[2023-06-17 09:32:35,627] [INFO] DFAST_QC pipeline started.
[2023-06-17 09:32:35,636] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 09:32:35,636] [INFO] DQC Reference Directory: /var/lib/cwl/stgccca9f6b-6c73-4026-8f7f-30a156c119ec/dqc_reference
[2023-06-17 09:32:39,513] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 09:32:39,515] [INFO] Task started: Prodigal
[2023-06-17 09:32:39,515] [INFO] Running command: gunzip -c /var/lib/cwl/stgabb621b9-7af1-4065-99ea-410f87c77767/GCA_028290065.1_ASM2829006v1_genomic.fna.gz | prodigal -d GCA_028290065.1_ASM2829006v1_genomic.fna/cds.fna -a GCA_028290065.1_ASM2829006v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 09:32:49,975] [INFO] Task succeeded: Prodigal
[2023-06-17 09:32:49,976] [INFO] Task started: HMMsearch
[2023-06-17 09:32:49,976] [INFO] Running command: hmmsearch --tblout GCA_028290065.1_ASM2829006v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgccca9f6b-6c73-4026-8f7f-30a156c119ec/dqc_reference/reference_markers.hmm GCA_028290065.1_ASM2829006v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 09:32:50,256] [INFO] Task succeeded: HMMsearch
[2023-06-17 09:32:50,257] [INFO] Found 6/6 markers.
[2023-06-17 09:32:50,295] [INFO] Query marker FASTA was written to GCA_028290065.1_ASM2829006v1_genomic.fna/markers.fasta
[2023-06-17 09:32:50,296] [INFO] Task started: Blastn
[2023-06-17 09:32:50,296] [INFO] Running command: blastn -query GCA_028290065.1_ASM2829006v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgccca9f6b-6c73-4026-8f7f-30a156c119ec/dqc_reference/reference_markers.fasta -out GCA_028290065.1_ASM2829006v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 09:32:51,186] [INFO] Task succeeded: Blastn
[2023-06-17 09:32:51,190] [INFO] Selected 21 target genomes.
[2023-06-17 09:32:51,190] [INFO] Target genome list was writen to GCA_028290065.1_ASM2829006v1_genomic.fna/target_genomes.txt
[2023-06-17 09:32:51,199] [INFO] Task started: fastANI
[2023-06-17 09:32:51,199] [INFO] Running command: fastANI --query /var/lib/cwl/stgabb621b9-7af1-4065-99ea-410f87c77767/GCA_028290065.1_ASM2829006v1_genomic.fna.gz --refList GCA_028290065.1_ASM2829006v1_genomic.fna/target_genomes.txt --output GCA_028290065.1_ASM2829006v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 09:33:06,658] [INFO] Task succeeded: fastANI
[2023-06-17 09:33:06,659] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgccca9f6b-6c73-4026-8f7f-30a156c119ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 09:33:06,659] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgccca9f6b-6c73-4026-8f7f-30a156c119ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 09:33:06,680] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 09:33:06,680] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 09:33:06,680] [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
Cypionkella psychrotolerans	strain=PAMC 27389	GCA_001294535.1	1678131	1678131	type	True	83.7876	837	1068	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	77.5586	313	1068	95	below_threshold
Gemmobacter aquatilis	strain=DSM 3857	GCA_900110025.1	933059	933059	type	True	77.4587	314	1068	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	77.4391	258	1068	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	77.4057	272	1068	95	below_threshold
Gemmobacter straminiformis	strain=CAM-8	GCA_014243445.1	2045119	2045119	type	True	77.3721	275	1068	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	77.325	328	1068	95	below_threshold
Gemmobacter aquarius	strain=HYN0069	GCA_003060865.1	2169400	2169400	type	True	77.2478	293	1068	95	below_threshold
Pseudorhodobacter ferrugineus	strain=DSM 5888	GCA_000420745.1	77008	77008	type	True	77.1645	188	1068	95	below_threshold
Cereibacter changlensis	strain=JA139	GCA_003034985.1	402884	402884	type	True	77.0725	264	1068	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	77.0263	271	1068	95	below_threshold
Pseudorhodobacter wandonensis	strain=KCTC 23672	GCA_001202035.1	1120568	1120568	type	True	76.9482	194	1068	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009881095.1	1465486	1465486	type	True	76.7806	207	1068	95	below_threshold
Frigidibacter albus	strain=CGMCC 1.13995	GCA_014640395.1	1465486	1465486	type	True	76.7716	208	1068	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009908165.1	1465486	1465486	type	True	76.7676	209	1068	95	below_threshold
Gemmobacter tilapiae	strain=KCTC 23310	GCA_014652215.1	875041	875041	type	True	76.7644	217	1068	95	below_threshold
Gemmobacter aquaticus	strain=CGMCC 1.7029	GCA_014645295.1	490185	490185	type	True	76.6653	200	1068	95	below_threshold
Pseudogemmobacter bohemicus	strain=Cd-10	GCA_003290025.1	2250708	2250708	type	True	76.6022	202	1068	95	below_threshold
Pseudogemmobacter hezensis	strain=D13-10-4-6	GCA_013155295.1	2737662	2737662	type	True	76.5978	208	1068	95	below_threshold
