[2023-06-27 14:08:10,598] [INFO] DFAST_QC pipeline started.
[2023-06-27 14:08:10,600] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 14:08:10,600] [INFO] DQC Reference Directory: /var/lib/cwl/stg99f15491-3a82-4553-b695-e50074a04c0a/dqc_reference
[2023-06-27 14:08:12,033] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 14:08:12,034] [INFO] Task started: Prodigal
[2023-06-27 14:08:12,034] [INFO] Running command: gunzip -c /var/lib/cwl/stgee5441c0-0bcb-43ed-8fb2-544d5ff23e15/GCA_002404035.1_ASM240403v1_genomic.fna.gz | prodigal -d GCA_002404035.1_ASM240403v1_genomic.fna/cds.fna -a GCA_002404035.1_ASM240403v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 14:08:27,243] [INFO] Task succeeded: Prodigal
[2023-06-27 14:08:27,244] [INFO] Task started: HMMsearch
[2023-06-27 14:08:27,244] [INFO] Running command: hmmsearch --tblout GCA_002404035.1_ASM240403v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99f15491-3a82-4553-b695-e50074a04c0a/dqc_reference/reference_markers.hmm GCA_002404035.1_ASM240403v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 14:08:27,428] [INFO] Task succeeded: HMMsearch
[2023-06-27 14:08:27,430] [INFO] Found 6/6 markers.
[2023-06-27 14:08:27,457] [INFO] Query marker FASTA was written to GCA_002404035.1_ASM240403v1_genomic.fna/markers.fasta
[2023-06-27 14:08:27,457] [INFO] Task started: Blastn
[2023-06-27 14:08:27,457] [INFO] Running command: blastn -query GCA_002404035.1_ASM240403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99f15491-3a82-4553-b695-e50074a04c0a/dqc_reference/reference_markers.fasta -out GCA_002404035.1_ASM240403v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 14:08:28,059] [INFO] Task succeeded: Blastn
[2023-06-27 14:08:28,062] [INFO] Selected 27 target genomes.
[2023-06-27 14:08:28,062] [INFO] Target genome list was writen to GCA_002404035.1_ASM240403v1_genomic.fna/target_genomes.txt
[2023-06-27 14:08:28,092] [INFO] Task started: fastANI
[2023-06-27 14:08:28,092] [INFO] Running command: fastANI --query /var/lib/cwl/stgee5441c0-0bcb-43ed-8fb2-544d5ff23e15/GCA_002404035.1_ASM240403v1_genomic.fna.gz --refList GCA_002404035.1_ASM240403v1_genomic.fna/target_genomes.txt --output GCA_002404035.1_ASM240403v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 14:08:45,770] [INFO] Task succeeded: fastANI
[2023-06-27 14:08:45,770] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99f15491-3a82-4553-b695-e50074a04c0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 14:08:45,771] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99f15491-3a82-4553-b695-e50074a04c0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 14:08:45,781] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 14:08:45,781] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 14:08:45,781] [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
Gaiella occulta	strain=F2-233	GCA_003351045.1	1002870	1002870	type	True	75.0591	107	1067	95	below_threshold
Microbacterium ulmi	strain=CECT 5976	GCA_011759705.1	179095	179095	type	True	74.9377	89	1067	95	below_threshold
Saccharothrix ecbatanensis	strain=DSM 45486	GCA_014205015.1	1105145	1105145	type	True	74.9186	90	1067	95	below_threshold
Microbacterium ulmi	strain=JCM 14282	GCA_013004565.1	179095	179095	type	True	74.9115	88	1067	95	below_threshold
Rhodococcus rhodnii	strain=NBRC 100604	GCA_001894925.1	38312	38312	type	True	74.9055	83	1067	95	below_threshold
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	74.8634	201	1067	95	below_threshold
Aeromicrobium stalagmiti	strain=YC3-14	GCA_013283745.1	2738988	2738988	type	True	74.856	65	1067	95	below_threshold
Elioraea tepida	strain=MS-P2	GCA_019203965.1	2843330	2843330	type	True	74.8305	61	1067	95	below_threshold
Aromatoleum petrolei	strain=ToN1	GCA_012910985.1	76116	76116	type	True	74.8119	56	1067	95	below_threshold
Aromatoleum petrolei	strain=ToN1	GCA_017894385.1	76116	76116	type	True	74.8119	56	1067	95	below_threshold
Kocuria turfanensis	strain=HO-9042	GCA_001580365.1	388357	388357	type	True	74.789	56	1067	95	below_threshold
Nocardiopsis chromatogenes	strain=YIM 90109	GCA_000341185.1	280239	280239	type	True	74.7717	75	1067	95	below_threshold
Kocuria sediminis	strain=JCM 17929	GCA_009735315.1	1038857	1038857	type	True	74.6994	66	1067	95	below_threshold
Actinoplanes consettensis	strain=NBRC 14913	GCA_018332715.1	113560	113560	type	True	74.6866	109	1067	95	below_threshold
Aromatoleum toluvorans	strain=Td21	GCA_012910905.1	92002	92002	type	True	74.6742	71	1067	95	below_threshold
Actinoplanes humidus	strain=NBRC 14915	GCA_016862215.1	113566	113566	type	True	74.6416	103	1067	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 14:08:45,783] [INFO] DFAST Taxonomy check result was written to GCA_002404035.1_ASM240403v1_genomic.fna/tc_result.tsv
[2023-06-27 14:08:45,784] [INFO] ===== Taxonomy check completed =====
[2023-06-27 14:08:45,784] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 14:08:45,784] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99f15491-3a82-4553-b695-e50074a04c0a/dqc_reference/checkm_data
[2023-06-27 14:08:45,785] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 14:08:45,819] [INFO] Task started: CheckM
[2023-06-27 14:08:45,819] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002404035.1_ASM240403v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002404035.1_ASM240403v1_genomic.fna/checkm_input GCA_002404035.1_ASM240403v1_genomic.fna/checkm_result
[2023-06-27 14:09:19,325] [INFO] Task succeeded: CheckM
[2023-06-27 14:09:19,326] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 14:09:19,343] [INFO] ===== Completeness check finished =====
[2023-06-27 14:09:19,344] [INFO] ===== Start GTDB Search =====
[2023-06-27 14:09:19,345] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002404035.1_ASM240403v1_genomic.fna/markers.fasta)
[2023-06-27 14:09:19,345] [INFO] Task started: Blastn
[2023-06-27 14:09:19,345] [INFO] Running command: blastn -query GCA_002404035.1_ASM240403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99f15491-3a82-4553-b695-e50074a04c0a/dqc_reference/reference_markers_gtdb.fasta -out GCA_002404035.1_ASM240403v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 14:09:20,260] [INFO] Task succeeded: Blastn
[2023-06-27 14:09:20,264] [INFO] Selected 20 target genomes.
