[2023-07-01 01:28:47,138] [INFO] DFAST_QC pipeline started.
[2023-07-01 01:28:47,220] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 01:28:47,220] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b6c35fe-cbbb-4acc-b3cc-d24647222e70/dqc_reference
[2023-07-01 01:28:49,615] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 01:28:49,616] [INFO] Task started: Prodigal
[2023-07-01 01:28:49,617] [INFO] Running command: gunzip -c /var/lib/cwl/stg99f7f68d-ab6f-4f83-bb64-084370ea24ca/GCA_019236735.1_ASM1923673v1_genomic.fna.gz | prodigal -d GCA_019236735.1_ASM1923673v1_genomic.fna/cds.fna -a GCA_019236735.1_ASM1923673v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 01:28:59,242] [INFO] Task succeeded: Prodigal
[2023-07-01 01:28:59,243] [INFO] Task started: HMMsearch
[2023-07-01 01:28:59,243] [INFO] Running command: hmmsearch --tblout GCA_019236735.1_ASM1923673v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b6c35fe-cbbb-4acc-b3cc-d24647222e70/dqc_reference/reference_markers.hmm GCA_019236735.1_ASM1923673v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 01:28:59,515] [INFO] Task succeeded: HMMsearch
[2023-07-01 01:28:59,517] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg99f7f68d-ab6f-4f83-bb64-084370ea24ca/GCA_019236735.1_ASM1923673v1_genomic.fna.gz]
[2023-07-01 01:28:59,548] [INFO] Query marker FASTA was written to GCA_019236735.1_ASM1923673v1_genomic.fna/markers.fasta
[2023-07-01 01:28:59,549] [INFO] Task started: Blastn
[2023-07-01 01:28:59,549] [INFO] Running command: blastn -query GCA_019236735.1_ASM1923673v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b6c35fe-cbbb-4acc-b3cc-d24647222e70/dqc_reference/reference_markers.fasta -out GCA_019236735.1_ASM1923673v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 01:29:00,363] [INFO] Task succeeded: Blastn
[2023-07-01 01:29:00,368] [INFO] Selected 28 target genomes.
[2023-07-01 01:29:00,369] [INFO] Target genome list was writen to GCA_019236735.1_ASM1923673v1_genomic.fna/target_genomes.txt
[2023-07-01 01:29:00,373] [INFO] Task started: fastANI
[2023-07-01 01:29:00,373] [INFO] Running command: fastANI --query /var/lib/cwl/stg99f7f68d-ab6f-4f83-bb64-084370ea24ca/GCA_019236735.1_ASM1923673v1_genomic.fna.gz --refList GCA_019236735.1_ASM1923673v1_genomic.fna/target_genomes.txt --output GCA_019236735.1_ASM1923673v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 01:29:22,582] [INFO] Task succeeded: fastANI
[2023-07-01 01:29:22,582] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b6c35fe-cbbb-4acc-b3cc-d24647222e70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 01:29:22,583] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b6c35fe-cbbb-4acc-b3cc-d24647222e70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 01:29:22,604] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 01:29:22,604] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 01:29:22,604] [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
Aromatoleum petrolei	strain=ToN1	GCA_017894385.1	76116	76116	type	True	76.7534	104	1054	95	below_threshold
Aromatoleum petrolei	strain=ToN1	GCA_012910985.1	76116	76116	type	True	76.683	105	1054	95	below_threshold
Aromatoleum toluvorans	strain=Td21	GCA_012910905.1	92002	92002	type	True	76.521	122	1054	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	76.4683	162	1054	95	below_threshold
Massilia agilis	strain=JCM 31605	GCA_024756255.1	1811226	1811226	type	True	76.4656	139	1054	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	76.4651	126	1054	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	76.3938	164	1054	95	below_threshold
Massilia glaciei	strain=B448-2	GCA_003011895.2	1524097	1524097	type	True	76.337	151	1054	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	76.3162	157	1054	95	below_threshold
Derxia gummosa	strain=DSM 723	GCA_000482785.1	203699	203699	type	True	76.3041	157	1054	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	76.2705	140	1054	95	below_threshold
Burkholderia multivorans	strain=ATCC BAA-247	GCA_000959525.1	87883	87883	type	True	76.2565	176	1054	95	below_threshold
Aromatoleum toluclasticum	strain=MF63	GCA_000378245.1	92003	92003	type	True	76.238	129	1054	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	76.2164	156	1054	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	76.142	130	1054	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_014197755.1	1066	1066	type	True	76.108	91	1054	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_009469755.1	1066	1066	type	True	76.0927	92	1054	95	below_threshold
Massilia forsythiae	strain=GN2-R2	GCA_012849555.1	2728020	2728020	type	True	76.0371	175	1054	95	below_threshold
Burkholderia thailandensis	strain=E264; ATCC 700388	GCA_000012365.1	57975	57975	type	True	76.0326	181	1054	95	below_threshold
Burkholderia plantarii	strain=ATCC 43733	GCA_001411805.1	41899	41899	type	True	75.9858	220	1054	95	below_threshold
Burkholderia plantarii	strain=LMG 9035	GCA_902832905.1	41899	41899	type	True	75.9822	214	1054	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	75.9389	168	1054	95	below_threshold
Duganella aquatilis	strain=FT26W	GCA_009674565.1	2666082	2666082	type	True	75.9351	136	1054	95	below_threshold
