[2023-06-05 14:48:30,480] [INFO] DFAST_QC pipeline started.
[2023-06-05 14:48:30,482] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 14:48:30,482] [INFO] DQC Reference Directory: /var/lib/cwl/stg0985b348-c00c-4880-93a7-f885e98bce00/dqc_reference
[2023-06-05 14:48:31,831] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 14:48:31,831] [INFO] Task started: Prodigal
[2023-06-05 14:48:31,832] [INFO] Running command: gunzip -c /var/lib/cwl/stg6d930b61-6e39-40ea-8176-788ec5e9886b/GCA_934401795.1_ERR7746411_bin.65_genomic.fna.gz | prodigal -d GCA_934401795.1_ERR7746411_bin.65_genomic.fna/cds.fna -a GCA_934401795.1_ERR7746411_bin.65_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 14:48:37,005] [INFO] Task succeeded: Prodigal
[2023-06-05 14:48:37,005] [INFO] Task started: HMMsearch
[2023-06-05 14:48:37,005] [INFO] Running command: hmmsearch --tblout GCA_934401795.1_ERR7746411_bin.65_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0985b348-c00c-4880-93a7-f885e98bce00/dqc_reference/reference_markers.hmm GCA_934401795.1_ERR7746411_bin.65_genomic.fna/protein.faa > /dev/null
[2023-06-05 14:48:37,206] [INFO] Task succeeded: HMMsearch
[2023-06-05 14:48:37,207] [INFO] Found 6/6 markers.
[2023-06-05 14:48:37,230] [INFO] Query marker FASTA was written to GCA_934401795.1_ERR7746411_bin.65_genomic.fna/markers.fasta
[2023-06-05 14:48:37,230] [INFO] Task started: Blastn
[2023-06-05 14:48:37,230] [INFO] Running command: blastn -query GCA_934401795.1_ERR7746411_bin.65_genomic.fna/markers.fasta -db /var/lib/cwl/stg0985b348-c00c-4880-93a7-f885e98bce00/dqc_reference/reference_markers.fasta -out GCA_934401795.1_ERR7746411_bin.65_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 14:48:37,833] [INFO] Task succeeded: Blastn
[2023-06-05 14:48:37,836] [INFO] Selected 23 target genomes.
[2023-06-05 14:48:37,837] [INFO] Target genome list was writen to GCA_934401795.1_ERR7746411_bin.65_genomic.fna/target_genomes.txt
[2023-06-05 14:48:37,841] [INFO] Task started: fastANI
[2023-06-05 14:48:37,841] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d930b61-6e39-40ea-8176-788ec5e9886b/GCA_934401795.1_ERR7746411_bin.65_genomic.fna.gz --refList GCA_934401795.1_ERR7746411_bin.65_genomic.fna/target_genomes.txt --output GCA_934401795.1_ERR7746411_bin.65_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 14:48:49,994] [INFO] Task succeeded: fastANI
[2023-06-05 14:48:49,994] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0985b348-c00c-4880-93a7-f885e98bce00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 14:48:49,995] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0985b348-c00c-4880-93a7-f885e98bce00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 14:48:50,005] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 14:48:50,005] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 14:48:50,005] [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
Marvinbryantia formatexigens	strain=I-52	GCA_900102475.1	168384	168384	type	True	78.002	92	695	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	77.9765	93	695	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_000173815.1	168384	168384	type	True	77.9591	90	695	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	77.917	90	695	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	77.6269	87	695	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	77.2262	80	695	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	76.9097	59	695	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	76.9096	58	695	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	76.801	54	695	95	below_threshold
Merdimonas faecis	strain=BR31	GCA_001754075.1	1653435	1653435	type	True	76.6849	57	695	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	76.6009	67	695	95	below_threshold
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	76.5961	66	695	95	below_threshold
Roseburia faecis	strain=M72	GCA_001406815.1	301302	301302	type	True	76.3451	54	695	95	below_threshold
Hespellia stercorisuis	strain=DSM 15480	GCA_900142165.1	180311	180311	type	True	76.141	53	695	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 14:48:50,007] [INFO] DFAST Taxonomy check result was written to GCA_934401795.1_ERR7746411_bin.65_genomic.fna/tc_result.tsv
[2023-06-05 14:48:50,007] [INFO] ===== Taxonomy check completed =====
[2023-06-05 14:48:50,008] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 14:48:50,008] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0985b348-c00c-4880-93a7-f885e98bce00/dqc_reference/checkm_data