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	76.5521	196	1068	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	75.869	90	1068	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 09:33:06,682] [INFO] DFAST Taxonomy check result was written to GCA_028290065.1_ASM2829006v1_genomic.fna/tc_result.tsv
[2023-06-17 09:33:06,683] [INFO] ===== Taxonomy check completed =====
[2023-06-17 09:33:06,683] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 09:33:06,684] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgccca9f6b-6c73-4026-8f7f-30a156c119ec/dqc_reference/checkm_data
[2023-06-17 09:33:06,685] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 09:33:06,726] [INFO] Task started: CheckM
[2023-06-17 09:33:06,726] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028290065.1_ASM2829006v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028290065.1_ASM2829006v1_genomic.fna/checkm_input GCA_028290065.1_ASM2829006v1_genomic.fna/checkm_result
[2023-06-17 09:33:40,742] [INFO] Task succeeded: CheckM
[2023-06-17 09:33:40,744] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.61%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 09:33:40,765] [INFO] ===== Completeness check finished =====
[2023-06-17 09:33:40,765] [INFO] ===== Start GTDB Search =====
[2023-06-17 09:33:40,766] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028290065.1_ASM2829006v1_genomic.fna/markers.fasta)
[2023-06-17 09:33:40,766] [INFO] Task started: Blastn
[2023-06-17 09:33:40,766] [INFO] Running command: blastn -query GCA_028290065.1_ASM2829006v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgccca9f6b-6c73-4026-8f7f-30a156c119ec/dqc_reference/reference_markers_gtdb.fasta -out GCA_028290065.1_ASM2829006v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 09:33:41,997] [INFO] Task succeeded: Blastn
[2023-06-17 09:33:42,002] [INFO] Selected 15 target genomes.
[2023-06-17 09:33:42,003] [INFO] Target genome list was writen to GCA_028290065.1_ASM2829006v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 09:33:42,030] [INFO] Task started: fastANI
[2023-06-17 09:33:42,030] [INFO] Running command: fastANI --query /var/lib/cwl/stgabb621b9-7af1-4065-99ea-410f87c77767/GCA_028290065.1_ASM2829006v1_genomic.fna.gz --refList GCA_028290065.1_ASM2829006v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028290065.1_ASM2829006v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 09:33:52,638] [INFO] Task succeeded: fastANI
[2023-06-17 09:33:52,651] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 09:33:52,652] [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_001294535.1	s__Cypionkella psychrotolerans	83.7988	836	1068	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cypionkella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002256245.1	s__Cypionkella sp002256245	82.7505	800	1068	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cypionkella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009773375.1	s__Cypionkella sp009773375	80.4715	606	1068	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cypionkella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001828855.1	s__Cypionkella sp001828855	78.9196	498	1068	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cypionkella	95.0	99.95	99.91	0.99	0.97	3	-
GCA_018063485.1	s__Cypionkella sp018063485	78.0294	247	1068	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cypionkella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003443995.1	s__ETT8 sp003443995	77.5586	313	1068	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010915705.1	s__ETT8 sp010915705	77.4419	257	1068	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014243445.1	s__Gemmobacter_B straminiformis	77.3721	275	1068	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869835.1	s__KMS-5 sp016869835	77.3007	262	1068	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__KMS-5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003060865.1	s__Gemmobacter_B sp003060865	77.2574	292	1068	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298675.1	s__Cypionkella sp013298675	77.2013	173	1068	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cypionkella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792925.1	s__Gemmobacter sp016792925	76.8298	229	1068	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003243455.1	s__Rhodobacter_F sphaeroides_A	76.7976	225	1068	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001620265.1	s__Frigidibacter mobilis	76.5411	197	1068	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003990445.1	s__Pararhodobacter zhoushanensis	76.332	156	1068	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 09:33:52,654] [INFO] GTDB search result was written to GCA_028290065.1_ASM2829006v1_genomic.fna/result_gtdb.tsv
[2023-06-17 09:33:52,654] [INFO] ===== GTDB Search completed =====
[2023-06-17 09:33:52,659] [INFO] DFAST_QC result json was written to GCA_028290065.1_ASM2829006v1_genomic.fna/dqc_result.json
[2023-06-17 09:33:52,659] [INFO] DFAST_QC completed!
[2023-06-17 09:33:52,659] [INFO] Total running time: 0h1m17s