Burkholderia mallei	strain=ATCC 23344	GCA_000011705.1	13373	13373	type	True	75.9229	172	1054	95	below_threshold
Duganella alba	strain=FT9W	GCA_009674495.1	2666081	2666081	type	True	75.9227	150	1054	95	below_threshold
Burkholderia mallei	strain=NCTC12938	GCA_900446245.1	13373	13373	type	True	75.916	171	1054	95	below_threshold
Caballeronia concitans		GCA_001544615.2	1777133	1777133	type	True	75.8336	100	1054	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	75.7612	133	1054	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 01:29:22,607] [INFO] DFAST Taxonomy check result was written to GCA_019236735.1_ASM1923673v1_genomic.fna/tc_result.tsv
[2023-07-01 01:29:22,607] [INFO] ===== Taxonomy check completed =====
[2023-07-01 01:29:22,607] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 01:29:22,608] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b6c35fe-cbbb-4acc-b3cc-d24647222e70/dqc_reference/checkm_data
[2023-07-01 01:29:22,609] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 01:29:22,645] [INFO] Task started: CheckM
[2023-07-01 01:29:22,646] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019236735.1_ASM1923673v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019236735.1_ASM1923673v1_genomic.fna/checkm_input GCA_019236735.1_ASM1923673v1_genomic.fna/checkm_result
[2023-07-01 01:29:54,156] [INFO] Task succeeded: CheckM
[2023-07-01 01:29:54,157] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 01:29:54,179] [INFO] ===== Completeness check finished =====
[2023-07-01 01:29:54,179] [INFO] ===== Start GTDB Search =====
[2023-07-01 01:29:54,180] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019236735.1_ASM1923673v1_genomic.fna/markers.fasta)
[2023-07-01 01:29:54,180] [INFO] Task started: Blastn
[2023-07-01 01:29:54,180] [INFO] Running command: blastn -query GCA_019236735.1_ASM1923673v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b6c35fe-cbbb-4acc-b3cc-d24647222e70/dqc_reference/reference_markers_gtdb.fasta -out GCA_019236735.1_ASM1923673v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 01:29:55,634] [INFO] Task succeeded: Blastn
[2023-07-01 01:29:55,639] [INFO] Selected 13 target genomes.
[2023-07-01 01:29:55,639] [INFO] Target genome list was writen to GCA_019236735.1_ASM1923673v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 01:29:55,643] [INFO] Task started: fastANI
[2023-07-01 01:29:55,643] [INFO] Running command: fastANI --query /var/lib/cwl/stg99f7f68d-ab6f-4f83-bb64-084370ea24ca/GCA_019236735.1_ASM1923673v1_genomic.fna.gz --refList GCA_019236735.1_ASM1923673v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019236735.1_ASM1923673v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 01:30:04,057] [INFO] Task succeeded: fastANI
[2023-07-01 01:30:04,074] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 01:30:04,074] [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_019236735.1	s__VBCK01 sp019236735	100.0	1048	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__VBCK01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_005882215.1	s__VBCK01 sp005882215	79.3443	527	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__VBCK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011056935.1	s__DSNY01 sp011056935	77.7114	263	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__DSNY01	95.0	98.37	98.37	0.91	0.91	2	-
GCA_016716275.1	s__JADJWR01 sp016716275	77.6517	264	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JADJWR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016861185.1	s__DSNY01 sp016861185	77.5411	265	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__DSNY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000828975.1	s__GJ-E10 sp000828975	77.3635	172	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__GJ-E10	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008039575.1	s__SCN-69-89 sp008039575	77.3294	157	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724855.1	s__SCN-69-89 sp001724855	77.1441	176	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403875.1	s__Burkholderia guangdongensis	76.3552	159	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903831455.1	s__CAIKXV01 sp903831455	76.293	92	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__CAIKXV01;g__CAIKXV01	95.0	99.62	99.56	0.92	0.90	5	-
GCA_017880775.1	s__JADGRQ01 sp017880775	76.022	113	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__JADGRQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003153475.1	s__PALSA-1003 sp003153475	75.8944	74	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__PALSA-1003	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013389055.1	s__Sulfuritortus sp013389055	75.7996	53	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Sulfuritortus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 01:30:04,076] [INFO] GTDB search result was written to GCA_019236735.1_ASM1923673v1_genomic.fna/result_gtdb.tsv
[2023-07-01 01:30:04,076] [INFO] ===== GTDB Search completed =====
[2023-07-01 01:30:04,104] [INFO] DFAST_QC result json was written to GCA_019236735.1_ASM1923673v1_genomic.fna/dqc_result.json
[2023-07-01 01:30:04,104] [INFO] DFAST_QC completed!
[2023-07-01 01:30:04,104] [INFO] Total running time: 0h1m17s