[2023-06-17 09:32:10,603] [INFO] DFAST_QC pipeline started.
[2023-06-17 09:32:10,606] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 09:32:10,606] [INFO] DQC Reference Directory: /var/lib/cwl/stgac4ccb3f-c11c-4546-8950-0f3777d6109b/dqc_reference
[2023-06-17 09:32:13,267] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 09:32:13,268] [INFO] Task started: Prodigal
[2023-06-17 09:32:13,269] [INFO] Running command: gunzip -c /var/lib/cwl/stgda752a5d-461c-47fa-a05c-8a24ff8e89e6/GCA_028821955.1_ASM2882195v1_genomic.fna.gz | prodigal -d GCA_028821955.1_ASM2882195v1_genomic.fna/cds.fna -a GCA_028821955.1_ASM2882195v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 09:32:24,376] [INFO] Task succeeded: Prodigal
[2023-06-17 09:32:24,376] [INFO] Task started: HMMsearch
[2023-06-17 09:32:24,377] [INFO] Running command: hmmsearch --tblout GCA_028821955.1_ASM2882195v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac4ccb3f-c11c-4546-8950-0f3777d6109b/dqc_reference/reference_markers.hmm GCA_028821955.1_ASM2882195v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 09:32:24,663] [INFO] Task succeeded: HMMsearch
[2023-06-17 09:32:24,664] [INFO] Found 6/6 markers.
[2023-06-17 09:32:24,710] [INFO] Query marker FASTA was written to GCA_028821955.1_ASM2882195v1_genomic.fna/markers.fasta
[2023-06-17 09:32:24,710] [INFO] Task started: Blastn
[2023-06-17 09:32:24,710] [INFO] Running command: blastn -query GCA_028821955.1_ASM2882195v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac4ccb3f-c11c-4546-8950-0f3777d6109b/dqc_reference/reference_markers.fasta -out GCA_028821955.1_ASM2882195v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 09:32:25,448] [INFO] Task succeeded: Blastn
[2023-06-17 09:32:25,453] [INFO] Selected 39 target genomes.
[2023-06-17 09:32:25,454] [INFO] Target genome list was writen to GCA_028821955.1_ASM2882195v1_genomic.fna/target_genomes.txt
[2023-06-17 09:32:25,462] [INFO] Task started: fastANI
[2023-06-17 09:32:25,462] [INFO] Running command: fastANI --query /var/lib/cwl/stgda752a5d-461c-47fa-a05c-8a24ff8e89e6/GCA_028821955.1_ASM2882195v1_genomic.fna.gz --refList GCA_028821955.1_ASM2882195v1_genomic.fna/target_genomes.txt --output GCA_028821955.1_ASM2882195v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 09:32:55,363] [INFO] Task succeeded: fastANI
[2023-06-17 09:32:55,364] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac4ccb3f-c11c-4546-8950-0f3777d6109b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 09:32:55,364] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac4ccb3f-c11c-4546-8950-0f3777d6109b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 09:32:55,392] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 09:32:55,392] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 09:32:55,393] [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
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.0593	86	916	95	below_threshold
Rhodothalassium salexigens	strain=DSM 2132	GCA_016583875.1	1086	1086	type	True	76.0568	52	916	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	75.7036	64	916	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	75.7009	76	916	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	75.6581	62	916	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_000513295.1	55518	55518	type	True	75.631	71	916	95	below_threshold
Niveispirillum cyanobacteriorum	strain=TH16	GCA_002868735.1	1612173	1612173	type	True	75.6075	59	916	95	below_threshold
Niveispirillum cyanobacteriorum	strain=CGMCC 1.12958	GCA_014640215.1	1612173	1612173	type	True	75.5565	58	916	95	below_threshold
Nitrospirillum iridis	strain=DSM 22198	GCA_014205765.1	765888	765888	type	True	75.5295	98	916	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	75.4658	54	916	95	below_threshold
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	75.461	53	916	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	75.4442	84	916	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	75.384	64	916	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	75.3593	56	916	95	below_threshold
