[2023-06-14 01:26:27,506] [INFO] DFAST_QC pipeline started.
[2023-06-14 01:26:27,508] [INFO] DFAST_QC version: 0.5.7
[2023-06-14 01:26:27,508] [INFO] DQC Reference Directory: /var/lib/cwl/stg47a0cb9f-b386-46f3-93c5-40a643f4273f/dqc_reference
[2023-06-14 01:26:28,750] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-14 01:26:28,751] [INFO] Task started: Prodigal
[2023-06-14 01:26:28,751] [INFO] Running command: gunzip -c /var/lib/cwl/stg3e8302c0-2e99-486e-872f-86b1be6905da/GCA_947178795.1_SRR13713032_bin.9_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947178795.1_SRR13713032_bin.9_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947178795.1_SRR13713032_bin.9_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-14 01:26:41,546] [INFO] Task succeeded: Prodigal
[2023-06-14 01:26:41,546] [INFO] Task started: HMMsearch
[2023-06-14 01:26:41,547] [INFO] Running command: hmmsearch --tblout GCA_947178795.1_SRR13713032_bin.9_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47a0cb9f-b386-46f3-93c5-40a643f4273f/dqc_reference/reference_markers.hmm GCA_947178795.1_SRR13713032_bin.9_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-14 01:26:41,779] [INFO] Task succeeded: HMMsearch
[2023-06-14 01:26:41,780] [INFO] Found 6/6 markers.
[2023-06-14 01:26:41,804] [INFO] Query marker FASTA was written to GCA_947178795.1_SRR13713032_bin.9_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-14 01:26:41,804] [INFO] Task started: Blastn
[2023-06-14 01:26:41,804] [INFO] Running command: blastn -query GCA_947178795.1_SRR13713032_bin.9_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg47a0cb9f-b386-46f3-93c5-40a643f4273f/dqc_reference/reference_markers.fasta -out GCA_947178795.1_SRR13713032_bin.9_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:26:42,451] [INFO] Task succeeded: Blastn
[2023-06-14 01:26:42,455] [INFO] Selected 21 target genomes.
[2023-06-14 01:26:42,455] [INFO] Target genome list was writen to GCA_947178795.1_SRR13713032_bin.9_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-14 01:26:42,464] [INFO] Task started: fastANI
[2023-06-14 01:26:42,465] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e8302c0-2e99-486e-872f-86b1be6905da/GCA_947178795.1_SRR13713032_bin.9_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947178795.1_SRR13713032_bin.9_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947178795.1_SRR13713032_bin.9_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-14 01:26:54,016] [INFO] Task succeeded: fastANI
[2023-06-14 01:26:54,016] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47a0cb9f-b386-46f3-93c5-40a643f4273f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-14 01:26:54,017] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47a0cb9f-b386-46f3-93c5-40a643f4273f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-14 01:26:54,025] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-14 01:26:54,025] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-14 01:26:54,025] [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
Muribaculum intestinale	strain=YL27	GCA_016696845.1	1796646	1796646	type	True	77.1008	68	615	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_001688845.2	1796646	1796646	type	True	77.0212	70	615	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_002201515.1	1796646	1796646	type	True	76.9893	71	615	95	below_threshold
Paramuribaculum intestinale	strain=DSM 100749	GCA_003024925.1	2094151	2094151	type	True	76.9363	64	615	95	below_threshold
Duncaniella dubosii	strain=H5	GCA_004803915.1	2518971	2518971	type	True	76.7586	62	615	95	below_threshold
Duncaniella muris	strain=DSM 103720	GCA_003024805.1	2094150	2094150	type	True	76.751	66	615	95	below_threshold
Muribaculum gordoncarteri	strain=TLL-A4	GCA_004803695.1	2530390	2530390	type	True	76.2354	70	615	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-14 01:26:54,027] [INFO] DFAST Taxonomy check result was written to GCA_947178795.1_SRR13713032_bin.9_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-14 01:26:54,028] [INFO] ===== Taxonomy check completed =====
[2023-06-14 01:26:54,028] [INFO] ===== Start completeness check using CheckM =====
[2023-06-14 01:26:54,029] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47a0cb9f-b386-46f3-93c5-40a643f4273f/dqc_reference/checkm_data
[2023-06-14 01:26:54,030] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-14 01:26:54,054] [INFO] Task started: CheckM
[2023-06-14 01:26:54,054] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947178795.1_SRR13713032_bin.9_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947178795.1_SRR13713032_bin.9_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947178795.1_SRR13713032_bin.9_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-14 01:27:32,693] [INFO] Task succeeded: CheckM
[2023-06-14 01:27:32,695] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.69%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-14 01:27:32,716] [INFO] ===== Completeness check finished =====
[2023-06-14 01:27:32,716] [INFO] ===== Start GTDB Search =====
[2023-06-14 01:27:32,716] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947178795.1_SRR13713032_bin.9_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-14 01:27:32,717] [INFO] Task started: Blastn
[2023-06-14 01:27:32,717] [INFO] Running command: blastn -query GCA_947178795.1_SRR13713032_bin.9_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg47a0cb9f-b386-46f3-93c5-40a643f4273f/dqc_reference/reference_markers_gtdb.fasta -out GCA_947178795.1_SRR13713032_bin.9_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:27:33,762] [INFO] Task succeeded: Blastn
[2023-06-14 01:27:33,768] [INFO] Selected 18 target genomes.
