[2023-06-13 05:13:02,444] [INFO] DFAST_QC pipeline started.
[2023-06-13 05:13:02,447] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 05:13:02,447] [INFO] DQC Reference Directory: /var/lib/cwl/stga51f4b88-8b98-4be9-aede-08520bca1afa/dqc_reference
[2023-06-13 05:13:04,820] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 05:13:04,821] [INFO] Task started: Prodigal
[2023-06-13 05:13:04,821] [INFO] Running command: gunzip -c /var/lib/cwl/stg3bc6335a-1ec0-45c7-bfde-6a5c969d42b0/GCA_947002565.1_SRR19721639_bin.17_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947002565.1_SRR19721639_bin.17_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947002565.1_SRR19721639_bin.17_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 05:13:11,951] [INFO] Task succeeded: Prodigal
[2023-06-13 05:13:11,952] [INFO] Task started: HMMsearch
[2023-06-13 05:13:11,952] [INFO] Running command: hmmsearch --tblout GCA_947002565.1_SRR19721639_bin.17_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga51f4b88-8b98-4be9-aede-08520bca1afa/dqc_reference/reference_markers.hmm GCA_947002565.1_SRR19721639_bin.17_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 05:13:12,220] [INFO] Task succeeded: HMMsearch
[2023-06-13 05:13:12,222] [INFO] Found 6/6 markers.
[2023-06-13 05:13:12,279] [INFO] Query marker FASTA was written to GCA_947002565.1_SRR19721639_bin.17_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-13 05:13:12,279] [INFO] Task started: Blastn
[2023-06-13 05:13:12,279] [INFO] Running command: blastn -query GCA_947002565.1_SRR19721639_bin.17_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stga51f4b88-8b98-4be9-aede-08520bca1afa/dqc_reference/reference_markers.fasta -out GCA_947002565.1_SRR19721639_bin.17_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 05:13:12,919] [INFO] Task succeeded: Blastn
[2023-06-13 05:13:12,938] [INFO] Selected 17 target genomes.
[2023-06-13 05:13:12,939] [INFO] Target genome list was writen to GCA_947002565.1_SRR19721639_bin.17_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-13 05:13:12,940] [INFO] Task started: fastANI
[2023-06-13 05:13:12,941] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bc6335a-1ec0-45c7-bfde-6a5c969d42b0/GCA_947002565.1_SRR19721639_bin.17_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947002565.1_SRR19721639_bin.17_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947002565.1_SRR19721639_bin.17_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 05:13:22,113] [INFO] Task succeeded: fastANI
[2023-06-13 05:13:22,114] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga51f4b88-8b98-4be9-aede-08520bca1afa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 05:13:22,114] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga51f4b88-8b98-4be9-aede-08520bca1afa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 05:13:22,130] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 05:13:22,131] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 05:13:22,131] [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
Blautia obeum	strain=ATCC 29174	GCA_000153905.1	40520	40520	type	True	79.254	238	1014	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	79.2319	273	1014	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	79.209	278	1014	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	79.1468	289	1014	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	79.1442	241	1014	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	79.0457	266	1014	95	below_threshold
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	78.8285	233	1014	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	78.269	206	1014	95	below_threshold
Eubacterium ramulus	strain=ATCC 29099	GCA_000469345.1	39490	39490	type	True	77.2234	80	1014	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	76.9166	67	1014	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_002221555.2	1796616	1796616	type	True	76.3295	101	1014	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_001689125.2	1796616	1796616	type	True	76.3234	100	1014	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 05:13:22,133] [INFO] DFAST Taxonomy check result was written to GCA_947002565.1_SRR19721639_bin.17_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-13 05:13:22,133] [INFO] ===== Taxonomy check completed =====
[2023-06-13 05:13:22,133] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 05:13:22,134] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga51f4b88-8b98-4be9-aede-08520bca1afa/dqc_reference/checkm_data
