[2024-01-24 13:48:59,520] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:59,526] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:59,526] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a4dad77-e650-411f-a4ec-5a9294a27f27/dqc_reference
[2024-01-24 13:49:00,798] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:00,799] [INFO] Task started: Prodigal
[2024-01-24 13:49:00,799] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb1f9189-af6d-4253-b422-2fd88d8009cf/GCF_019042275.1_ASM1904227v1_genomic.fna.gz | prodigal -d GCF_019042275.1_ASM1904227v1_genomic.fna/cds.fna -a GCF_019042275.1_ASM1904227v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:14,570] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:14,571] [INFO] Task started: HMMsearch
[2024-01-24 13:49:14,571] [INFO] Running command: hmmsearch --tblout GCF_019042275.1_ASM1904227v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a4dad77-e650-411f-a4ec-5a9294a27f27/dqc_reference/reference_markers.hmm GCF_019042275.1_ASM1904227v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:14,891] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:14,892] [INFO] Found 6/6 markers.
[2024-01-24 13:49:14,941] [INFO] Query marker FASTA was written to GCF_019042275.1_ASM1904227v1_genomic.fna/markers.fasta
[2024-01-24 13:49:14,941] [INFO] Task started: Blastn
[2024-01-24 13:49:14,941] [INFO] Running command: blastn -query GCF_019042275.1_ASM1904227v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a4dad77-e650-411f-a4ec-5a9294a27f27/dqc_reference/reference_markers.fasta -out GCF_019042275.1_ASM1904227v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:15,589] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:15,593] [INFO] Selected 22 target genomes.
[2024-01-24 13:49:15,593] [INFO] Target genome list was writen to GCF_019042275.1_ASM1904227v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:15,602] [INFO] Task started: fastANI
[2024-01-24 13:49:15,603] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb1f9189-af6d-4253-b422-2fd88d8009cf/GCF_019042275.1_ASM1904227v1_genomic.fna.gz --refList GCF_019042275.1_ASM1904227v1_genomic.fna/target_genomes.txt --output GCF_019042275.1_ASM1904227v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:33,523] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:33,523] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a4dad77-e650-411f-a4ec-5a9294a27f27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:33,524] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a4dad77-e650-411f-a4ec-5a9294a27f27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:33,537] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:33,538] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:33,538] [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
Diplocloster agilis	strain=ASD5720	GCA_019042275.1	2850323	2850323	type	True	100.0	1843	1859	95	conclusive
Diplocloster modestus	strain=ASD4241	GCA_019042245.1	2850322	2850322	type	True	88.2721	1330	1859	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	78.6216	102	1859	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	78.0745	99	1859	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	77.2587	62	1859	95	below_threshold
Hungatella effluvii	strain=DSM 24995	GCA_003201875.1	1096246	1096246	type	True	76.7003	88	1859	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_001689125.2	1796616	1796616	type	True	76.6588	72	1859	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_002221555.2	1796616	1796616	type	True	76.6521	71	1859	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_016696745.1	1796616	1796616	type	True	76.6469	70	1859	95	below_threshold
Murimonas intestini	strain=DSM 26524	GCA_024622195.1	1337051	1337051	type	True	76.5281	79	1859	95	below_threshold
Marvinbryantia formatexigens	strain=I-52	GCA_900102475.1	168384	168384	type	True	76.4336	65	1859	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_000173815.1	168384	168384	type	True	76.4161	63	1859	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	76.3778	64	1859	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	76.3608	91	1859	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	76.3326	89	1859	95	below_threshold
Lacrimispora sphenoides	strain=ATCC 19403	GCA_900105615.1	29370	29370	type	True	76.1727	53	1859	95	below_threshold
Lacrimispora sphenoides	strain=NCTC507	GCA_900461315.1	29370	29370	type	True	76.1593	52	1859	95	below_threshold
Anaerobium acetethylicum	strain=GluBS11	GCA_900096945.1	1619234	1619234	type	True	76.0455	50	1859	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:33,539] [INFO] DFAST Taxonomy check result was written to GCF_019042275.1_ASM1904227v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:33,540] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:33,540] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:33,540] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a4dad77-e650-411f-a4ec-5a9294a27f27/dqc_reference/checkm_data
[2024-01-24 13:49:33,541] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:33,595] [INFO] Task started: CheckM
[2024-01-24 13:49:33,595] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019042275.1_ASM1904227v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019042275.1_ASM1904227v1_genomic.fna/checkm_input GCF_019042275.1_ASM1904227v1_genomic.fna/checkm_result
[2024-01-24 13:50:19,600] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:19,601] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:19,624] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:19,624] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:19,625] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019042275.1_ASM1904227v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:19,625] [INFO] Task started: Blastn
[2024-01-24 13:50:19,625] [INFO] Running command: blastn -query GCF_019042275.1_ASM1904227v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a4dad77-e650-411f-a4ec-5a9294a27f27/dqc_reference/reference_markers_gtdb.fasta -out GCF_019042275.1_ASM1904227v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:20,700] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:20,703] [INFO] Selected 23 target genomes.
