[2023-06-30 07:43:35,472] [INFO] DFAST_QC pipeline started.
[2023-06-30 07:43:35,474] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 07:43:35,475] [INFO] DQC Reference Directory: /var/lib/cwl/stg31780d8b-ac4d-4c80-8845-508b2f177555/dqc_reference
[2023-06-30 07:43:36,825] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 07:43:36,825] [INFO] Task started: Prodigal
[2023-06-30 07:43:36,826] [INFO] Running command: gunzip -c /var/lib/cwl/stg24fc6e92-0f5d-4463-b644-9b69df88a0ac/GCA_016708465.1_ASM1670846v1_genomic.fna.gz | prodigal -d GCA_016708465.1_ASM1670846v1_genomic.fna/cds.fna -a GCA_016708465.1_ASM1670846v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 07:43:47,975] [INFO] Task succeeded: Prodigal
[2023-06-30 07:43:47,975] [INFO] Task started: HMMsearch
[2023-06-30 07:43:47,976] [INFO] Running command: hmmsearch --tblout GCA_016708465.1_ASM1670846v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31780d8b-ac4d-4c80-8845-508b2f177555/dqc_reference/reference_markers.hmm GCA_016708465.1_ASM1670846v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 07:43:48,219] [INFO] Task succeeded: HMMsearch
[2023-06-30 07:43:48,225] [INFO] Found 6/6 markers.
[2023-06-30 07:43:48,261] [INFO] Query marker FASTA was written to GCA_016708465.1_ASM1670846v1_genomic.fna/markers.fasta
[2023-06-30 07:43:48,262] [INFO] Task started: Blastn
[2023-06-30 07:43:48,262] [INFO] Running command: blastn -query GCA_016708465.1_ASM1670846v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31780d8b-ac4d-4c80-8845-508b2f177555/dqc_reference/reference_markers.fasta -out GCA_016708465.1_ASM1670846v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 07:43:49,090] [INFO] Task succeeded: Blastn
[2023-06-30 07:43:49,096] [INFO] Selected 33 target genomes.
[2023-06-30 07:43:49,096] [INFO] Target genome list was writen to GCA_016708465.1_ASM1670846v1_genomic.fna/target_genomes.txt
[2023-06-30 07:43:49,106] [INFO] Task started: fastANI
[2023-06-30 07:43:49,106] [INFO] Running command: fastANI --query /var/lib/cwl/stg24fc6e92-0f5d-4463-b644-9b69df88a0ac/GCA_016708465.1_ASM1670846v1_genomic.fna.gz --refList GCA_016708465.1_ASM1670846v1_genomic.fna/target_genomes.txt --output GCA_016708465.1_ASM1670846v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 07:44:09,847] [INFO] Task succeeded: fastANI
[2023-06-30 07:44:09,848] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31780d8b-ac4d-4c80-8845-508b2f177555/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 07:44:09,849] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31780d8b-ac4d-4c80-8845-508b2f177555/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 07:44:09,876] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 07:44:09,877] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 07:44:09,877] [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
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	77.2654	180	1072	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	77.1409	166	1072	95	below_threshold
Pseudoxanthomonas dokdonensis	strain=DSM 21858	GCA_001431405.1	344882	344882	type	True	77.093	125	1072	95	below_threshold
Ahniella affigens	strain=D13	GCA_003015185.1	2021234	2021234	type	True	77.0562	175	1072	95	below_threshold
Luteimonas fraxinea	strain=D4P002	GCA_021233355.1	2901869	2901869	type	True	77.0002	157	1072	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	76.9771	213	1072	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	76.9703	162	1072	95	below_threshold
Rudaea cellulosilytica	strain=DSM 22992	GCA_000378125.1	540746	540746	type	True	76.9623	167	1072	95	below_threshold
Pseudoxanthomonas gei	strain=KCTC 32298	GCA_010119615.1	1383030	1383030	type	True	76.9586	128	1072	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	76.9144	142	1072	95	below_threshold
Luteimonas cucumeris	strain=CGMCC 1.10821	GCA_007830035.1	985012	985012	type	True	76.908	158	1072	95	below_threshold