[2023-06-27 14:09:20,264] [INFO] Target genome list was writen to GCA_002404035.1_ASM240403v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 14:09:20,293] [INFO] Task started: fastANI
[2023-06-27 14:09:20,294] [INFO] Running command: fastANI --query /var/lib/cwl/stgee5441c0-0bcb-43ed-8fb2-544d5ff23e15/GCA_002404035.1_ASM240403v1_genomic.fna.gz --refList GCA_002404035.1_ASM240403v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002404035.1_ASM240403v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 14:09:30,551] [INFO] Task succeeded: fastANI
[2023-06-27 14:09:30,562] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 14:09:30,563] [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_002404155.1	s__UBA4735 sp002404155	99.9587	1015	1067	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__P2-11E;f__P2-11E;g__UBA4735	95.0	99.90	99.84	0.93	0.89	5	conclusive
GCA_016194865.1	s__JACQAT01 sp016194865	78.5783	225	1067	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__P2-11E;f__P2-11E;g__JACQAT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875795.1	s__JACPOT01 sp016875795	78.2558	245	1067	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__P2-11E;f__P2-11E;g__JACPOT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005883625.1	s__3-1-20CM-2-70-9 sp001919195	78.057	376	1067	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__P2-11E;f__P2-11E;g__3-1-20CM-2-70-9	95.0	98.45	97.34	0.95	0.95	6	-
GCA_005887995.1	s__CF-39 sp005887995	77.8439	298	1067	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__P2-11E;f__P2-11E;g__CF-39	95.0	99.25	99.03	0.88	0.87	6	-
GCA_005882255.1	s__CF-39 sp005882255	77.8419	286	1067	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__P2-11E;f__P2-11E;g__CF-39	95.0	98.81	98.81	0.77	0.77	2	-
GCA_016183435.1	s__JACPOT01 sp016183435	77.8102	258	1067	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__P2-11E;f__P2-11E;g__JACPOT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005889275.1	s__3-1-20CM-2-70-9 sp005889275	77.7814	284	1067	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__P2-11E;f__P2-11E;g__3-1-20CM-2-70-9	95.0	98.44	98.44	0.90	0.90	2	-
GCA_001795345.1	s__GWC2-70-10 sp001795345	77.7187	249	1067	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__P2-11E;f__P2-11E;g__GWC2-70-10	95.0	98.93	98.93	0.81	0.81	2	-
GCA_005889445.1	s__3-1-20CM-2-70-9 sp005889445	77.6841	212	1067	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__P2-11E;f__P2-11E;g__3-1-20CM-2-70-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013695575.1	s__JACDAF01 sp013695575	77.6251	217	1067	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__P2-11E;f__P2-11E;g__JACDAF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005889075.1	s__3-1-20CM-2-70-9 sp005889075	77.4989	270	1067	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__P2-11E;f__P2-11E;g__3-1-20CM-2-70-9	95.0	99.43	99.43	0.93	0.93	2	-
GCA_016191385.1	s__JACPOT01 sp016191385	77.4352	170	1067	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__P2-11E;f__P2-11E;g__JACPOT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875665.1	s__SHYN01 sp016875665	77.4174	136	1067	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__P2-11E;f__P2-11E;g__SHYN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016191435.1	s__JACPOQ01 sp016191435	75.1483	54	1067	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__JACPOQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016866775.1	s__VGLJ01 sp016866775	74.9319	128	1067	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__VGLJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001014645.1	s__Luteimonas sp001014645	74.923	79	1067	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018122625.2	s__Coralloluteibacterium stylophorae	74.7894	76	1067	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Coralloluteibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 14:09:30,564] [INFO] GTDB search result was written to GCA_002404035.1_ASM240403v1_genomic.fna/result_gtdb.tsv
[2023-06-27 14:09:30,565] [INFO] ===== GTDB Search completed =====
[2023-06-27 14:09:30,568] [INFO] DFAST_QC result json was written to GCA_002404035.1_ASM240403v1_genomic.fna/dqc_result.json
[2023-06-27 14:09:30,568] [INFO] DFAST_QC completed!
[2023-06-27 14:09:30,568] [INFO] Total running time: 0h1m20s