[2024-01-24 13:50:20,703] [INFO] Target genome list was writen to GCF_019042275.1_ASM1904227v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:20,720] [INFO] Task started: fastANI
[2024-01-24 13:50:20,720] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb1f9189-af6d-4253-b422-2fd88d8009cf/GCF_019042275.1_ASM1904227v1_genomic.fna.gz --refList GCF_019042275.1_ASM1904227v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019042275.1_ASM1904227v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:36,808] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:36,831] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:36,832] [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_902362855.1	s__GCA-900066755 sp900066755	98.9012	1630	1859	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__GCA-900066755	95.0	99.21	98.73	0.90	0.82	4	conclusive
GCA_902363085.1	s__GCA-900066755 sp902363085	88.1971	1318	1859	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__GCA-900066755	95.0	99.73	99.73	0.92	0.92	2	-
GCF_000225345.1	s__Roseburia hominis	77.7691	58	1859	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.94	95.20	0.88	0.81	15	-
GCA_018223385.1	s__JAGTTR01 sp018223385	77.3226	86	1859	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__JAGTTR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002361955.1	s__CAG-56 sp002361955	77.0085	55	1859	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-56	95.0	99.90	99.85	0.92	0.90	5	-
GCA_019120315.1	s__Ruminococcus_G avistercoris	76.8845	70	1859	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ruminococcus_G	95.0	99.47	98.95	0.89	0.84	3	-
GCA_910575555.1	s__14-2 sp011960065	76.4974	76	1859	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	99.61	97.67	0.95	0.76	7	-
GCA_910583895.1	s__Choladocola sp910583895	76.363	55	1859	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019115665.1	s__Eisenbergiella pullistercoris	76.2203	76	1859	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eisenbergiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018711275.1	s__Pullilachnospira intestinigallinarum	76.1502	79	1859	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pullilachnospira	95.0	99.92	99.92	0.90	0.90	2	-
GCA_910583615.1	s__Choladocola sp910583615	76.1256	69	1859	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018713585.1	s__Pullilachnospira stercoravium	76.0833	80	1859	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pullilachnospira	95.0	97.91	97.84	0.85	0.79	6	-
GCA_018715565.1	s__Ventrimonas merdavium	76.072	65	1859	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_009911175.1	s__Schaedlerella sp009911175	76.0655	95	1859	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	98.09	98.08	0.79	0.79	3	-
GCF_900626075.1	s__Clostridium_Q transplantifaecale	76.0202	66	1859	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588285.1	s__14-2 sp910588285	75.8223	72	1859	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586965.1	s__MD308 sp910586965	75.7333	50	1859	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__MD308	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:36,834] [INFO] GTDB search result was written to GCF_019042275.1_ASM1904227v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:36,835] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:36,839] [INFO] DFAST_QC result json was written to GCF_019042275.1_ASM1904227v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:36,840] [INFO] DFAST_QC completed!
[2024-01-24 13:50:36,840] [INFO] Total running time: 0h1m37s