[2023-06-13 04:13:02,239] [INFO] DFAST_QC pipeline started.
[2023-06-13 04:13:02,241] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 04:13:02,241] [INFO] DQC Reference Directory: /var/lib/cwl/stg1efc9bbb-58a1-40a7-a215-293cbb44b9a6/dqc_reference
[2023-06-13 04:13:03,484] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 04:13:03,485] [INFO] Task started: Prodigal
[2023-06-13 04:13:03,485] [INFO] Running command: gunzip -c /var/lib/cwl/stg604de794-ddc0-427f-925b-22d45184eb06/GCA_947644475.1_SRR15633999_bin.11_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947644475.1_SRR15633999_bin.11_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947644475.1_SRR15633999_bin.11_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 04:13:18,924] [INFO] Task succeeded: Prodigal
[2023-06-13 04:13:18,924] [INFO] Task started: HMMsearch
[2023-06-13 04:13:18,924] [INFO] Running command: hmmsearch --tblout GCA_947644475.1_SRR15633999_bin.11_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1efc9bbb-58a1-40a7-a215-293cbb44b9a6/dqc_reference/reference_markers.hmm GCA_947644475.1_SRR15633999_bin.11_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 04:13:19,206] [INFO] Task succeeded: HMMsearch
[2023-06-13 04:13:19,208] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg604de794-ddc0-427f-925b-22d45184eb06/GCA_947644475.1_SRR15633999_bin.11_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-13 04:13:19,232] [INFO] Query marker FASTA was written to GCA_947644475.1_SRR15633999_bin.11_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-13 04:13:19,233] [INFO] Task started: Blastn
[2023-06-13 04:13:19,233] [INFO] Running command: blastn -query GCA_947644475.1_SRR15633999_bin.11_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg1efc9bbb-58a1-40a7-a215-293cbb44b9a6/dqc_reference/reference_markers.fasta -out GCA_947644475.1_SRR15633999_bin.11_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 04:13:19,883] [INFO] Task succeeded: Blastn
[2023-06-13 04:13:19,886] [INFO] Selected 22 target genomes.
[2023-06-13 04:13:19,887] [INFO] Target genome list was writen to GCA_947644475.1_SRR15633999_bin.11_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-13 04:13:19,889] [INFO] Task started: fastANI
[2023-06-13 04:13:19,889] [INFO] Running command: fastANI --query /var/lib/cwl/stg604de794-ddc0-427f-925b-22d45184eb06/GCA_947644475.1_SRR15633999_bin.11_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947644475.1_SRR15633999_bin.11_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947644475.1_SRR15633999_bin.11_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 04:13:32,395] [INFO] Task succeeded: fastANI
[2023-06-13 04:13:32,396] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1efc9bbb-58a1-40a7-a215-293cbb44b9a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 04:13:32,396] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1efc9bbb-58a1-40a7-a215-293cbb44b9a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 04:13:32,406] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 04:13:32,406] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 04:13:32,407] [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
Duncaniella muris	strain=DSM 103720	GCA_003024805.1	2094150	2094150	type	True	76.8371	82	722	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_001688845.2	1796646	1796646	type	True	76.8229	61	722	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_002201515.1	1796646	1796646	type	True	76.807	58	722	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_016696845.1	1796646	1796646	type	True	76.7854	63	722	95	below_threshold
Paramuribaculum intestinale	strain=DSM 100749	GCA_003024925.1	2094151	2094151	type	True	76.3126	59	722	95	below_threshold
Heminiphilus faecis	strain=AM35	GCA_008728965.1	2601703	2601703	type	True	76.1706	50	722	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 04:13:32,409] [INFO] DFAST Taxonomy check result was written to GCA_947644475.1_SRR15633999_bin.11_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-13 04:13:32,410] [INFO] ===== Taxonomy check completed =====
[2023-06-13 04:13:32,410] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 04:13:32,410] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1efc9bbb-58a1-40a7-a215-293cbb44b9a6/dqc_reference/checkm_data
[2023-06-13 04:13:32,412] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 04:13:32,447] [INFO] Task started: CheckM
[2023-06-13 04:13:32,448] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947644475.1_SRR15633999_bin.11_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947644475.1_SRR15633999_bin.11_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947644475.1_SRR15633999_bin.11_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-13 04:14:17,778] [INFO] Task succeeded: CheckM
[2023-06-13 04:14:17,780] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.98%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 04:14:17,807] [INFO] ===== Completeness check finished =====
[2023-06-13 04:14:17,808] [INFO] ===== Start GTDB Search =====
[2023-06-13 04:14:17,809] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947644475.1_SRR15633999_bin.11_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-13 04:14:17,809] [INFO] Task started: Blastn
[2023-06-13 04:14:17,809] [INFO] Running command: blastn -query GCA_947644475.1_SRR15633999_bin.11_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg1efc9bbb-58a1-40a7-a215-293cbb44b9a6/dqc_reference/reference_markers_gtdb.fasta -out GCA_947644475.1_SRR15633999_bin.11_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 04:14:18,850] [INFO] Task succeeded: Blastn
[2023-06-13 04:14:18,856] [INFO] Selected 22 target genomes.