Rhodanobacter denitrificans	strain=2APBS1	GCA_000230695.3	666685	666685	type	True	76.8769	174	1072	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	76.874	147	1072	95	below_threshold
Arenimonas donghaensis	strain=HO3-R19	GCA_000743535.1	375061	375061	type	True	76.8673	156	1072	95	below_threshold
Dokdonella fugitiva	strain=A3	GCA_004342425.1	328517	328517	type	True	76.7673	203	1072	95	below_threshold
Pseudoxanthomonas winnipegensis	strain=NML 130738	GCA_004283755.1	2480810	2480810	type	True	76.7546	132	1072	95	below_threshold
Rhodanobacter fulvus	strain=Jip2	GCA_000264315.1	219571	219571	type	True	76.7519	117	1072	95	below_threshold
Oleiagrimonas soli	strain=DSM 107085	GCA_014201555.1	1543381	1543381	type	True	76.7252	144	1072	95	below_threshold
Luteibacter anthropi	strain=CCUG 25036	GCA_011759365.1	564369	564369	type	True	76.6991	97	1072	95	below_threshold
Oleiagrimonas soli	strain=3.5X	GCA_000761445.1	1543381	1543381	type	True	76.6871	147	1072	95	below_threshold
Xanthomonas phaseoli	strain=CFBP2534	GCA_017745345.1	1985254	1985254	pathovar	True	76.6293	116	1072	95	below_threshold
Xanthomonas phaseoli	strain=NCPPB 3035	GCA_000774035.2	1985254	1985254	pathovar	True	76.6115	117	1072	95	below_threshold
Tahibacter aquaticus	strain=DSM 21667	GCA_004363655.1	520092	520092	type	True	76.6008	200	1072	95	below_threshold
Xanthomonas phaseoli	strain=LMG784	GCA_001482665.1	1985254	1985254	pathovar	True	76.5595	116	1072	95	below_threshold
Xanthomonas citri	strain=LMG 941	GCA_000263335.1	346	346	pathovar	True	76.5576	120	1072	95	below_threshold
Nevskia ramosa	strain=DSM 11499	GCA_000420645.1	64002	64002	type	True	76.5421	90	1072	95	below_threshold
Pseudoxanthomonas beigongshangi	strain=REN9	GCA_016820515.1	2782537	2782537	type	True	76.5357	166	1072	95	below_threshold
Stenotrophomonas bentonitica	strain=DSM 103927	GCA_013185915.1	1450134	1450134	type	True	76.5171	131	1072	95	below_threshold
Pseudolysobacter antarcticus	strain=AQ6-296	GCA_004168365.1	2511995	2511995	type	True	76.4936	146	1072	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	76.4697	139	1072	95	below_threshold
Solimonas variicoloris	strain=DSM 15731	GCA_000382285.1	254408	254408	type	True	76.0899	100	1072	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 07:44:09,879] [INFO] DFAST Taxonomy check result was written to GCA_016708465.1_ASM1670846v1_genomic.fna/tc_result.tsv
[2023-06-30 07:44:09,879] [INFO] ===== Taxonomy check completed =====
[2023-06-30 07:44:09,880] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 07:44:09,880] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31780d8b-ac4d-4c80-8845-508b2f177555/dqc_reference/checkm_data
[2023-06-30 07:44:09,881] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 07:44:09,914] [INFO] Task started: CheckM
[2023-06-30 07:44:09,914] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708465.1_ASM1670846v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708465.1_ASM1670846v1_genomic.fna/checkm_input GCA_016708465.1_ASM1670846v1_genomic.fna/checkm_result
[2023-06-30 07:44:46,965] [INFO] Task succeeded: CheckM
[2023-06-30 07:44:46,967] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.07%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 07:44:46,988] [INFO] ===== Completeness check finished =====
[2023-06-30 07:44:46,989] [INFO] ===== Start GTDB Search =====
[2023-06-30 07:44:46,989] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708465.1_ASM1670846v1_genomic.fna/markers.fasta)
[2023-06-30 07:44:46,989] [INFO] Task started: Blastn
[2023-06-30 07:44:46,990] [INFO] Running command: blastn -query GCA_016708465.1_ASM1670846v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31780d8b-ac4d-4c80-8845-508b2f177555/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708465.1_ASM1670846v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 07:44:48,471] [INFO] Task succeeded: Blastn
[2023-06-30 07:44:48,475] [INFO] Selected 17 target genomes.
