[2023-06-08 10:52:39,048] [INFO] DFAST_QC pipeline started.
[2023-06-08 10:52:39,051] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 10:52:39,051] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e00c9c9-bb59-44b7-b49b-6ea65d9531c2/dqc_reference
[2023-06-08 10:52:40,379] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 10:52:40,380] [INFO] Task started: Prodigal
[2023-06-08 10:52:40,381] [INFO] Running command: gunzip -c /var/lib/cwl/stg1f3de2fe-e836-4ec4-9b27-472d6458c412/GCA_947074735.1_SRR13169512_bin.25_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947074735.1_SRR13169512_bin.25_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947074735.1_SRR13169512_bin.25_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 10:52:50,690] [INFO] Task succeeded: Prodigal
[2023-06-08 10:52:50,690] [INFO] Task started: HMMsearch
[2023-06-08 10:52:50,690] [INFO] Running command: hmmsearch --tblout GCA_947074735.1_SRR13169512_bin.25_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e00c9c9-bb59-44b7-b49b-6ea65d9531c2/dqc_reference/reference_markers.hmm GCA_947074735.1_SRR13169512_bin.25_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 10:52:50,980] [INFO] Task succeeded: HMMsearch
[2023-06-08 10:52:50,982] [INFO] Found 6/6 markers.
[2023-06-08 10:52:51,029] [INFO] Query marker FASTA was written to GCA_947074735.1_SRR13169512_bin.25_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 10:52:51,030] [INFO] Task started: Blastn
[2023-06-08 10:52:51,030] [INFO] Running command: blastn -query GCA_947074735.1_SRR13169512_bin.25_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e00c9c9-bb59-44b7-b49b-6ea65d9531c2/dqc_reference/reference_markers.fasta -out GCA_947074735.1_SRR13169512_bin.25_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 10:52:51,685] [INFO] Task succeeded: Blastn
[2023-06-08 10:52:51,689] [INFO] Selected 27 target genomes.
[2023-06-08 10:52:51,689] [INFO] Target genome list was writen to GCA_947074735.1_SRR13169512_bin.25_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 10:52:51,690] [INFO] Task started: fastANI
[2023-06-08 10:52:51,691] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f3de2fe-e836-4ec4-9b27-472d6458c412/GCA_947074735.1_SRR13169512_bin.25_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947074735.1_SRR13169512_bin.25_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947074735.1_SRR13169512_bin.25_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 10:53:09,275] [INFO] Task succeeded: fastANI
[2023-06-08 10:53:09,276] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e00c9c9-bb59-44b7-b49b-6ea65d9531c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 10:53:09,276] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e00c9c9-bb59-44b7-b49b-6ea65d9531c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 10:53:09,287] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 10:53:09,287] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 10:53:09,287] [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
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	76.5463	114	1325	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	76.535	115	1325	95	below_threshold
Lacrimispora sphenoides	strain=NCTC507	GCA_900461315.1	29370	29370	type	True	76.2895	78	1325	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	76.2858	105	1325	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_000160095.1	154046	154046	suspected-type	True	76.2747	99	1325	95	below_threshold
Lacrimispora sphenoides	strain=ATCC 19403	GCA_900105615.1	29370	29370	type	True	76.2352	78	1325	95	below_threshold
Lacrimispora aerotolerans	strain=DSM 5434	GCA_000687555.1	36832	36832	type	True	76.1986	55	1325	95	below_threshold
Diplocloster agilis	strain=ASD5720	GCA_019042275.1	2850323	2850323	type	True	76.1838	53	1325	95	below_threshold
Lacrimispora celerecrescens	strain=18A	GCA_002797975.1	29354	29354	type	True	76.0719	80	1325	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	75.9996	63	1325	95	below_threshold
Marvinbryantia formatexigens	strain=I-52	GCA_900102475.1	168384	168384	type	True	75.974	64	1325	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	75.5926	50	1325	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 10:53:09,289] [INFO] DFAST Taxonomy check result was written to GCA_947074735.1_SRR13169512_bin.25_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 10:53:09,290] [INFO] ===== Taxonomy check completed =====
[2023-06-08 10:53:09,290] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 10:53:09,290] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e00c9c9-bb59-44b7-b49b-6ea65d9531c2/dqc_reference/checkm_data
[2023-06-08 10:53:09,291] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 10:53:09,338] [INFO] Task started: CheckM
[2023-06-08 10:53:09,338] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947074735.1_SRR13169512_bin.25_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947074735.1_SRR13169512_bin.25_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947074735.1_SRR13169512_bin.25_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 10:53:44,754] [INFO] Task succeeded: CheckM
[2023-06-08 10:53:44,756] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-08 10:53:44,776] [INFO] ===== Completeness check finished =====
[2023-06-08 10:53:44,777] [INFO] ===== Start GTDB Search =====
[2023-06-08 10:53:44,777] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947074735.1_SRR13169512_bin.25_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 10:53:44,778] [INFO] Task started: Blastn
[2023-06-08 10:53:44,778] [INFO] Running command: blastn -query GCA_947074735.1_SRR13169512_bin.25_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e00c9c9-bb59-44b7-b49b-6ea65d9531c2/dqc_reference/reference_markers_gtdb.fasta -out GCA_947074735.1_SRR13169512_bin.25_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 10:53:45,838] [INFO] Task succeeded: Blastn
[2023-06-08 10:53:45,844] [INFO] Selected 19 target genomes.
