[2023-06-28 04:20:32,171] [INFO] DFAST_QC pipeline started.
[2023-06-28 04:20:32,173] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 04:20:32,173] [INFO] DQC Reference Directory: /var/lib/cwl/stgae61b609-66f0-475a-adf6-128b7e4c9b1a/dqc_reference
[2023-06-28 04:20:33,480] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 04:20:33,481] [INFO] Task started: Prodigal
[2023-06-28 04:20:33,481] [INFO] Running command: gunzip -c /var/lib/cwl/stg80b0c1eb-926d-40d9-a8da-3c0a1188a152/GCA_944384175.1_BRZ_II_bin38_genomic.fna.gz | prodigal -d GCA_944384175.1_BRZ_II_bin38_genomic.fna/cds.fna -a GCA_944384175.1_BRZ_II_bin38_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 04:20:41,118] [INFO] Task succeeded: Prodigal
[2023-06-28 04:20:41,118] [INFO] Task started: HMMsearch
[2023-06-28 04:20:41,118] [INFO] Running command: hmmsearch --tblout GCA_944384175.1_BRZ_II_bin38_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgae61b609-66f0-475a-adf6-128b7e4c9b1a/dqc_reference/reference_markers.hmm GCA_944384175.1_BRZ_II_bin38_genomic.fna/protein.faa > /dev/null
[2023-06-28 04:20:41,410] [INFO] Task succeeded: HMMsearch
[2023-06-28 04:20:41,412] [INFO] Found 6/6 markers.
[2023-06-28 04:20:41,442] [INFO] Query marker FASTA was written to GCA_944384175.1_BRZ_II_bin38_genomic.fna/markers.fasta
[2023-06-28 04:20:41,443] [INFO] Task started: Blastn
[2023-06-28 04:20:41,443] [INFO] Running command: blastn -query GCA_944384175.1_BRZ_II_bin38_genomic.fna/markers.fasta -db /var/lib/cwl/stgae61b609-66f0-475a-adf6-128b7e4c9b1a/dqc_reference/reference_markers.fasta -out GCA_944384175.1_BRZ_II_bin38_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:20:42,110] [INFO] Task succeeded: Blastn
[2023-06-28 04:20:42,114] [INFO] Selected 28 target genomes.
[2023-06-28 04:20:42,115] [INFO] Target genome list was writen to GCA_944384175.1_BRZ_II_bin38_genomic.fna/target_genomes.txt
[2023-06-28 04:20:42,118] [INFO] Task started: fastANI
[2023-06-28 04:20:42,118] [INFO] Running command: fastANI --query /var/lib/cwl/stg80b0c1eb-926d-40d9-a8da-3c0a1188a152/GCA_944384175.1_BRZ_II_bin38_genomic.fna.gz --refList GCA_944384175.1_BRZ_II_bin38_genomic.fna/target_genomes.txt --output GCA_944384175.1_BRZ_II_bin38_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 04:20:59,783] [INFO] Task succeeded: fastANI
[2023-06-28 04:20:59,784] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgae61b609-66f0-475a-adf6-128b7e4c9b1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 04:20:59,785] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgae61b609-66f0-475a-adf6-128b7e4c9b1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 04:20:59,803] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 04:20:59,803] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 04:20:59,803] [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 bolteae	strain=ATCC BAA-613	GCA_002234575.2	208479	208479	type	True	77.2604	121	1061	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_000154365.1	208479	208479	type	True	77.2225	120	1061	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002959675.1	208479	208479	type	True	77.2187	121	1061	95	below_threshold
Clostridium porci	strain=WCA-389-WT-23D1	GCA_009696375.1	2605778	2605778	type	True	76.8536	86	1061	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	76.8379	89	1061	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_000160095.1	154046	154046	suspected-type	True	76.7147	85	1061	95	below_threshold
Enterocloster clostridioformis	strain=FDAARGOS_1529	GCA_020297485.1	1531	1531	suspected-type	True	76.7107	123	1061	95	below_threshold
Enterocloster clostridioformis	strain=NCTC11224	GCA_900447015.1	1531	1531	suspected-type	True	76.7062	126	1061	95	below_threshold
Enterocloster clostridioformis	strain=ATCC 25537	GCA_900113155.1	1531	1531	type	True	76.691	123	1061	95	below_threshold
Lacrimispora celerecrescens	strain=18A	GCA_002797975.1	29354	29354	type	True	76.6453	87	1061	95	below_threshold
Lachnoclostridium edouardi	strain=Marseille-P3397	GCA_900240245.1	1926283	1926283	type	True	76.6431	98	1061	95	below_threshold
Hungatella effluvii	strain=DSM 24995	GCA_003201875.1	1096246	1096246	type	True	76.5057	87	1061	95	below_threshold
Cuneatibacter caecimuris	strain=DSM 29486	GCA_004216775.1	1796618	1796618	type	True	76.2534	54	1061	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	76.0542	62	1061	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	75.6675	63	1061	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 04:20:59,806] [INFO] DFAST Taxonomy check result was written to GCA_944384175.1_BRZ_II_bin38_genomic.fna/tc_result.tsv
[2023-06-28 04:20:59,807] [INFO] ===== Taxonomy check completed =====
