[2023-06-05 13:48:30,126] [INFO] DFAST_QC pipeline started.
[2023-06-05 13:48:30,127] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 13:48:30,128] [INFO] DQC Reference Directory: /var/lib/cwl/stgbbdbb5a1-62a3-4722-9770-fa6be8f60e8e/dqc_reference
[2023-06-05 13:48:31,223] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 13:48:31,224] [INFO] Task started: Prodigal
[2023-06-05 13:48:31,224] [INFO] Running command: gunzip -c /var/lib/cwl/stg44fbe6cc-ed35-4832-8a61-56ad048180a8/GCA_934876045.1_MTG247_bin.2.fa_genomic.fna.gz | prodigal -d GCA_934876045.1_MTG247_bin.2.fa_genomic.fna/cds.fna -a GCA_934876045.1_MTG247_bin.2.fa_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 13:48:36,530] [INFO] Task succeeded: Prodigal
[2023-06-05 13:48:36,530] [INFO] Task started: HMMsearch
[2023-06-05 13:48:36,530] [INFO] Running command: hmmsearch --tblout GCA_934876045.1_MTG247_bin.2.fa_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbbdbb5a1-62a3-4722-9770-fa6be8f60e8e/dqc_reference/reference_markers.hmm GCA_934876045.1_MTG247_bin.2.fa_genomic.fna/protein.faa > /dev/null
[2023-06-05 13:48:36,714] [INFO] Task succeeded: HMMsearch
[2023-06-05 13:48:36,715] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg44fbe6cc-ed35-4832-8a61-56ad048180a8/GCA_934876045.1_MTG247_bin.2.fa_genomic.fna.gz]
[2023-06-05 13:48:36,735] [INFO] Query marker FASTA was written to GCA_934876045.1_MTG247_bin.2.fa_genomic.fna/markers.fasta
[2023-06-05 13:48:36,735] [INFO] Task started: Blastn
[2023-06-05 13:48:36,735] [INFO] Running command: blastn -query GCA_934876045.1_MTG247_bin.2.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbdbb5a1-62a3-4722-9770-fa6be8f60e8e/dqc_reference/reference_markers.fasta -out GCA_934876045.1_MTG247_bin.2.fa_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 13:48:37,304] [INFO] Task succeeded: Blastn
[2023-06-05 13:48:37,307] [INFO] Selected 20 target genomes.
[2023-06-05 13:48:37,307] [INFO] Target genome list was writen to GCA_934876045.1_MTG247_bin.2.fa_genomic.fna/target_genomes.txt
[2023-06-05 13:48:37,308] [INFO] Task started: fastANI
[2023-06-05 13:48:37,309] [INFO] Running command: fastANI --query /var/lib/cwl/stg44fbe6cc-ed35-4832-8a61-56ad048180a8/GCA_934876045.1_MTG247_bin.2.fa_genomic.fna.gz --refList GCA_934876045.1_MTG247_bin.2.fa_genomic.fna/target_genomes.txt --output GCA_934876045.1_MTG247_bin.2.fa_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 13:48:50,393] [INFO] Task succeeded: fastANI
[2023-06-05 13:48:50,394] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbbdbb5a1-62a3-4722-9770-fa6be8f60e8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 13:48:50,394] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbbdbb5a1-62a3-4722-9770-fa6be8f60e8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 13:48:50,403] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2023-06-05 13:48:50,403] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-05 13:48:50,403] [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	97.6652	725	794	95	conclusive
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	77.3368	61	794	95	below_threshold
Hungatella effluvii	strain=DSM 24995	GCA_003201875.1	1096246	1096246	type	True	77.1932	100	794	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	77.179	52	794	95	below_threshold
[Clostridium] aminophilum	strain=F	GCA_900112885.1	1526	1526	type	True	77.1353	98	794	95	below_threshold
[Clostridium] aminophilum	strain=DSM 10710	GCA_000711825.1	1526	1526	type	True	77.1172	98	794	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	77.0935	82	794	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	77.0479	82	794	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	77.0462	68	794	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	76.9637	96	794	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	76.8036	70	794	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	76.7357	71	794	95	below_threshold
Eubacterium ramulus	strain=ATCC 29099	GCA_000469345.1	39490	39490	type	True	76.4878	58	794	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 13:48:50,405] [INFO] DFAST Taxonomy check result was written to GCA_934876045.1_MTG247_bin.2.fa_genomic.fna/tc_result.tsv
[2023-06-05 13:48:50,406] [INFO] ===== Taxonomy check completed =====
[2023-06-05 13:48:50,406] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 13:48:50,406] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbbdbb5a1-62a3-4722-9770-fa6be8f60e8e/dqc_reference/checkm_data
[2023-06-05 13:48:50,407] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 13:48:50,435] [INFO] Task started: CheckM
[2023-06-05 13:48:50,435] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934876045.1_MTG247_bin.2.fa_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934876045.1_MTG247_bin.2.fa_genomic.fna/checkm_input GCA_934876045.1_MTG247_bin.2.fa_genomic.fna/checkm_result
[2023-06-05 13:49:10,875] [INFO] Task succeeded: CheckM
[2023-06-05 13:49:10,876] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 13:49:10,892] [INFO] ===== Completeness check finished =====
[2023-06-05 13:49:10,892] [INFO] ===== Start GTDB Search =====
[2023-06-05 13:49:10,893] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934876045.1_MTG247_bin.2.fa_genomic.fna/markers.fasta)
[2023-06-05 13:49:10,893] [INFO] Task started: Blastn
[2023-06-05 13:49:10,894] [INFO] Running command: blastn -query GCA_934876045.1_MTG247_bin.2.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbdbb5a1-62a3-4722-9770-fa6be8f60e8e/dqc_reference/reference_markers_gtdb.fasta -out GCA_934876045.1_MTG247_bin.2.fa_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 13:49:11,802] [INFO] Task succeeded: Blastn
[2023-06-05 13:49:11,805] [INFO] Selected 20 target genomes.