[2023-06-05 14:48:50,009] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 14:48:50,037] [INFO] Task started: CheckM
[2023-06-05 14:48:50,037] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934401795.1_ERR7746411_bin.65_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934401795.1_ERR7746411_bin.65_genomic.fna/checkm_input GCA_934401795.1_ERR7746411_bin.65_genomic.fna/checkm_result
[2023-06-05 14:49:10,569] [INFO] Task succeeded: CheckM
[2023-06-05 14:49:10,570] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 14:49:10,585] [INFO] ===== Completeness check finished =====
[2023-06-05 14:49:10,586] [INFO] ===== Start GTDB Search =====
[2023-06-05 14:49:10,587] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934401795.1_ERR7746411_bin.65_genomic.fna/markers.fasta)
[2023-06-05 14:49:10,587] [INFO] Task started: Blastn
[2023-06-05 14:49:10,587] [INFO] Running command: blastn -query GCA_934401795.1_ERR7746411_bin.65_genomic.fna/markers.fasta -db /var/lib/cwl/stg0985b348-c00c-4880-93a7-f885e98bce00/dqc_reference/reference_markers_gtdb.fasta -out GCA_934401795.1_ERR7746411_bin.65_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 14:49:11,638] [INFO] Task succeeded: Blastn
[2023-06-05 14:49:11,642] [INFO] Selected 17 target genomes.
[2023-06-05 14:49:11,642] [INFO] Target genome list was writen to GCA_934401795.1_ERR7746411_bin.65_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 14:49:11,664] [INFO] Task started: fastANI
[2023-06-05 14:49:11,664] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d930b61-6e39-40ea-8176-788ec5e9886b/GCA_934401795.1_ERR7746411_bin.65_genomic.fna.gz --refList GCA_934401795.1_ERR7746411_bin.65_genomic.fna/target_genomes_gtdb.txt --output GCA_934401795.1_ERR7746411_bin.65_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 14:49:20,927] [INFO] Task succeeded: fastANI
[2023-06-05 14:49:20,936] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 14:49:20,936] [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_902363135.1	s__Choladousia sp902363135	95.6475	649	695	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	98.66	98.47	0.96	0.95	4	conclusive
GCA_902363665.1	s__Choladousia sp902363665	80.0079	303	695	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	97.59	97.59	0.93	0.93	2	-
GCA_002491565.1	s__Choladousia sp002491565	78.0675	192	695	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018223435.1	s__Limivivens sp900543575	78.0459	92	695	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Limivivens	95.0	98.02	97.88	0.92	0.90	4	-
GCF_015557635.1	s__Fusicatenibacter saccharivorans	78.0417	81	695	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Fusicatenibacter	95.0	97.82	97.27	0.86	0.77	91	-
GCA_004557975.1	s__Choladousia sp004557975	77.9901	151	695	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000173815.1	s__Marvinbryantia formatexigens	77.9503	91	695	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Marvinbryantia	95.0	99.98	99.98	0.99	0.99	3	-
GCA_003612585.1	s__Choladousia sp003612585	77.7585	126	695	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018711885.1	s__Choladousia intestinipullorum	77.6952	110	695	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900757145.1	s__Choladousia sp900757145	77.5859	99	695	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	99.16	99.16	0.96	0.96	2	-
GCA_905201705.1	s__Marvinbryantia sp900550755	77.5531	101	695	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Marvinbryantia	95.0	99.85	99.71	0.93	0.91	3	-
GCF_003470905.1	s__Roseburia sp003470905	76.6615	53	695	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.69	98.30	0.90	0.82	7	-
GCA_905207905.1	s__Merdiplasma sp905207905	76.5567	61	695	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdiplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009696065.1	s__Oliverpabstia intestinalis	76.5483	62	695	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	97.25	96.88	0.81	0.78	19	-
--------------------------------------------------------------------------------
[2023-06-05 14:49:20,938] [INFO] GTDB search result was written to GCA_934401795.1_ERR7746411_bin.65_genomic.fna/result_gtdb.tsv
[2023-06-05 14:49:20,938] [INFO] ===== GTDB Search completed =====
[2023-06-05 14:49:20,941] [INFO] DFAST_QC result json was written to GCA_934401795.1_ERR7746411_bin.65_genomic.fna/dqc_result.json
[2023-06-05 14:49:20,941] [INFO] DFAST_QC completed!
[2023-06-05 14:49:20,941] [INFO] Total running time: 0h0m50s