[2024-01-24 13:01:26,552] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:26,559] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:26,559] [INFO] DQC Reference Directory: /var/lib/cwl/stg0dabcc80-7a09-415b-9318-c7ce737b4dd9/dqc_reference
[2024-01-24 13:01:28,064] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:28,065] [INFO] Task started: Prodigal
[2024-01-24 13:01:28,065] [INFO] Running command: gunzip -c /var/lib/cwl/stg2f805754-e3d4-4945-a37c-82cb092d6c2c/GCF_001045555.1_ASM104555v1_genomic.fna.gz | prodigal -d GCF_001045555.1_ASM104555v1_genomic.fna/cds.fna -a GCF_001045555.1_ASM104555v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:42,901] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:42,901] [INFO] Task started: HMMsearch
[2024-01-24 13:01:42,901] [INFO] Running command: hmmsearch --tblout GCF_001045555.1_ASM104555v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0dabcc80-7a09-415b-9318-c7ce737b4dd9/dqc_reference/reference_markers.hmm GCF_001045555.1_ASM104555v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:43,254] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:43,255] [INFO] Found 6/6 markers.
[2024-01-24 13:01:43,299] [INFO] Query marker FASTA was written to GCF_001045555.1_ASM104555v1_genomic.fna/markers.fasta
[2024-01-24 13:01:43,300] [INFO] Task started: Blastn
[2024-01-24 13:01:43,300] [INFO] Running command: blastn -query GCF_001045555.1_ASM104555v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0dabcc80-7a09-415b-9318-c7ce737b4dd9/dqc_reference/reference_markers.fasta -out GCF_001045555.1_ASM104555v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:44,133] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:44,138] [INFO] Selected 13 target genomes.
[2024-01-24 13:01:44,138] [INFO] Target genome list was writen to GCF_001045555.1_ASM104555v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:44,145] [INFO] Task started: fastANI
[2024-01-24 13:01:44,145] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f805754-e3d4-4945-a37c-82cb092d6c2c/GCF_001045555.1_ASM104555v1_genomic.fna.gz --refList GCF_001045555.1_ASM104555v1_genomic.fna/target_genomes.txt --output GCF_001045555.1_ASM104555v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:56,394] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:56,394] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0dabcc80-7a09-415b-9318-c7ce737b4dd9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:56,395] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0dabcc80-7a09-415b-9318-c7ce737b4dd9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:56,407] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:01:56,407] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:56,407] [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 subterrani	strain=JG233	GCA_001045555.1	1658765	1658765	type	True	100.0	1481	1483	95	conclusive
Marinobacter guineae	strain=M3B	GCA_002744735.1	432303	432303	type	True	84.7481	1063	1483	95	below_threshold
Marinobacter maroccanus	strain=N4	GCA_002933275.1	2055143	2055143	type	True	83.4993	973	1483	95	below_threshold
Marinobacter flavimaris	strain=KCTC 12185	GCA_003363485.1	262076	262076	type	True	82.8338	940	1483	95	below_threshold
Marinobacter adhaerens	strain=HP15	GCA_000166295.1	1033846	1033846	type	True	82.7884	920	1483	95	below_threshold
Marinobacter flavimaris	strain=LMG 23834	GCA_002933295.1	262076	262076	type	True	82.773	942	1483	95	below_threshold
Marinobacter gudaonensis	strain=CGMCC 1.6294	GCA_900115175.1	375760	375760	type	True	81.8032	859	1483	95	below_threshold
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	80.4898	635	1483	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	80.3898	632	1483	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	80.3313	747	1483	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	80.2321	682	1483	95	below_threshold
Marinobacter bryozoorum	strain=DSM 15401	GCA_023156245.1	256324	256324	type	True	79.1552	438	1483	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	78.6791	487	1483	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:56,409] [INFO] DFAST Taxonomy check result was written to GCF_001045555.1_ASM104555v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:56,409] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:56,410] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:56,410] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0dabcc80-7a09-415b-9318-c7ce737b4dd9/dqc_reference/checkm_data
[2024-01-24 13:01:56,411] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:56,457] [INFO] Task started: CheckM
[2024-01-24 13:01:56,457] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001045555.1_ASM104555v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001045555.1_ASM104555v1_genomic.fna/checkm_input GCF_001045555.1_ASM104555v1_genomic.fna/checkm_result
[2024-01-24 13:02:40,478] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:40,480] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:40,503] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:40,503] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:40,503] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001045555.1_ASM104555v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:40,504] [INFO] Task started: Blastn
[2024-01-24 13:02:40,504] [INFO] Running command: blastn -query GCF_001045555.1_ASM104555v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0dabcc80-7a09-415b-9318-c7ce737b4dd9/dqc_reference/reference_markers_gtdb.fasta -out GCF_001045555.1_ASM104555v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:41,917] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:41,922] [INFO] Selected 12 target genomes.
[2024-01-24 13:02:41,923] [INFO] Target genome list was writen to GCF_001045555.1_ASM104555v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:41,933] [INFO] Task started: fastANI
[2024-01-24 13:02:41,933] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f805754-e3d4-4945-a37c-82cb092d6c2c/GCF_001045555.1_ASM104555v1_genomic.fna.gz --refList GCF_001045555.1_ASM104555v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001045555.1_ASM104555v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:52,670] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:52,681] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:52,682] [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_001045555.1	s__Marinobacter subterrani	100.0	1480	1483	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.05	97.05	0.84	0.84	2	conclusive
GCF_002744735.1	s__Marinobacter guineae	84.7481	1063	1483	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003441595.1	s__Marinobacter sp003441595	84.512	994	1483	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650915.1	s__Marinobacter sp001650915	83.5201	962	1483	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.33	97.47	0.91	0.86	4	-
GCA_002707215.1	s__Marinobacter sp002707215	83.5089	503	1483	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002933275.1	s__Marinobacter maroccanus	83.502	971	1483	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003030785.1	s__Marinobacter sp003030785	83.0891	560	1483	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000235625.1	s__Marinobacter manganoxydans_A	82.9603	902	1483	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.5877	97.20	96.90	0.83	0.80	5	-
GCF_900188435.1	s__Marinobacter sp900188435	82.8433	897	1483	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000166295.1	s__Marinobacter adhaerens	82.7777	920	1483	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.6719	98.39	97.71	0.91	0.87	5	-
GCF_900188315.1	s__Marinobacter sp900188315	82.7477	854	1483	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.8497	N/A	N/A	N/A	N/A	1	-
GCF_009617755.1	s__Marinobacter salsuginis	82.7422	891	1483	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.38	96.64	0.89	0.80	12	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:52,684] [INFO] GTDB search result was written to GCF_001045555.1_ASM104555v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:52,685] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:52,690] [INFO] DFAST_QC result json was written to GCF_001045555.1_ASM104555v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:52,690] [INFO] DFAST_QC completed!
[2024-01-24 13:02:52,690] [INFO] Total running time: 0h1m26s