[2023-06-28 16:15:28,877] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:15:28,879] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:15:28,879] [INFO] DQC Reference Directory: /var/lib/cwl/stg37737045-7616-4cb5-a127-4744bdbc574d/dqc_reference
[2023-06-28 16:15:30,033] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:15:30,033] [INFO] Task started: Prodigal
[2023-06-28 16:15:30,034] [INFO] Running command: gunzip -c /var/lib/cwl/stg28018dc3-b9f7-490c-b2c4-2ab91a3cd555/GCA_005877705.1_ASM587770v1_genomic.fna.gz | prodigal -d GCA_005877705.1_ASM587770v1_genomic.fna/cds.fna -a GCA_005877705.1_ASM587770v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:15:36,800] [INFO] Task succeeded: Prodigal
[2023-06-28 16:15:36,800] [INFO] Task started: HMMsearch
[2023-06-28 16:15:36,800] [INFO] Running command: hmmsearch --tblout GCA_005877705.1_ASM587770v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37737045-7616-4cb5-a127-4744bdbc574d/dqc_reference/reference_markers.hmm GCA_005877705.1_ASM587770v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:15:36,974] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:15:36,975] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg28018dc3-b9f7-490c-b2c4-2ab91a3cd555/GCA_005877705.1_ASM587770v1_genomic.fna.gz]
[2023-06-28 16:15:37,003] [INFO] Query marker FASTA was written to GCA_005877705.1_ASM587770v1_genomic.fna/markers.fasta
[2023-06-28 16:15:37,003] [INFO] Task started: Blastn
[2023-06-28 16:15:37,003] [INFO] Running command: blastn -query GCA_005877705.1_ASM587770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37737045-7616-4cb5-a127-4744bdbc574d/dqc_reference/reference_markers.fasta -out GCA_005877705.1_ASM587770v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:15:37,591] [INFO] Task succeeded: Blastn
[2023-06-28 16:15:37,594] [INFO] Selected 29 target genomes.
[2023-06-28 16:15:37,595] [INFO] Target genome list was writen to GCA_005877705.1_ASM587770v1_genomic.fna/target_genomes.txt
[2023-06-28 16:15:37,595] [INFO] Task started: fastANI
[2023-06-28 16:15:37,595] [INFO] Running command: fastANI --query /var/lib/cwl/stg28018dc3-b9f7-490c-b2c4-2ab91a3cd555/GCA_005877705.1_ASM587770v1_genomic.fna.gz --refList GCA_005877705.1_ASM587770v1_genomic.fna/target_genomes.txt --output GCA_005877705.1_ASM587770v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:15:57,265] [INFO] Task succeeded: fastANI
[2023-06-28 16:15:57,266] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37737045-7616-4cb5-a127-4744bdbc574d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:15:57,266] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37737045-7616-4cb5-a127-4744bdbc574d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:15:57,279] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:15:57,279] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 16:15:57,279] [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
Steroidobacter agariperforans	strain=KA5-B	GCA_004138335.1	268404	268404	type	True	76.8763	108	767	95	below_threshold
Povalibacter uvarum	strain=DSM 26723	GCA_014202975.1	732238	732238	type	True	76.7973	97	767	95	below_threshold
Steroidobacter gossypii	strain=S1-65	GCA_016801985.1	2805490	2805490	type	True	76.6335	110	767	95	below_threshold
Steroidobacter agaridevorans	strain=SA29-B	GCA_009932555.1	2695856	2695856	type	True	76.5207	119	767	95	below_threshold
Steroidobacter soli	strain=JW-3	GCA_004138485.1	2497877	2497877	type	True	76.4429	117	767	95	below_threshold
Steroidobacter cummioxidans	strain=35Y	GCA_003104955.1	1803913	1803913	type	True	76.434	98	767	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	76.3985	60	767	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	76.3125	63	767	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	76.2045	75	767	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	76.2012	62	767	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	76.17	87	767	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	75.9519	117	767	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	75.8309	67	767	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	75.7439	61	767	95	below_threshold
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	75.7123	58	767	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	75.6165	71	767	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	75.6153	73	767	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	75.5911	72	767	95	below_threshold
