[2023-06-17 06:44:38,535] [INFO] DFAST_QC pipeline started.
[2023-06-17 06:44:38,544] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 06:44:38,544] [INFO] DQC Reference Directory: /var/lib/cwl/stg167ac4d0-0e12-46fa-9462-71c06b573cd6/dqc_reference
[2023-06-17 06:44:40,116] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 06:44:40,117] [INFO] Task started: Prodigal
[2023-06-17 06:44:40,118] [INFO] Running command: gunzip -c /var/lib/cwl/stg81bd9589-799a-4cf9-ac7b-daf00f9edf10/GCA_905202645.1_ERR1430405-mag-bin.30_genomic.fna.gz | prodigal -d GCA_905202645.1_ERR1430405-mag-bin.30_genomic.fna/cds.fna -a GCA_905202645.1_ERR1430405-mag-bin.30_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 06:44:46,959] [INFO] Task succeeded: Prodigal
[2023-06-17 06:44:46,960] [INFO] Task started: HMMsearch
[2023-06-17 06:44:46,960] [INFO] Running command: hmmsearch --tblout GCA_905202645.1_ERR1430405-mag-bin.30_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg167ac4d0-0e12-46fa-9462-71c06b573cd6/dqc_reference/reference_markers.hmm GCA_905202645.1_ERR1430405-mag-bin.30_genomic.fna/protein.faa > /dev/null
[2023-06-17 06:44:47,220] [INFO] Task succeeded: HMMsearch
[2023-06-17 06:44:47,222] [INFO] Found 6/6 markers.
[2023-06-17 06:44:47,251] [INFO] Query marker FASTA was written to GCA_905202645.1_ERR1430405-mag-bin.30_genomic.fna/markers.fasta
[2023-06-17 06:44:47,251] [INFO] Task started: Blastn
[2023-06-17 06:44:47,251] [INFO] Running command: blastn -query GCA_905202645.1_ERR1430405-mag-bin.30_genomic.fna/markers.fasta -db /var/lib/cwl/stg167ac4d0-0e12-46fa-9462-71c06b573cd6/dqc_reference/reference_markers.fasta -out GCA_905202645.1_ERR1430405-mag-bin.30_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 06:44:47,919] [INFO] Task succeeded: Blastn
[2023-06-17 06:44:47,924] [INFO] Selected 27 target genomes.
[2023-06-17 06:44:47,925] [INFO] Target genome list was writen to GCA_905202645.1_ERR1430405-mag-bin.30_genomic.fna/target_genomes.txt
[2023-06-17 06:44:47,930] [INFO] Task started: fastANI
[2023-06-17 06:44:47,930] [INFO] Running command: fastANI --query /var/lib/cwl/stg81bd9589-799a-4cf9-ac7b-daf00f9edf10/GCA_905202645.1_ERR1430405-mag-bin.30_genomic.fna.gz --refList GCA_905202645.1_ERR1430405-mag-bin.30_genomic.fna/target_genomes.txt --output GCA_905202645.1_ERR1430405-mag-bin.30_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 06:45:04,898] [INFO] Task succeeded: fastANI
[2023-06-17 06:45:04,899] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg167ac4d0-0e12-46fa-9462-71c06b573cd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 06:45:04,899] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg167ac4d0-0e12-46fa-9462-71c06b573cd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 06:45:04,915] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 06:45:04,916] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 06:45:04,916] [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
Clostridium fessum	strain=SNUG30386	GCA_003024715.1	2126740	2126740	type	True	78.4621	150	844	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	77.3168	148	844	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	77.2062	147	844	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_000160095.1	154046	154046	suspected-type	True	77.0775	120	844	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	77.0466	137	844	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_000154365.1	208479	208479	type	True	77.0183	110	844	95	below_threshold
Hungatella effluvii	strain=DSM 24995	GCA_003201875.1	1096246	1096246	type	True	76.9167	130	844	95	below_threshold
Lachnoclostridium pacaense	strain=Marseille-P3100	GCA_900566185.1	1917870	1917870	type	True	76.8999	55	844	95	below_threshold
Lacrimispora celerecrescens	strain=18A	GCA_002797975.1	29354	29354	type	True	76.742	78	844	95	below_threshold
Enterocloster clostridioformis	strain=ATCC 25537	GCA_900113155.1	1531	1531	type	True	76.7311	126	844	95	below_threshold
Enterocloster clostridioformis	strain=NCTC11224	GCA_900447015.1	1531	1531	suspected-type	True	76.6963	118	844	95	below_threshold
Enterocloster clostridioformis	strain=FDAARGOS_1529	GCA_020297485.1	1531	1531	suspected-type	True	76.6639	118	844	95	below_threshold
Lacrimispora sphenoides	strain=NCTC507	GCA_900461315.1	29370	29370	type	True	76.5172	93	844	95	below_threshold
