[2024-01-24 14:05:59,264] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:59,266] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:59,266] [INFO] DQC Reference Directory: /var/lib/cwl/stgae139b56-1525-4adb-bac6-ff0900325179/dqc_reference
[2024-01-24 14:06:00,682] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:00,688] [INFO] Task started: Prodigal
[2024-01-24 14:06:00,689] [INFO] Running command: gunzip -c /var/lib/cwl/stg22b3ee00-e7f8-49bd-be00-7ee903a31b5c/GCF_008122265.1_ASM812226v1_genomic.fna.gz | prodigal -d GCF_008122265.1_ASM812226v1_genomic.fna/cds.fna -a GCF_008122265.1_ASM812226v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:14,914] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:14,915] [INFO] Task started: HMMsearch
[2024-01-24 14:06:14,915] [INFO] Running command: hmmsearch --tblout GCF_008122265.1_ASM812226v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgae139b56-1525-4adb-bac6-ff0900325179/dqc_reference/reference_markers.hmm GCF_008122265.1_ASM812226v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:15,243] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:15,244] [INFO] Found 6/6 markers.
[2024-01-24 14:06:15,301] [INFO] Query marker FASTA was written to GCF_008122265.1_ASM812226v1_genomic.fna/markers.fasta
[2024-01-24 14:06:15,302] [INFO] Task started: Blastn
[2024-01-24 14:06:15,302] [INFO] Running command: blastn -query GCF_008122265.1_ASM812226v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae139b56-1525-4adb-bac6-ff0900325179/dqc_reference/reference_markers.fasta -out GCF_008122265.1_ASM812226v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:16,217] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:16,221] [INFO] Selected 16 target genomes.
[2024-01-24 14:06:16,222] [INFO] Target genome list was writen to GCF_008122265.1_ASM812226v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:16,232] [INFO] Task started: fastANI
[2024-01-24 14:06:16,232] [INFO] Running command: fastANI --query /var/lib/cwl/stg22b3ee00-e7f8-49bd-be00-7ee903a31b5c/GCF_008122265.1_ASM812226v1_genomic.fna.gz --refList GCF_008122265.1_ASM812226v1_genomic.fna/target_genomes.txt --output GCF_008122265.1_ASM812226v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:30,222] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:30,222] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgae139b56-1525-4adb-bac6-ff0900325179/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:30,223] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgae139b56-1525-4adb-bac6-ff0900325179/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:30,236] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:30,237] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:30,237] [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
Marinobacter fonticola	strain=CS412	GCA_008122265.1	2603215	2603215	type	True	100.0	1513	1514	95	conclusive
Marinobacter nanhaiticus	strain=D15-8W	GCA_000364845.1	1305740	1305740	type	True	80.8842	922	1514	95	below_threshold
Marinobacter bohaiensis	strain=T17	GCA_003258515.1	2201898	2201898	type	True	79.8446	643	1514	95	below_threshold
Marinobacter mangrovi	strain=CHFG3-1-5	GCA_016798325.1	2803918	2803918	type	True	79.7486	656	1514	95	below_threshold
Marinobacter halodurans	strain=YJ-S3-2	GCA_004327985.1	2528979	2528979	type	True	79.5718	665	1514	95	below_threshold
Marinobacter salinus	strain=Hb8	GCA_001854125.1	1874317	1874317	type	True	78.3639	218	1514	95	below_threshold
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	78.3413	289	1514	95	below_threshold
Marinobacter subterrani	strain=JG233	GCA_001045555.1	1658765	1658765	type	True	78.1751	331	1514	95	below_threshold
Marinobacter shengliensis	strain=SL013A34A2	GCA_003007715.1	1389223	1389223	type	True	78.0483	254	1514	95	below_threshold
Marinobacter lipolyticus	strain=SM19	GCA_000397065.2	209639	209639	type	True	78.0352	278	1514	95	below_threshold
Marinobacter shengliensis subsp. alexandrii	strain=LZ-6	GCA_005871095.1	2570350	1389223	type	True	77.9612	245	1514	95	below_threshold
Marinobacter mobilis	strain=CGMCC 1.7059	GCA_900106945.1	488533	488533	type	True	77.6736	257	1514	95	below_threshold
Marinobacter caseinilyticus	strain=M3-13	GCA_011074955.1	2692195	2692195	type	True	77.6269	281	1514	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	76.9734	121	1514	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.424	55	1514	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	76.3074	101	1514	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:30,239] [INFO] DFAST Taxonomy check result was written to GCF_008122265.1_ASM812226v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:30,240] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:30,240] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:30,240] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgae139b56-1525-4adb-bac6-ff0900325179/dqc_reference/checkm_data
[2024-01-24 14:06:30,242] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:30,288] [INFO] Task started: CheckM
[2024-01-24 14:06:30,288] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008122265.1_ASM812226v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008122265.1_ASM812226v1_genomic.fna/checkm_input GCF_008122265.1_ASM812226v1_genomic.fna/checkm_result
[2024-01-24 14:07:12,886] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:12,888] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:12,907] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:12,907] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:12,908] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008122265.1_ASM812226v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:12,908] [INFO] Task started: Blastn
[2024-01-24 14:07:12,908] [INFO] Running command: blastn -query GCF_008122265.1_ASM812226v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae139b56-1525-4adb-bac6-ff0900325179/dqc_reference/reference_markers_gtdb.fasta -out GCF_008122265.1_ASM812226v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:14,316] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:14,320] [INFO] Selected 12 target genomes.
[2024-01-24 14:07:14,320] [INFO] Target genome list was writen to GCF_008122265.1_ASM812226v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:14,332] [INFO] Task started: fastANI
[2024-01-24 14:07:14,332] [INFO] Running command: fastANI --query /var/lib/cwl/stg22b3ee00-e7f8-49bd-be00-7ee903a31b5c/GCF_008122265.1_ASM812226v1_genomic.fna.gz --refList GCF_008122265.1_ASM812226v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008122265.1_ASM812226v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:24,786] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:24,803] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:24,804] [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_008122265.1	s__Marinobacter_A fonticola	100.0	1514	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000364845.1	s__Marinobacter_A nanhaiticus	80.8804	922	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258515.1	s__Marinobacter_A bohaiensis	79.8305	646	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	98.52	98.52	0.96	0.96	2	-
GCF_003789045.1	s__Marinobacter_A sp003789045	79.7798	635	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	97.70	97.70	0.91	0.91	2	-
GCF_004327985.1	s__Marinobacter_A halodurans	79.5717	665	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003994855.1	s__Marinobacter sp003994855	78.488	322	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001447155.2	s__Marinobacter sp001447155	78.1619	275	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001045555.1	s__Marinobacter subterrani	78.137	331	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.05	97.05	0.84	0.84	2	-
GCF_000397065.2	s__Marinobacter lipolyticus	78.0231	279	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011074955.1	s__Marinobacter caseinilyticus	77.7085	279	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106945.1	s__Marinobacter mobilis	77.6736	257	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016427555.1	s__Marinobacter litoralis_A	77.5367	187	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:24,805] [INFO] GTDB search result was written to GCF_008122265.1_ASM812226v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:24,806] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:24,809] [INFO] DFAST_QC result json was written to GCF_008122265.1_ASM812226v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:24,809] [INFO] DFAST_QC completed!
[2024-01-24 14:07:24,809] [INFO] Total running time: 0h1m26s