[2023-06-08 10:53:45,844] [INFO] Target genome list was writen to GCA_947074735.1_SRR13169512_bin.25_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 10:53:45,845] [INFO] Task started: fastANI
[2023-06-08 10:53:45,846] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f3de2fe-e836-4ec4-9b27-472d6458c412/GCA_947074735.1_SRR13169512_bin.25_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947074735.1_SRR13169512_bin.25_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947074735.1_SRR13169512_bin.25_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 10:54:00,536] [INFO] Task succeeded: fastANI
[2023-06-08 10:54:00,554] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 10:54:00,554] [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_910575255.1	s__Ventrimonas sp910575255	99.2103	1195	1325	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.31	99.12	0.89	0.88	4	conclusive
GCA_910588875.1	s__Ventrimonas sp910588875	83.213	580	1325	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586255.1	s__Ventrimonas sp910586255	81.3465	572	1325	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003669055.1	s__Ventrimonas sp003669055	80.76	555	1325	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003611875.1	s__Ventrimonas sp003611875	79.3866	497	1325	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.50	99.24	0.91	0.86	4	-
GCA_910586205.1	s__Ventrimonas sp910586205	79.1657	449	1325	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009911065.1	s__Ventrimonas sp009911065	78.3568	367	1325	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	95.78	95.73	0.75	0.73	3	-
GCA_910577655.1	s__Ventrimonas sp910577655	77.3631	250	1325	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584845.1	s__Ventrimonas sp910584845	77.2375	231	1325	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018715565.1	s__Ventrimonas merdavium	77.1482	174	1325	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.46	99.46	0.97	0.97	2	-
GCA_900540335.1	s__Ventrimonas sp900540335	76.9307	177	1325	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.37	99.36	0.86	0.81	3	-
GCA_004554205.1	s__Ventrimonas sp004554205	76.8547	120	1325	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584785.1	s__Caccovicinus sp910584785	76.7398	118	1325	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018715905.1	s__Caccovicinus merdipullorum	76.553	108	1325	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	98.94	98.69	0.87	0.79	3	-
GCF_000158075.1	s__Enterocloster asparagiformis	76.5463	114	1325	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.72	98.33	0.90	0.88	5	-
GCA_900770345.1	s__Enterocloster sp900770345	76.4426	130	1325	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003477885.1	s__AF33-28 sp003477885	75.4145	53	1325	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__AF33-28	95.0	99.55	99.29	0.96	0.92	4	-
--------------------------------------------------------------------------------
[2023-06-08 10:54:00,556] [INFO] GTDB search result was written to GCA_947074735.1_SRR13169512_bin.25_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 10:54:00,557] [INFO] ===== GTDB Search completed =====
[2023-06-08 10:54:00,564] [INFO] DFAST_QC result json was written to GCA_947074735.1_SRR13169512_bin.25_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 10:54:00,564] [INFO] DFAST_QC completed!
[2023-06-08 10:54:00,564] [INFO] Total running time: 0h1m22s