Lacrimispora sphenoides	strain=ATCC 19403	GCA_900105615.1	29370	29370	type	True	76.4851	97	844	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	76.0141	59	844	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	75.9494	50	844	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 06:45:04,918] [INFO] DFAST Taxonomy check result was written to GCA_905202645.1_ERR1430405-mag-bin.30_genomic.fna/tc_result.tsv
[2023-06-17 06:45:04,919] [INFO] ===== Taxonomy check completed =====
[2023-06-17 06:45:04,919] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 06:45:04,919] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg167ac4d0-0e12-46fa-9462-71c06b573cd6/dqc_reference/checkm_data
[2023-06-17 06:45:04,921] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 06:45:04,955] [INFO] Task started: CheckM
[2023-06-17 06:45:04,956] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905202645.1_ERR1430405-mag-bin.30_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905202645.1_ERR1430405-mag-bin.30_genomic.fna/checkm_input GCA_905202645.1_ERR1430405-mag-bin.30_genomic.fna/checkm_result
[2023-06-17 06:45:31,345] [INFO] Task succeeded: CheckM
[2023-06-17 06:45:31,346] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.38%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 06:45:31,368] [INFO] ===== Completeness check finished =====
[2023-06-17 06:45:31,368] [INFO] ===== Start GTDB Search =====
[2023-06-17 06:45:31,369] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905202645.1_ERR1430405-mag-bin.30_genomic.fna/markers.fasta)
[2023-06-17 06:45:31,369] [INFO] Task started: Blastn
[2023-06-17 06:45:31,370] [INFO] Running command: blastn -query GCA_905202645.1_ERR1430405-mag-bin.30_genomic.fna/markers.fasta -db /var/lib/cwl/stg167ac4d0-0e12-46fa-9462-71c06b573cd6/dqc_reference/reference_markers_gtdb.fasta -out GCA_905202645.1_ERR1430405-mag-bin.30_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 06:45:32,501] [INFO] Task succeeded: Blastn
[2023-06-17 06:45:32,507] [INFO] Selected 9 target genomes.
[2023-06-17 06:45:32,507] [INFO] Target genome list was writen to GCA_905202645.1_ERR1430405-mag-bin.30_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 06:45:32,511] [INFO] Task started: fastANI
[2023-06-17 06:45:32,512] [INFO] Running command: fastANI --query /var/lib/cwl/stg81bd9589-799a-4cf9-ac7b-daf00f9edf10/GCA_905202645.1_ERR1430405-mag-bin.30_genomic.fna.gz --refList GCA_905202645.1_ERR1430405-mag-bin.30_genomic.fna/target_genomes_gtdb.txt --output GCA_905202645.1_ERR1430405-mag-bin.30_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 06:45:38,735] [INFO] Task succeeded: fastANI
[2023-06-17 06:45:38,750] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 06:45:38,750] [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_900770535.1	s__Ventrimonas sp900770535	98.2676	464	844	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	98.72	98.72	0.86	0.86	2	conclusive
GCF_003478505.1	s__Ventrimonas sp003478505	89.2584	638	844	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.07	97.61	0.91	0.78	6	-
GCF_003480315.1	s__Ventrimonas sp003480315	87.1541	609	844	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	98.62	98.00	0.91	0.88	5	-
GCF_003481985.1	s__Ventrimonas sp003506385	85.1842	622	844	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	98.83	98.43	0.90	0.84	6	-
GCF_003481825.1	s__Ventrimonas sp003481825	84.368	585	844	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.33	98.65	0.93	0.87	3	-
GCF_003024715.1	s__Clostridium_Q fessum	78.447	150	844	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	98.33	97.70	0.88	0.81	31	-
GCA_900538475.1	s__Ventrimonas sp900538475	78.3358	186	844	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.39	99.20	0.94	0.93	3	-
GCA_900540335.1	s__Ventrimonas sp900540335	78.2119	185	844	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_910577765.1	s__Ventrimonas sp910577765	77.3397	146	844	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 06:45:38,752] [INFO] GTDB search result was written to GCA_905202645.1_ERR1430405-mag-bin.30_genomic.fna/result_gtdb.tsv
[2023-06-17 06:45:38,753] [INFO] ===== GTDB Search completed =====
[2023-06-17 06:45:38,757] [INFO] DFAST_QC result json was written to GCA_905202645.1_ERR1430405-mag-bin.30_genomic.fna/dqc_result.json
[2023-06-17 06:45:38,757] [INFO] DFAST_QC completed!
[2023-06-17 06:45:38,757] [INFO] Total running time: 0h1m0s