[2024-01-24 13:28:11,867] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:11,869] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:11,869] [INFO] DQC Reference Directory: /var/lib/cwl/stg4cbbe8aa-dd3c-4924-a993-bae9773a4862/dqc_reference
[2024-01-24 13:28:13,140] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:13,140] [INFO] Task started: Prodigal
[2024-01-24 13:28:13,141] [INFO] Running command: gunzip -c /var/lib/cwl/stg987b241f-21d5-4b59-b52a-2fea2db8829f/GCF_014651835.1_ASM1465183v1_genomic.fna.gz | prodigal -d GCF_014651835.1_ASM1465183v1_genomic.fna/cds.fna -a GCF_014651835.1_ASM1465183v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:32,261] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:32,261] [INFO] Task started: HMMsearch
[2024-01-24 13:28:32,261] [INFO] Running command: hmmsearch --tblout GCF_014651835.1_ASM1465183v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4cbbe8aa-dd3c-4924-a993-bae9773a4862/dqc_reference/reference_markers.hmm GCF_014651835.1_ASM1465183v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:32,582] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:32,583] [INFO] Found 6/6 markers.
[2024-01-24 13:28:32,633] [INFO] Query marker FASTA was written to GCF_014651835.1_ASM1465183v1_genomic.fna/markers.fasta
[2024-01-24 13:28:32,633] [INFO] Task started: Blastn
[2024-01-24 13:28:32,633] [INFO] Running command: blastn -query GCF_014651835.1_ASM1465183v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4cbbe8aa-dd3c-4924-a993-bae9773a4862/dqc_reference/reference_markers.fasta -out GCF_014651835.1_ASM1465183v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:33,618] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:33,622] [INFO] Selected 26 target genomes.
[2024-01-24 13:28:33,623] [INFO] Target genome list was writen to GCF_014651835.1_ASM1465183v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:33,720] [INFO] Task started: fastANI
[2024-01-24 13:28:33,720] [INFO] Running command: fastANI --query /var/lib/cwl/stg987b241f-21d5-4b59-b52a-2fea2db8829f/GCF_014651835.1_ASM1465183v1_genomic.fna.gz --refList GCF_014651835.1_ASM1465183v1_genomic.fna/target_genomes.txt --output GCF_014651835.1_ASM1465183v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:59,146] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:59,146] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4cbbe8aa-dd3c-4924-a993-bae9773a4862/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:59,147] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4cbbe8aa-dd3c-4924-a993-bae9773a4862/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:59,171] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:59,171] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:59,171] [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
Pigmentiphaga litoralis	strain=KCTC 22165	GCA_014651835.1	516702	516702	type	True	100.0	1860	1861	95	conclusive
Pigmentiphaga kullae	strain=K24	GCA_004216695.1	151784	151784	type	True	79.4732	715	1861	95	below_threshold
Achromobacter insuavis	strain=LMG 26845	GCA_902859645.1	1287735	1287735	type	True	78.3689	513	1861	95	below_threshold
Achromobacter dolens	strain=LMG 26840	GCA_902859745.1	1287738	1287738	type	True	78.3496	505	1861	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	78.3118	509	1861	95	below_threshold
Achromobacter xylosoxidans	strain=NCTC10807	GCA_001457475.1	85698	85698	type	True	78.3012	522	1861	95	below_threshold
Achromobacter pulmonis	strain=LMG 26696	GCA_902859765.1	1389932	1389932	type	True	78.2915	466	1861	95	below_threshold
Achromobacter ruhlandii	strain=LMG 1866	GCA_902859695.1	72557	72557	type	True	78.2789	513	1861	95	below_threshold
Achromobacter xylosoxidans	strain=NBRC 15126	GCA_001598595.1	85698	85698	type	True	78.2738	516	1861	95	below_threshold
Achromobacter veterisilvae	strain=LMG 30378	GCA_900496975.1	2069367	2069367	type	True	78.2717	471	1861	95	below_threshold
Achromobacter anxifer	strain=LMG 26857	GCA_903652925.1	1287737	1287737	type	True	78.2594	480	1861	95	below_threshold
Achromobacter deleyi	strain=LMG 3458	GCA_902859705.1	1353891	1353891	type	True	78.2093	507	1861	95	below_threshold
Achromobacter mucicolens	strain=LMG 26685	GCA_902859725.1	1389922	1389922	type	True	78.0961	443	1861	95	below_threshold
Achromobacter aegrifaciens	strain=LMG 26852	GCA_902859735.1	1287736	1287736	type	True	78.0834	491	1861	95	below_threshold
Achromobacter denitrificans	strain=FDAARGOS_786	GCA_013267395.1	32002	32002	type	True	78.0568	485	1861	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	78.0459	402	1861	95	below_threshold
Achromobacter denitrificans	strain=NBRC 15125	GCA_001571365.1	32002	32002	type	True	78.0238	478	1861	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	78.0223	426	1861	95	below_threshold
Bordetella bronchiseptica	strain=NBRC 13691	GCA_001598655.1	518	518	suspected-type	True	78.0213	403	1861	95	below_threshold
