[2024-01-25 18:54:20,604] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:54:20,606] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:54:20,606] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb131002-8cc7-4ca8-b209-c78790749bc8/dqc_reference
[2024-01-25 18:54:21,799] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:54:21,800] [INFO] Task started: Prodigal
[2024-01-25 18:54:21,800] [INFO] Running command: gunzip -c /var/lib/cwl/stg070c7682-18b6-4c1e-8870-6dc7078525af/GCF_025566885.1_ASM2556688v1_genomic.fna.gz | prodigal -d GCF_025566885.1_ASM2556688v1_genomic.fna/cds.fna -a GCF_025566885.1_ASM2556688v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:54:28,906] [INFO] Task succeeded: Prodigal
[2024-01-25 18:54:28,906] [INFO] Task started: HMMsearch
[2024-01-25 18:54:28,906] [INFO] Running command: hmmsearch --tblout GCF_025566885.1_ASM2556688v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb131002-8cc7-4ca8-b209-c78790749bc8/dqc_reference/reference_markers.hmm GCF_025566885.1_ASM2556688v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:54:29,152] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:54:29,153] [INFO] Found 6/6 markers.
[2024-01-25 18:54:29,181] [INFO] Query marker FASTA was written to GCF_025566885.1_ASM2556688v1_genomic.fna/markers.fasta
[2024-01-25 18:54:29,181] [INFO] Task started: Blastn
[2024-01-25 18:54:29,181] [INFO] Running command: blastn -query GCF_025566885.1_ASM2556688v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb131002-8cc7-4ca8-b209-c78790749bc8/dqc_reference/reference_markers.fasta -out GCF_025566885.1_ASM2556688v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:29,769] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:29,773] [INFO] Selected 32 target genomes.
[2024-01-25 18:54:29,773] [INFO] Target genome list was writen to GCF_025566885.1_ASM2556688v1_genomic.fna/target_genomes.txt
[2024-01-25 18:54:29,787] [INFO] Task started: fastANI
[2024-01-25 18:54:29,787] [INFO] Running command: fastANI --query /var/lib/cwl/stg070c7682-18b6-4c1e-8870-6dc7078525af/GCF_025566885.1_ASM2556688v1_genomic.fna.gz --refList GCF_025566885.1_ASM2556688v1_genomic.fna/target_genomes.txt --output GCF_025566885.1_ASM2556688v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:54:47,747] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:47,747] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb131002-8cc7-4ca8-b209-c78790749bc8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:54:47,748] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb131002-8cc7-4ca8-b209-c78790749bc8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:54:47,760] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:54:47,760] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:54:47,760] [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
Eubacterium ventriosum	strain=ATCC 27560	GCA_000153885.1	39496	39496	suspected-type	True	82.7643	54	1144	95	below_threshold
Eubacterium ventriosum	strain=ATCC 27560	GCA_025150745.1	39496	39496	suspected-type	True	82.6899	56	1144	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	81.3557	93	1144	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	79.6982	70	1144	95	below_threshold
Luxibacter massiliensis	strain=Marseille-P5551	GCA_900604355.1	2219695	2219695	type	True	79.5845	70	1144	95	below_threshold
Blautia argi	strain=KCTC 15426	GCA_003287895.1	1912897	1912897	type	True	79.3856	102	1144	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	78.7164	74	1144	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_000153905.1	40520	40520	type	True	78.6959	69	1144	95	below_threshold
Eubacterium ramulus	strain=ATCC 29099	GCA_000469345.1	39490	39490	type	True	78.5959	152	1144	95	below_threshold
Lachnoclostridium edouardi	strain=Marseille-P3397	GCA_900240245.1	1926283	1926283	type	True	77.9856	55	1144	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_002222595.2	1322	1322	type	True	77.8095	74	1144	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	77.7807	71	1144	95	below_threshold
Lactonifactor longoviformis	strain=DSM 17459	GCA_900129135.1	341220	341220	suspected-type	True	77.77	64	1144	95	below_threshold
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	77.661	58	1144	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_000156675.1	1322	1322	type	True	77.5555	73	1144	95	below_threshold
Dorea phocaeensis	strain=Marseille-P4003	GCA_900240315.1	2040291	2040291	type	True	77.4197	59	1144	95	below_threshold
Diplocloster agilis	strain=ASD5720	GCA_019042275.1	2850323	2850323	type	True	77.2432	50	1144	95	below_threshold
Wansuia hejianensis	strain=NSJ-29	GCA_014337215.1	2763667	2763667	type	True	76.7036	51	1144	95	below_threshold
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	76.6959	64	1144	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	76.6906	57	1144	95	below_threshold
Murimonas intestini	strain=DSM 26524	GCA_024622195.1	1337051	1337051	type	True	76.4875	67	1144	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:54:47,762] [INFO] DFAST Taxonomy check result was written to GCF_025566885.1_ASM2556688v1_genomic.fna/tc_result.tsv