[2023-06-30 07:44:48,475] [INFO] Target genome list was writen to GCA_016708465.1_ASM1670846v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 07:44:48,486] [INFO] Task started: fastANI
[2023-06-30 07:44:48,486] [INFO] Running command: fastANI --query /var/lib/cwl/stg24fc6e92-0f5d-4463-b644-9b69df88a0ac/GCA_016708465.1_ASM1670846v1_genomic.fna.gz --refList GCA_016708465.1_ASM1670846v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708465.1_ASM1670846v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 07:45:02,971] [INFO] Task succeeded: fastANI
[2023-06-30 07:45:02,990] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 07:45:02,990] [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_016708465.1	s__JADKHK01 sp016708465	100.0	1071	1072	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__JADKHK01	95.0	99.43	99.22	0.94	0.94	3	conclusive
GCA_016721845.1	s__JADKHK01 sp016721845	82.5844	791	1072	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__JADKHK01	95.0	99.21	98.90	0.96	0.94	3	-
GCA_016703225.1	s__JADKHK01 sp016703225	80.19	642	1072	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__JADKHK01	95.0	99.05	99.05	0.90	0.90	2	-
GCA_016182785.1	s__JADKHK01 sp016182785	80.0983	612	1072	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__JADKHK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712105.1	s__Ahniella sp016712105	77.6827	175	1072	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__Ahniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010119615.1	s__Pseudoxanthomonas_A gei	76.9586	128	1072	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014338185.1	s__Dokdonella_A sp014338185	76.8961	150	1072	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	96.24	96.24	0.88	0.88	2	-
GCF_014138265.1	s__Dokdonella_A fugitiva_A	76.8279	199	1072	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008329435.1	s__Rhodanobacter sp008329435	76.7967	147	1072	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241385.1	s__Dokdonella denitrificans_A	76.7899	195	1072	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483055.1	s__Dokdonella sp002483055	76.7823	161	1072	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342425.1	s__Dokdonella_A fugitiva	76.7566	204	1072	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	99.45	99.45	0.96	0.96	2	-
GCF_014192715.1	s__Luteibacter sp014192715	76.6987	90	1072	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002429615.1	s__Stenotrophomonas_A sp002429615	76.6968	138	1072	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000336385.2	s__Lysobacter antibioticus_A	76.6553	177	1072	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002785585.1	s__0-14-3-00-62-12 sp002785585	76.5315	132	1072	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__0-14-3-00-62-12	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013185915.1	s__Stenotrophomonas bentonitica	76.5171	131	1072	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-30 07:45:02,992] [INFO] GTDB search result was written to GCA_016708465.1_ASM1670846v1_genomic.fna/result_gtdb.tsv
[2023-06-30 07:45:02,993] [INFO] ===== GTDB Search completed =====
[2023-06-30 07:45:02,998] [INFO] DFAST_QC result json was written to GCA_016708465.1_ASM1670846v1_genomic.fna/dqc_result.json
[2023-06-30 07:45:02,998] [INFO] DFAST_QC completed!
[2023-06-30 07:45:02,998] [INFO] Total running time: 0h1m28s