt --output GCA_022009975.1_ASM2200997v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 00:24:18,899] [INFO] Task succeeded: fastANI
[2023-06-13 00:24:18,899] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d3c82fd-ffaf-4ae0-8f24-371638d03d85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 00:24:18,900] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d3c82fd-ffaf-4ae0-8f24-371638d03d85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 00:24:18,917] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 00:24:18,917] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 00:24:18,917] [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
Parabacteroides distasonis	strain=FDAARGOS_1565	GCA_020735945.1	823	823	type	True	82.2949	107	893	95	below_threshold
Parabacteroides distasonis	strain=ATCC 8503	GCA_000012845.1	823	823	type	True	82.2948	107	893	95	below_threshold
Parabacteroides distasonis	strain=NCTC11152	GCA_900445525.1	823	823	type	True	82.196	109	893	95	below_threshold
Parabacteroides bouchesdurhonensis	strain=Marseille-P3763	GCA_900186615.1	1936995	1936995	type	True	78.8039	83	893	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_002221665.1	1796613	1796613	type	True	78.796	73	893	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_016697125.1	1796613	1796613	type	True	78.3095	66	893	95	below_threshold
Parabacteroides gordonii	strain=FDAARGOS_1522	GCA_020297465.1	574930	574930	type	True	78.2216	99	893	95	below_threshold
Parabacteroides goldsteinii	strain=DSM 19448	GCA_000969835.1	328812	328812	type	True	78.1894	115	893	95	below_threshold
Parabacteroides gordonii	strain=MS-1	GCA_000969825.1	574930	574930	type	True	77.9915	97	893	95	below_threshold
Bacteroides salyersiae	strain=DSM 18765	GCA_000381365.1	291644	291644	type	True	77.941	52	893	95	below_threshold
Phocaeicola salanitronis	strain=DSM 18170	GCA_000190575.1	376805	376805	type	True	77.7424	51	893	95	below_threshold
Parabacteroides acidifaciens	strain=426_9	GCA_014385205.1	2290935	2290935	type	True	77.7249	101	893	95	below_threshold
Parabacteroides acidifaciens	strain=426-9	GCA_003363715.1	2290935	2290935	type	True	77.6945	102	893	95	below_threshold
Parabacteroides gordonii	strain=DSM 23371	GCA_000428565.1	574930	574930	type	True	77.26	91	893	95	below_threshold
Phocaeicola barnesiae	strain=DSM 18169	GCA_000374585.1	376804	376804	type	True	76.8404	62	893	95	below_threshold
Phocaeicola barnesiae	strain=JCM 13652	GCA_000613645.1	376804	376804	type	True	76.8186	62	893	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 00:24:18,921] [INFO] DFAST Taxonomy check result was written to GCA_022009975.1_ASM2200997v1_genomic.fna/tc_result.tsv
[2023-06-13 00:24:18,921] [INFO] ===== Taxonomy check completed =====
[2023-06-13 00:24:18,921] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 00:24:18,922] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d3c82fd-ffaf-4ae0-8f24-371638d03d85/dqc_reference/checkm_data
[2023-06-13 00:24:18,923] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 00:24:18,954] [INFO] Task started: CheckM
[2023-06-13 00:24:18,954] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022009975.1_ASM2200997v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022009975.1_ASM2200997v1_genomic.fna/checkm_input GCA_022009975.1_ASM2200997v1_genomic.fna/checkm_result
[2023-06-13 00:25:06,681] [INFO] Task succeeded: CheckM
[2023-06-13 00:25:06,682] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 00:25:06,706] [INFO] ===== Completeness check finished =====
[2023-06-13 00:25:06,707] [INFO] ===== Start GTDB Search =====
[2023-06-13 00:25:06,707] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022009975.1_ASM2200997v1_genomic.fna/markers.fasta)
[2023-06-13 00:25:06,708] [INFO] Task started: Blastn
[2023-06-13 00:25:06,708] [INFO] Running command: blastn -query GCA_022009975.1_ASM2200997v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d3c82fd-ffaf-4ae0-8f24-371638d03d85/dqc_reference/reference_markers_gtdb.fasta -out GCA_022009975.1_ASM2200997v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:25:07,179] [INFO] Task succeeded: Blastn
[2023-06-13 00:25:07,188] [INFO] Selected 19 target genomes.
[2023-06-13 00:25:07,188] [INFO] Target genome list was writen to GCA_022009975.1_ASM2200997v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 00:25:07,198] [INFO] Task started: fastANI
[2023-06-13 00:25:07,198] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ed62fab-179b-4c6f-a4ea-54c527554453/GCA_022009975.1_ASM2200997v1_genomic.fna.gz --refList GCA_022009975.1_ASM2200997v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022009975.1_ASM2200997v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 00:25:19,007] [INFO] Task succeeded: fastANI
[2023-06-13 00:25:19,025] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 00:25:19,026] [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_900549585.1	s__Parabacteroides sp900549585	98.1965	596	893	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.88	98.86	0.81	0.76	3	conclusive
GCF_000012845.1	s__Parabacteroides distasonis	82.4581	108	893	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.16	96.57	0.86	0.75	191	-
GCA_000436495.1	s__Parabacteroides faecavium	78.8105	139	893	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	96.87	96.42	0.81	0.77	5	-
GCF_900186615.1	s__Parabacteroides bouchesdurhonensis	78.6302	83	893	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	97.72	97.72	0.92	0.92	3	-
GCF_000969835.1	s__Parabacteroides goldsteinii	78.2652	115	893	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.03	95.33	0.85	0.78	37	-
GCF_002159645.1	s__Parabacteroides sp002159645	78.0356	100	893	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000969825.1	s__Parabacteroides gordonii	78.0116	92	893	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.64	96.69	0.92	0.81	6	-
GCF_900108035.1	s__Parabacteroides chinchillae	77.996	86	893	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	97.95	97.95	0.87	0.87	3	-
GCF_000381365.1	s__Bacteroides salyersiae	77.9919	50	893	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.03	96.77	0.88	0.58	55	-
GCA_900548175.1	s__Parabacteroides sp900548175	77.7658	110	893	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	96.23	96.23	0.78	0.78	2	-
GCF_003363715.1	s__Parabacteroides acidifaciens	77.7006	101	893	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.21	97.25	0.91	0.84	7	-
GCF_010500925.1	s__Barb7 sp010500925	77.3034	55	893	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Barb7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900547435.1	s__Parabacteroides sp900547435	77.2355	98	893	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	100.00	100.00	0.96	0.96	2	-
GCA_017937385.1	s__Parabacteroides sp017937385	77.1992	74	893	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374585.1	s__Phocaeicola barnesiae	76.8937	59	893	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.58	98.10	0.88	0.84	8	-
--------------------------------------------------------------------------------
[2023-06-13 00:25:19,029] [INFO] GTDB search result was written to GCA_022009975.1_ASM2200997v1_genomic.fna/result_gtdb.tsv
[2023-06-13 00:25:19,029] [INFO] ===== GTDB Search completed =====
[2023-06-13 00:25:19,034] [INFO] DFAST_QC result json was written to GCA_022009975.1_ASM2200997v1_genomic.fna/dqc_result.json
[2023-06-13 00:25:19,034] [INFO] DFAST_QC completed!
[2023-06-13 00:25:19,035] [INFO] Total running time: 0h1m31s