[2023-06-17 15:30:21,188] [INFO] DFAST_QC pipeline started.
[2023-06-17 15:30:21,191] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 15:30:21,191] [INFO] DQC Reference Directory: /var/lib/cwl/stgd8b14ea2-51c5-4184-a254-314057bedc72/dqc_reference
[2023-06-17 15:30:23,478] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 15:30:23,479] [INFO] Task started: Prodigal
[2023-06-17 15:30:23,480] [INFO] Running command: gunzip -c /var/lib/cwl/stg07e14c60-575e-4574-a131-98388841c57b/GCA_003456545.1_ASM345654v1_genomic.fna.gz | prodigal -d GCA_003456545.1_ASM345654v1_genomic.fna/cds.fna -a GCA_003456545.1_ASM345654v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 15:30:28,950] [INFO] Task succeeded: Prodigal
[2023-06-17 15:30:28,951] [INFO] Task started: HMMsearch
[2023-06-17 15:30:28,951] [INFO] Running command: hmmsearch --tblout GCA_003456545.1_ASM345654v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd8b14ea2-51c5-4184-a254-314057bedc72/dqc_reference/reference_markers.hmm GCA_003456545.1_ASM345654v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 15:30:29,195] [INFO] Task succeeded: HMMsearch
[2023-06-17 15:30:29,197] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg07e14c60-575e-4574-a131-98388841c57b/GCA_003456545.1_ASM345654v1_genomic.fna.gz]
[2023-06-17 15:30:29,225] [INFO] Query marker FASTA was written to GCA_003456545.1_ASM345654v1_genomic.fna/markers.fasta
[2023-06-17 15:30:29,225] [INFO] Task started: Blastn
[2023-06-17 15:30:29,225] [INFO] Running command: blastn -query GCA_003456545.1_ASM345654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8b14ea2-51c5-4184-a254-314057bedc72/dqc_reference/reference_markers.fasta -out GCA_003456545.1_ASM345654v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 15:30:30,028] [INFO] Task succeeded: Blastn
[2023-06-17 15:30:30,033] [INFO] Selected 19 target genomes.
[2023-06-17 15:30:30,034] [INFO] Target genome list was writen to GCA_003456545.1_ASM345654v1_genomic.fna/target_genomes.txt
[2023-06-17 15:30:30,038] [INFO] Task started: fastANI
[2023-06-17 15:30:30,038] [INFO] Running command: fastANI --query /var/lib/cwl/stg07e14c60-575e-4574-a131-98388841c57b/GCA_003456545.1_ASM345654v1_genomic.fna.gz --refList GCA_003456545.1_ASM345654v1_genomic.fna/target_genomes.txt --output GCA_003456545.1_ASM345654v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 15:30:43,961] [INFO] Task succeeded: fastANI
[2023-06-17 15:30:43,963] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd8b14ea2-51c5-4184-a254-314057bedc72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 15:30:43,965] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd8b14ea2-51c5-4184-a254-314057bedc72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 15:30:43,986] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 15:30:43,986] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 15:30:43,986] [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
Methyloceanibacter superfactus	strain=R-67175	GCA_001723305.1	1774969	1774969	type	True	79.8489	356	590	95	below_threshold
Methyloceanibacter marginalis	strain=R-67177	GCA_001723295.1	1774971	1774971	type	True	78.883	235	590	95	below_threshold
Methyloligella halotolerans	strain=VKM B-2706	GCA_001708935.1	1177755	1177755	type	True	77.4831	176	590	95	below_threshold
Methyloceanibacter methanicus	strain=R-67174	GCA_001723285.1	1774968	1774968	type	True	77.4302	212	590	95	below_threshold
Methyloceanibacter caenitepidi	strain=Gela4	GCA_000828475.1	1384459	1384459	type	True	77.2313	180	590	95	below_threshold
Methyloceanibacter stevinii	strain=R-67176	GCA_001723355.1	1774970	1774970	type	True	77.1603	202	590	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	76.5456	131	590	95	below_threshold
Methylobacterium marchantiae	strain=DSM 21328	GCA_022179405.1	600331	600331	type	True	76.4998	78	590	95	below_threshold
Rhodomicrobium lacus	strain=JA980	GCA_003992725.1	2498452	2498452	type	True	76.4036	60	590	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	76.1337	136	590	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	76.0508	114	590	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	75.75	68	590	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	75.5576	59	590	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	75.4757	75	590	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 15:30:43,988] [INFO] DFAST Taxonomy check result was written to GCA_003456545.1_ASM345654v1_genomic.fna/tc_result.tsv