[2023-06-14 01:27:33,768] [INFO] Target genome list was writen to GCA_947178795.1_SRR13713032_bin.9_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-14 01:27:33,780] [INFO] Task started: fastANI
[2023-06-14 01:27:33,780] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e8302c0-2e99-486e-872f-86b1be6905da/GCA_947178795.1_SRR13713032_bin.9_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947178795.1_SRR13713032_bin.9_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947178795.1_SRR13713032_bin.9_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-14 01:27:41,190] [INFO] Task succeeded: fastANI
[2023-06-14 01:27:41,208] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-14 01:27:41,208] [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_002490635.1	s__CAG-873 sp002490635	99.8075	575	615	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	99.68	99.16	0.94	0.92	13	conclusive
GCA_900541865.1	s__CAG-873 sp900541865	78.1191	203	615	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548975.1	s__CAG-873 sp900548975	78.1186	149	615	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	99.98	99.96	0.94	0.89	3	-
GCA_910579035.1	s__CAG-873 sp011959565	77.772	150	615	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	97.99	96.96	0.89	0.75	5	-
GCA_014800735.1	s__CAG-873 sp014800735	77.7622	151	615	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	97.24	97.04	0.84	0.82	3	-
GCA_009775225.1	s__CAG-873 sp009775225	77.7531	143	615	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	98.13	98.13	0.88	0.86	3	-
GCA_017621055.1	s__CAG-873 sp017621055	77.7487	181	615	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554265.1	s__CAG-873 sp900554265	77.6979	143	615	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	99.86	99.86	0.88	0.88	2	-
GCA_002493945.1	s__CAG-873 sp002493945	77.4913	155	615	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	99.61	97.51	0.95	0.88	8	-
GCA_009775195.1	s__CAG-873 sp009775195	77.4476	123	615	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	97.01	95.47	0.84	0.74	3	-
GCA_910584495.1	s__CAG-873 sp910584495	77.3164	108	615	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587915.1	s__CAG-873 sp910587915	77.2323	112	615	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579995.1	s__CAG-873 sp009775135	77.1613	120	615	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	99.86	99.86	0.96	0.96	2	-
GCA_004552485.1	s__CAG-873 sp004552485	77.0287	116	615	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	99.38	99.38	0.89	0.89	2	-
GCA_910576935.1	s__CAG-873 sp910576935	76.972	86	615	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586565.1	s__UBA7173 sp910586565	76.8295	88	615	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014800065.1	s__CAG-873 sp014800065	76.3601	51	615	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-14 01:27:41,210] [INFO] GTDB search result was written to GCA_947178795.1_SRR13713032_bin.9_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-14 01:27:41,211] [INFO] ===== GTDB Search completed =====
[2023-06-14 01:27:41,215] [INFO] DFAST_QC result json was written to GCA_947178795.1_SRR13713032_bin.9_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-14 01:27:41,215] [INFO] DFAST_QC completed!
[2023-06-14 01:27:41,215] [INFO] Total running time: 0h1m14s