Achromobacter denitrificans	strain=LMG 1231	GCA_902859715.1	32002	32002	type	True	78.0087	473	1861	95	below_threshold
Achromobacter aloeverae	strain=AVA-1	GCA_004121055.1	1750518	1750518	type	True	77.8074	422	1861	95	below_threshold
Bordetella bronchialis	strain=AU3182	GCA_001676705.1	463025	463025	type	True	77.579	433	1861	95	below_threshold
Verticiella sediminum	strain=DSM 27279	GCA_007558815.1	1247510	1247510	type	True	77.575	381	1861	95	below_threshold
Parapusillimonas granuli	strain=LMG 24012	GCA_013416525.1	380911	380911	type	True	77.1934	292	1861	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	77.1704	289	1861	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	76.5843	321	1861	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:59,173] [INFO] DFAST Taxonomy check result was written to GCF_014651835.1_ASM1465183v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:59,173] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:59,174] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:59,174] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4cbbe8aa-dd3c-4924-a993-bae9773a4862/dqc_reference/checkm_data
[2024-01-24 13:28:59,175] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:59,231] [INFO] Task started: CheckM
[2024-01-24 13:28:59,231] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651835.1_ASM1465183v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651835.1_ASM1465183v1_genomic.fna/checkm_input GCF_014651835.1_ASM1465183v1_genomic.fna/checkm_result
[2024-01-24 13:30:05,238] [INFO] Task succeeded: CheckM
[2024-01-24 13:30:05,239] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:30:05,263] [INFO] ===== Completeness check finished =====
[2024-01-24 13:30:05,264] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:30:05,264] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651835.1_ASM1465183v1_genomic.fna/markers.fasta)
[2024-01-24 13:30:05,264] [INFO] Task started: Blastn
[2024-01-24 13:30:05,265] [INFO] Running command: blastn -query GCF_014651835.1_ASM1465183v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4cbbe8aa-dd3c-4924-a993-bae9773a4862/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651835.1_ASM1465183v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:07,156] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:07,160] [INFO] Selected 11 target genomes.
[2024-01-24 13:30:07,160] [INFO] Target genome list was writen to GCF_014651835.1_ASM1465183v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:30:07,500] [INFO] Task started: fastANI
[2024-01-24 13:30:07,502] [INFO] Running command: fastANI --query /var/lib/cwl/stg987b241f-21d5-4b59-b52a-2fea2db8829f/GCF_014651835.1_ASM1465183v1_genomic.fna.gz --refList GCF_014651835.1_ASM1465183v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651835.1_ASM1465183v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:20,748] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:20,760] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:30:20,760] [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
GCF_014651835.1	s__Pigmentiphaga litoralis	100.0	1860	1861	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013408655.1	s__Pigmentiphaga litoralis_A	89.255	1628	1861	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004216695.1	s__Pigmentiphaga kullae	79.4978	711	1861	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003854895.1	s__Pigmentiphaga sp003854895	79.4878	682	1861	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002188635.1	s__Pigmentiphaga sp002188635	79.3481	697	1861	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	99.65	99.31	0.97	0.93	3	-
GCA_001898625.1	s__Pigmentiphaga sp001898625	79.3476	684	1861	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	99.98	99.98	0.96	0.93	3	-
GCF_900606115.1	s__Pigmentiphaga humi	79.3459	621	1861	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009360345.1	s__Pigmentiphaga sp009360345	79.2561	659	1861	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	99.85	99.84	0.97	0.96	3	-
GCF_002188465.1	s__Pigmentiphaga sp002188465	78.8675	662	1861	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002192695.1	s__Achromobacter xylosoxidans_C	78.1775	496	1861	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.40	98.40	0.91	0.91	2	-
GCF_002975275.1	s__Achromobacter sp002975275	77.9806	428	1861	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:30:20,928] [INFO] GTDB search result was written to GCF_014651835.1_ASM1465183v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:20,929] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:20,938] [INFO] DFAST_QC result json was written to GCF_014651835.1_ASM1465183v1_genomic.fna/dqc_result.json
[2024-01-24 13:30:20,939] [INFO] DFAST_QC completed!
[2024-01-24 13:30:20,939] [INFO] Total running time: 0h2m9s