[2023-06-13 05:13:22,135] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 05:13:22,175] [INFO] Task started: CheckM
[2023-06-13 05:13:22,175] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947002565.1_SRR19721639_bin.17_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947002565.1_SRR19721639_bin.17_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947002565.1_SRR19721639_bin.17_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-13 05:13:50,015] [INFO] Task succeeded: CheckM
[2023-06-13 05:13:50,016] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.06%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 05:13:50,043] [INFO] ===== Completeness check finished =====
[2023-06-13 05:13:50,043] [INFO] ===== Start GTDB Search =====
[2023-06-13 05:13:50,044] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947002565.1_SRR19721639_bin.17_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-13 05:13:50,044] [INFO] Task started: Blastn
[2023-06-13 05:13:50,044] [INFO] Running command: blastn -query GCA_947002565.1_SRR19721639_bin.17_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stga51f4b88-8b98-4be9-aede-08520bca1afa/dqc_reference/reference_markers_gtdb.fasta -out GCA_947002565.1_SRR19721639_bin.17_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 05:13:51,066] [INFO] Task succeeded: Blastn
[2023-06-13 05:13:51,071] [INFO] Selected 13 target genomes.
[2023-06-13 05:13:51,071] [INFO] Target genome list was writen to GCA_947002565.1_SRR19721639_bin.17_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 05:13:51,073] [INFO] Task started: fastANI
[2023-06-13 05:13:51,073] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bc6335a-1ec0-45c7-bfde-6a5c969d42b0/GCA_947002565.1_SRR19721639_bin.17_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947002565.1_SRR19721639_bin.17_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947002565.1_SRR19721639_bin.17_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 05:14:00,749] [INFO] Task succeeded: fastANI
[2023-06-13 05:14:00,767] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 05:14:00,768] [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
GCF_016908695.1	s__Blautia_A faecis	97.5518	896	1014	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.52	97.01	0.80	0.69	30	conclusive
GCA_905206915.1	s__Blautia_A sp905206915	87.5242	509	1014	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003460605.1	s__Blautia_A sp900066145	84.2637	665	1014	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	99.04	98.72	0.92	0.85	9	-
GCA_900763175.1	s__Blautia_A sp900763175	83.1111	481	1014	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003461955.1	s__Blautia_A sp900066335	79.4641	258	1014	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.91	98.25	0.89	0.82	13	-
GCA_000285855.2	s__Blautia_A sp000285855	79.4513	289	1014	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.62	95.80	0.88	0.79	6	-
GCF_013304385.1	s__Blautia_A sp900066505	79.2957	284	1014	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.06	97.97	0.82	0.78	4	-
GCA_900316115.1	s__Blautia_A sp900316115	79.2245	264	1014	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	99.53	99.48	0.92	0.90	3	-
GCF_009707925.1	s__Blautia_A luti	79.2212	277	1014	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.33	97.04	0.87	0.84	5	-
GCF_013304735.1	s__Blautia_A sp900066205	79.2109	279	1014	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.18	96.89	0.89	0.81	11	-
GCF_003477525.1	s__Blautia_A sp003477525	78.9383	290	1014	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	99.30	98.60	0.90	0.81	3	-
GCA_900764225.1	s__Blautia_A sp900764225	78.6769	202	1014	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544395.1	s__Ruminococcus_B sp900544395	76.4567	68	1014	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ruminococcus_B	95.0	99.21	99.21	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-06-13 05:14:00,770] [INFO] GTDB search result was written to GCA_947002565.1_SRR19721639_bin.17_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 05:14:00,771] [INFO] ===== GTDB Search completed =====
[2023-06-13 05:14:00,778] [INFO] DFAST_QC result json was written to GCA_947002565.1_SRR19721639_bin.17_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-13 05:14:00,779] [INFO] DFAST_QC completed!
[2023-06-13 05:14:00,779] [INFO] Total running time: 0h0m58s