[2023-06-28 04:20:59,807] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 04:20:59,808] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgae61b609-66f0-475a-adf6-128b7e4c9b1a/dqc_reference/checkm_data
[2023-06-28 04:20:59,809] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 04:20:59,843] [INFO] Task started: CheckM
[2023-06-28 04:20:59,843] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944384175.1_BRZ_II_bin38_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944384175.1_BRZ_II_bin38_genomic.fna/checkm_input GCA_944384175.1_BRZ_II_bin38_genomic.fna/checkm_result
[2023-06-28 04:21:28,162] [INFO] Task succeeded: CheckM
[2023-06-28 04:21:28,164] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 04:21:28,185] [INFO] ===== Completeness check finished =====
[2023-06-28 04:21:28,185] [INFO] ===== Start GTDB Search =====
[2023-06-28 04:21:28,186] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944384175.1_BRZ_II_bin38_genomic.fna/markers.fasta)
[2023-06-28 04:21:28,186] [INFO] Task started: Blastn
[2023-06-28 04:21:28,186] [INFO] Running command: blastn -query GCA_944384175.1_BRZ_II_bin38_genomic.fna/markers.fasta -db /var/lib/cwl/stgae61b609-66f0-475a-adf6-128b7e4c9b1a/dqc_reference/reference_markers_gtdb.fasta -out GCA_944384175.1_BRZ_II_bin38_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:21:29,259] [INFO] Task succeeded: Blastn
[2023-06-28 04:21:29,263] [INFO] Selected 17 target genomes.
[2023-06-28 04:21:29,264] [INFO] Target genome list was writen to GCA_944384175.1_BRZ_II_bin38_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 04:21:29,275] [INFO] Task started: fastANI
[2023-06-28 04:21:29,275] [INFO] Running command: fastANI --query /var/lib/cwl/stg80b0c1eb-926d-40d9-a8da-3c0a1188a152/GCA_944384175.1_BRZ_II_bin38_genomic.fna.gz --refList GCA_944384175.1_BRZ_II_bin38_genomic.fna/target_genomes_gtdb.txt --output GCA_944384175.1_BRZ_II_bin38_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 04:21:40,329] [INFO] Task succeeded: fastANI
[2023-06-28 04:21:40,346] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 04:21:40,347] [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_018713255.1	s__Caccovicinus excrementipullorum	99.6254	979	1061	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	99.99	99.99	0.96	0.96	2	conclusive
GCA_018715905.1	s__Caccovicinus merdipullorum	79.6252	438	1061	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	98.94	98.69	0.87	0.79	3	-
GCA_017889125.1	s__Caccovicinus sp017889125	79.2966	431	1061	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_009774615.1	s__Caccovicinus sp009774615	77.5009	154	1061	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	99.13	99.13	0.87	0.87	2	-
GCA_910575565.1	s__Caccovicinus sp910575565	77.3455	212	1061	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	99.12	99.12	0.93	0.93	2	-
GCA_910584785.1	s__Caccovicinus sp910584785	77.2869	143	1061	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_905215625.1	s__UMGS1370 sp905215625	77.2627	97	1061	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UMGS1370	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001517625.2	s__Enterocloster sp001517625	77.2441	123	1061	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.90	98.46	0.89	0.80	9	-
GCA_905215775.1	s__Copromonas sp905215775	77.104	61	1061	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904395885.1	s__UMGS1370 sp904395885	77.0807	134	1061	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UMGS1370	95.0	99.37	99.37	0.90	0.90	2	-
GCF_005845215.1	s__Enterocloster sp005845215	76.9877	107	1061	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.62	99.13	0.95	0.86	6	-
GCA_900540335.1	s__Ventrimonas sp900540335	76.8455	104	1061	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_018223375.1	s__Clostridium_Q sp000435655	76.8308	81	1061	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	98.36	96.90	0.90	0.85	8	-
GCF_018785315.1	s__CHH4-2 sp018785315	76.6994	107	1061	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CHH4-2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002899675.1	s__CHH4-2 sp002899675	76.458	106	1061	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CHH4-2	95.0	100.00	100.00	0.98	0.98	2	-
GCA_910588325.1	s__UBA3402 sp910588325	76.2073	102	1061	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 04:21:40,349] [INFO] GTDB search result was written to GCA_944384175.1_BRZ_II_bin38_genomic.fna/result_gtdb.tsv
[2023-06-28 04:21:40,349] [INFO] ===== GTDB Search completed =====
[2023-06-28 04:21:40,353] [INFO] DFAST_QC result json was written to GCA_944384175.1_BRZ_II_bin38_genomic.fna/dqc_result.json
[2023-06-28 04:21:40,353] [INFO] DFAST_QC completed!
[2023-06-28 04:21:40,353] [INFO] Total running time: 0h1m8s