[2023-06-05 13:49:11,805] [INFO] Target genome list was writen to GCA_934876045.1_MTG247_bin.2.fa_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 13:49:11,818] [INFO] Task started: fastANI
[2023-06-05 13:49:11,818] [INFO] Running command: fastANI --query /var/lib/cwl/stg44fbe6cc-ed35-4832-8a61-56ad048180a8/GCA_934876045.1_MTG247_bin.2.fa_genomic.fna.gz --refList GCA_934876045.1_MTG247_bin.2.fa_genomic.fna/target_genomes_gtdb.txt --output GCA_934876045.1_MTG247_bin.2.fa_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 13:49:24,005] [INFO] Task succeeded: fastANI
[2023-06-05 13:49:24,017] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 13:49:24,018] [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
GCF_003024715.1	s__Clostridium_Q fessum	97.6652	725	794	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	conclusive
GCF_003435375.1	s__Copromonas sp900066535	78.3669	156	794	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	97.23	95.52	0.82	0.74	22	-
GCA_016302185.1	s__Clostridium_Q sp016302185	78.3305	179	794	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	-
GCF_003478505.1	s__Ventrimonas sp003478505	78.3119	150	794	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_000466485.1	s__Clostridium_Q symbiosum	78.0793	165	794	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	98.86	98.57	0.86	0.81	32	-
GCA_018377235.1	s__Clostridium_Q sp018377235	77.961	115	794	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	-
GCF_900626075.1	s__Clostridium_Q transplantifaecale	77.9214	180	794	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	-
GCF_003480315.1	s__Ventrimonas sp003480315	77.8663	153	794	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	98.62	98.00	0.91	0.88	5	-
GCA_900547735.1	s__Clostridium_Q sp900547735	77.8305	184	794	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_018223375.1	s__Clostridium_Q sp000435655	77.6926	145	794	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_000235505.1	s__Hungatella_A hathewayi_A	77.6314	82	794	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Hungatella_A	95.0	99.27	96.59	0.97	0.86	6	-
GCA_900555625.1	s__Ventrimonas sp900555625	77.5906	94	794	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	98.73	98.70	0.86	0.85	3	-
GCA_900540335.1	s__Ventrimonas sp900540335	77.5894	85	794	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_900770535.1	s__Ventrimonas sp900770535	77.5378	81	794	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	98.72	98.72	0.86	0.86	2	-
GCA_001304875.1	s__Ventrisoma faecale	77.3575	126	794	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrisoma	95.0	98.23	97.74	0.91	0.86	4	-
GCA_009911305.1	s__Clostridium_Q sp009911305	77.3518	161	794	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	98.99	98.99	0.91	0.91	2	-
GCA_900538475.1	s__Ventrimonas sp900538475	77.1334	88	794	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.39	99.20	0.94	0.93	3	-
GCF_000711825.1	s__Clostridium_R aminophilum	77.1172	98	794	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_R	95.0	100.00	100.00	0.99	0.99	2	-
GCA_910585435.1	s__UBA3402 sp910585435	76.6468	72	794	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004554205.1	s__Ventrimonas sp004554205	76.6132	80	794	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 13:49:24,020] [INFO] GTDB search result was written to GCA_934876045.1_MTG247_bin.2.fa_genomic.fna/result_gtdb.tsv
[2023-06-05 13:49:24,021] [INFO] ===== GTDB Search completed =====
[2023-06-05 13:49:24,024] [INFO] DFAST_QC result json was written to GCA_934876045.1_MTG247_bin.2.fa_genomic.fna/dqc_result.json
[2023-06-05 13:49:24,024] [INFO] DFAST_QC completed!
[2023-06-05 13:49:24,024] [INFO] Total running time: 0h0m54s