Solimonas soli	strain=DSM 21787	GCA_000474945.1	413479	413479	type	True	75.5346	89	767	95	below_threshold
Tahibacter aquaticus	strain=DSM 21667	GCA_004363655.1	520092	520092	type	True	75.4125	77	767	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 16:15:57,280] [INFO] DFAST Taxonomy check result was written to GCA_005877705.1_ASM587770v1_genomic.fna/tc_result.tsv
[2023-06-28 16:15:57,281] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:15:57,281] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:15:57,281] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37737045-7616-4cb5-a127-4744bdbc574d/dqc_reference/checkm_data
[2023-06-28 16:15:57,282] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:15:57,314] [INFO] Task started: CheckM
[2023-06-28 16:15:57,314] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_005877705.1_ASM587770v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_005877705.1_ASM587770v1_genomic.fna/checkm_input GCA_005877705.1_ASM587770v1_genomic.fna/checkm_result
[2023-06-28 16:16:20,852] [INFO] Task succeeded: CheckM
[2023-06-28 16:16:20,853] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 16:16:20,868] [INFO] ===== Completeness check finished =====
[2023-06-28 16:16:20,868] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:16:20,869] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_005877705.1_ASM587770v1_genomic.fna/markers.fasta)
[2023-06-28 16:16:20,869] [INFO] Task started: Blastn
[2023-06-28 16:16:20,869] [INFO] Running command: blastn -query GCA_005877705.1_ASM587770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37737045-7616-4cb5-a127-4744bdbc574d/dqc_reference/reference_markers_gtdb.fasta -out GCA_005877705.1_ASM587770v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:16:21,779] [INFO] Task succeeded: Blastn
[2023-06-28 16:16:21,783] [INFO] Selected 11 target genomes.
[2023-06-28 16:16:21,783] [INFO] Target genome list was writen to GCA_005877705.1_ASM587770v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:16:21,786] [INFO] Task started: fastANI
[2023-06-28 16:16:21,786] [INFO] Running command: fastANI --query /var/lib/cwl/stg28018dc3-b9f7-490c-b2c4-2ab91a3cd555/GCA_005877705.1_ASM587770v1_genomic.fna.gz --refList GCA_005877705.1_ASM587770v1_genomic.fna/target_genomes_gtdb.txt --output GCA_005877705.1_ASM587770v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:16:28,689] [INFO] Task succeeded: fastANI
[2023-06-28 16:16:28,696] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 16:16:28,696] [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_005877705.1	s__13-2-20CM-66-19 sp005877705	99.9999	761	767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	97.92	97.92	0.70	0.70	2	conclusive
GCA_005878835.1	s__13-2-20CM-66-19 sp005878835	79.9348	392	767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	98.03	96.96	0.89	0.85	6	-
GCA_005878095.1	s__13-2-20CM-66-19 sp005878095	79.8885	353	767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	99.52	99.52	0.84	0.84	2	-
GCA_005877965.1	s__13-2-20CM-66-19 sp005877965	79.8629	302	767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001914695.1	s__13-2-20CM-66-19 sp001914695	79.2861	317	767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	98.00	96.94	0.81	0.73	19	-
GCA_003242685.1	s__ZC4RG24 sp003242685	78.8807	225	767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__ZC4RG24	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241505.1	s__13-2-20CM-66-19 sp018241505	77.0911	171	767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010031985.1	s__UBA964 sp010031985	76.6854	61	767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	98.93	98.76	0.80	0.76	12	-
GCA_016790695.1	s__JAEUOS01 sp016790695	75.3012	87	767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__JAEUOS01;g__JAEUOS01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 16:16:28,699] [INFO] GTDB search result was written to GCA_005877705.1_ASM587770v1_genomic.fna/result_gtdb.tsv
[2023-06-28 16:16:28,700] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:16:28,706] [INFO] DFAST_QC result json was written to GCA_005877705.1_ASM587770v1_genomic.fna/dqc_result.json
[2023-06-28 16:16:28,706] [INFO] DFAST_QC completed!
[2023-06-28 16:16:28,706] [INFO] Total running time: 0h0m60s