Azospirillum formosense	strain=CC-NFb-7	GCA_013340925.1	861533	861533	type	True	75.3453	76	916	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	75.3055	82	916	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	75.2753	77	916	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_001315015.1	192	192	type	True	75.2428	87	916	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_007827425.1	192	192	type	True	75.2364	88	916	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	75.1957	86	916	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_008274945.1	192	192	type	True	75.1775	88	916	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 09:32:55,395] [INFO] DFAST Taxonomy check result was written to GCA_028821955.1_ASM2882195v1_genomic.fna/tc_result.tsv
[2023-06-17 09:32:55,396] [INFO] ===== Taxonomy check completed =====
[2023-06-17 09:32:55,396] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 09:32:55,397] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac4ccb3f-c11c-4546-8950-0f3777d6109b/dqc_reference/checkm_data
[2023-06-17 09:32:55,398] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 09:32:55,443] [INFO] Task started: CheckM
[2023-06-17 09:32:55,443] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028821955.1_ASM2882195v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028821955.1_ASM2882195v1_genomic.fna/checkm_input GCA_028821955.1_ASM2882195v1_genomic.fna/checkm_result
[2023-06-17 09:33:31,567] [INFO] Task succeeded: CheckM
[2023-06-17 09:33:31,568] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 09:33:31,601] [INFO] ===== Completeness check finished =====
[2023-06-17 09:33:31,602] [INFO] ===== Start GTDB Search =====
[2023-06-17 09:33:31,602] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028821955.1_ASM2882195v1_genomic.fna/markers.fasta)
[2023-06-17 09:33:31,603] [INFO] Task started: Blastn
[2023-06-17 09:33:31,603] [INFO] Running command: blastn -query GCA_028821955.1_ASM2882195v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac4ccb3f-c11c-4546-8950-0f3777d6109b/dqc_reference/reference_markers_gtdb.fasta -out GCA_028821955.1_ASM2882195v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 09:33:32,866] [INFO] Task succeeded: Blastn
[2023-06-17 09:33:32,871] [INFO] Selected 13 target genomes.
[2023-06-17 09:33:32,871] [INFO] Target genome list was writen to GCA_028821955.1_ASM2882195v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 09:33:32,881] [INFO] Task started: fastANI
[2023-06-17 09:33:32,881] [INFO] Running command: fastANI --query /var/lib/cwl/stgda752a5d-461c-47fa-a05c-8a24ff8e89e6/GCA_028821955.1_ASM2882195v1_genomic.fna.gz --refList GCA_028821955.1_ASM2882195v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028821955.1_ASM2882195v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 09:33:42,808] [INFO] Task succeeded: fastANI
[2023-06-17 09:33:42,818] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 09:33:42,818] [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_018667855.1	s__GCA-2731375 sp018667855	79.9925	625	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	99.62	99.58	0.85	0.84	3	-
GCA_018701215.1	s__GCA-2731375 sp018701215	78.6879	571	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	99.97	99.95	0.98	0.97	15	-
GCA_016776605.1	s__GCA-2731375 sp016776605	78.4471	458	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002731375.1	s__GCA-2731375 sp002731375	78.4461	428	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	99.58	99.58	0.91	0.91	2	-
GCA_018660265.1	s__GCA-2731375 sp018660265	77.8526	424	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	99.92	99.87	0.96	0.94	11	-
GCA_002706405.1	s__UBA1479 sp002706405	75.6892	60	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	99.68	99.68	0.89	0.89	2	-
GCF_002868735.1	s__Niveispirillum cyanobacteriorum	75.6075	59	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Niveispirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001314655.1	s__Salibaculum sp001314655	75.5869	56	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192915.1	s__Azospirillum sp014192915	75.3394	79	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 09:33:42,835] [INFO] GTDB search result was written to GCA_028821955.1_ASM2882195v1_genomic.fna/result_gtdb.tsv
[2023-06-17 09:33:42,836] [INFO] ===== GTDB Search completed =====
[2023-06-17 09:33:42,843] [INFO] DFAST_QC result json was written to GCA_028821955.1_ASM2882195v1_genomic.fna/dqc_result.json
[2023-06-17 09:33:42,843] [INFO] DFAST_QC completed!
[2023-06-17 09:33:42,844] [INFO] Total running time: 0h1m32s