[2023-06-13 04:14:18,856] [INFO] Target genome list was writen to GCA_947644475.1_SRR15633999_bin.11_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 04:14:18,863] [INFO] Task started: fastANI
[2023-06-13 04:14:18,863] [INFO] Running command: fastANI --query /var/lib/cwl/stg604de794-ddc0-427f-925b-22d45184eb06/GCA_947644475.1_SRR15633999_bin.11_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947644475.1_SRR15633999_bin.11_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947644475.1_SRR15633999_bin.11_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 04:14:27,693] [INFO] Task succeeded: fastANI
[2023-06-13 04:14:27,711] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 04:14:27,711] [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_009775125.1	s__CAG-873 sp001689665	89.3374	614	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	98.51	97.14	0.87	0.85	3	-
GCA_910577315.1	s__CAG-873 sp910577315	77.6064	130	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	97.79	97.79	0.88	0.88	2	-
GCA_910584905.1	s__CAG-873 sp910584905	77.5618	99	722	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_004552485.1	s__CAG-873 sp004552485	77.348	106	722	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_910579035.1	s__CAG-873 sp011959565	77.1835	99	722	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_009775265.1	s__CAG-873 sp009775265	77.1363	82	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	99.34	99.23	0.92	0.92	3	-
GCA_905193995.1	s__CAG-873 sp905193995	77.0418	68	722	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_900759815.1	s__HGM05190 sp900759815	77.0273	71	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__HGM05190	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578095.1	s__CAG-873 sp910578095	76.9112	116	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	99.96	99.96	0.98	0.98	2	-
GCA_900550395.1	s__CAG-873 sp900550395	76.8904	95	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	97.34	95.74	0.88	0.82	4	-
GCA_001689495.1	s__Duncaniella sp001689495	76.8719	105	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	99.23	99.23	0.93	0.93	2	-
GCF_002201515.1	s__Muribaculum intestinale	76.8064	57	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	99.09	97.90	0.92	0.80	20	-
GCA_900554715.1	s__CAG-873 sp900554715	76.7985	63	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	97.36	96.96	0.90	0.86	3	-
GCA_905207535.1	s__UBA7173 sp905207535	76.7641	81	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900752535.1	s__CAG-1031 sp900752535	76.7225	57	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-1031	95.0	99.62	99.62	0.86	0.86	2	-
GCA_001689405.1	s__Muribaculum arabinoxylanisolvens	76.7222	60	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	99.46	99.01	0.94	0.92	3	-
GCA_900555165.1	s__UBA7173 sp900555165	76.6752	77	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	98.22	96.90	0.89	0.88	3	-
GCA_004102805.1	s__UBA7173 sp004102805	76.5147	90	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	98.86	98.86	0.92	0.89	3	-
GCA_017624155.1	s__CAG-873 sp017624155	76.4816	85	722	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_910579105.1	s__UBA7173 sp910579105	76.3554	77	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 04:14:27,714] [INFO] GTDB search result was written to GCA_947644475.1_SRR15633999_bin.11_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 04:14:27,715] [INFO] ===== GTDB Search completed =====
[2023-06-13 04:14:27,719] [INFO] DFAST_QC result json was written to GCA_947644475.1_SRR15633999_bin.11_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-13 04:14:27,719] [INFO] DFAST_QC completed!
[2023-06-13 04:14:27,719] [INFO] Total running time: 0h1m25s