[2023-06-17 15:30:43,989] [INFO] ===== Taxonomy check completed =====
[2023-06-17 15:30:43,989] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 15:30:43,990] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd8b14ea2-51c5-4184-a254-314057bedc72/dqc_reference/checkm_data
[2023-06-17 15:30:43,991] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 15:30:44,022] [INFO] Task started: CheckM
[2023-06-17 15:30:44,022] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003456545.1_ASM345654v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003456545.1_ASM345654v1_genomic.fna/checkm_input GCA_003456545.1_ASM345654v1_genomic.fna/checkm_result
[2023-06-17 15:31:05,373] [INFO] Task succeeded: CheckM
[2023-06-17 15:31:05,375] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.97%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 15:31:05,399] [INFO] ===== Completeness check finished =====
[2023-06-17 15:31:05,399] [INFO] ===== Start GTDB Search =====
[2023-06-17 15:31:05,400] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003456545.1_ASM345654v1_genomic.fna/markers.fasta)
[2023-06-17 15:31:05,400] [INFO] Task started: Blastn
[2023-06-17 15:31:05,400] [INFO] Running command: blastn -query GCA_003456545.1_ASM345654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8b14ea2-51c5-4184-a254-314057bedc72/dqc_reference/reference_markers_gtdb.fasta -out GCA_003456545.1_ASM345654v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 15:31:06,767] [INFO] Task succeeded: Blastn
[2023-06-17 15:31:06,773] [INFO] Selected 9 target genomes.
[2023-06-17 15:31:06,773] [INFO] Target genome list was writen to GCA_003456545.1_ASM345654v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 15:31:06,782] [INFO] Task started: fastANI
[2023-06-17 15:31:06,782] [INFO] Running command: fastANI --query /var/lib/cwl/stg07e14c60-575e-4574-a131-98388841c57b/GCA_003456545.1_ASM345654v1_genomic.fna.gz --refList GCA_003456545.1_ASM345654v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003456545.1_ASM345654v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 15:31:11,417] [INFO] Task succeeded: fastANI
[2023-06-17 15:31:11,430] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 15:31:11,430] [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_002383105.1	s__Methyloceanibacter sp002383105	99.0181	443	590	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	99.16	99.02	0.80	0.75	10	conclusive
GCA_016649675.1	s__Methyloceanibacter sp016649675	88.6684	393	590	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014380485.1	s__Methyloceanibacter sp014380485	81.3062	316	590	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003135455.1	s__Methyloceanibacter sp003135455	80.5673	361	590	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	99.05	98.64	0.83	0.80	5	-
GCF_001723305.1	s__Methyloceanibacter superfactus	79.8489	356	590	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869535.1	s__Methyloceanibacter sp016869535	79.5906	313	590	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001723295.1	s__Methyloceanibacter marginalis	78.883	235	590	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001708935.1	s__Methyloligella halotolerans	77.4831	176	590	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloligella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_901457705.2	s__RH-AL1 sp901457705	76.053	116	590	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__RH-AL1	95.0	99.94	99.94	0.99	0.99	3	-
--------------------------------------------------------------------------------
[2023-06-17 15:31:11,432] [INFO] GTDB search result was written to GCA_003456545.1_ASM345654v1_genomic.fna/result_gtdb.tsv
[2023-06-17 15:31:11,433] [INFO] ===== GTDB Search completed =====
[2023-06-17 15:31:11,437] [INFO] DFAST_QC result json was written to GCA_003456545.1_ASM345654v1_genomic.fna/dqc_result.json
[2023-06-17 15:31:11,437] [INFO] DFAST_QC completed!
[2023-06-17 15:31:11,437] [INFO] Total running time: 0h0m50s