[2024-01-25 18:54:47,763] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:54:47,763] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:54:47,763] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb131002-8cc7-4ca8-b209-c78790749bc8/dqc_reference/checkm_data
[2024-01-25 18:54:47,764] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:54:47,800] [INFO] Task started: CheckM
[2024-01-25 18:54:47,800] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025566885.1_ASM2556688v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025566885.1_ASM2556688v1_genomic.fna/checkm_input GCF_025566885.1_ASM2556688v1_genomic.fna/checkm_result
[2024-01-25 18:55:13,041] [INFO] Task succeeded: CheckM
[2024-01-25 18:55:13,042] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:55:13,060] [INFO] ===== Completeness check finished =====
[2024-01-25 18:55:13,060] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:55:13,060] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025566885.1_ASM2556688v1_genomic.fna/markers.fasta)
[2024-01-25 18:55:13,060] [INFO] Task started: Blastn
[2024-01-25 18:55:13,060] [INFO] Running command: blastn -query GCF_025566885.1_ASM2556688v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb131002-8cc7-4ca8-b209-c78790749bc8/dqc_reference/reference_markers_gtdb.fasta -out GCF_025566885.1_ASM2556688v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:55:14,118] [INFO] Task succeeded: Blastn
[2024-01-25 18:55:14,121] [INFO] Selected 26 target genomes.
[2024-01-25 18:55:14,121] [INFO] Target genome list was writen to GCF_025566885.1_ASM2556688v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:55:14,142] [INFO] Task started: fastANI
[2024-01-25 18:55:14,142] [INFO] Running command: fastANI --query /var/lib/cwl/stg070c7682-18b6-4c1e-8870-6dc7078525af/GCF_025566885.1_ASM2556688v1_genomic.fna.gz --refList GCF_025566885.1_ASM2556688v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025566885.1_ASM2556688v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:55:29,329] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:29,341] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:55:29,341] [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_902362715.1	s__Eubacterium_I sp900066595	100.0	1141	1144	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_I	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_014287635.1	s__1XD42-69 sp014287635	79.3872	109	1144	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__1XD42-69	95.0	98.20	98.20	0.93	0.93	2	-
GCF_014287615.1	s__Blautia sp001304935	78.6877	69	1144	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.32	98.73	0.92	0.87	9	-
GCF_002161285.1	s__Blautia ornithocaccae	78.6796	98	1144	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	98.34	98.05	0.87	0.83	4	-
GCF_000469345.1	s__Eubacterium_I ramulus	78.6073	151	1144	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_I	95.0	98.54	98.22	0.85	0.78	13	-
GCF_000403845.2	s__14-2 sp000403845	78.5705	98	1144	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_019116105.1	s__Eubacterium_I avistercoris	78.0212	218	1144	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_I	95.0	99.96	99.96	0.87	0.87	2	-
GCA_900557275.1	s__Eubacterium_I sp900557275	77.6166	128	1144	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_I	95.0	100.00	100.00	1.00	1.00	2	-
GCA_910575555.1	s__14-2 sp011960065	77.4347	104	1144	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	-
GCF_003479605.1	s__RUG115 sp900066395	77.3161	83	1144	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG115	95.0	98.27	97.78	0.88	0.83	29	-
GCF_001940225.1	s__14-2 sp001940225	77.294	93	1144	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_910578885.1	s__RUG115 sp910578885	77.2373	74	1144	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018366495.1	s__JAGZHZ01 sp018366495	77.1847	67	1144	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__JAGZHZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546495.1	s__Eubacterium_I sp900546495	77.1203	135	1144	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_I	95.0	99.94	99.87	0.93	0.88	3	-
GCA_012519695.1	s__14-2 sp012519695	76.8977	95	1144	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	97.81	97.81	0.86	0.86	2	-
GCA_910585825.1	s__1XD42-69 sp910585825	76.816	78	1144	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__1XD42-69	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002299665.1	s__CAG-45 sp002299665	76.6349	58	1144	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-45	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588285.1	s__14-2 sp910588285	76.2101	63	1144	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_017625255.1	s__1XD42-69 sp017625255	76.167	69	1144	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__1XD42-69	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:55:29,342] [INFO] GTDB search result was written to GCF_025566885.1_ASM2556688v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:55:29,343] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:55:29,346] [INFO] DFAST_QC result json was written to GCF_025566885.1_ASM2556688v1_genomic.fna/dqc_result.json
[2024-01-25 18:55:29,346] [INFO] DFAST_QC completed!
[2024-01-25 18:55:29,346] [INFO] Total running time: 0h1m9s