[2024-01-24 13:13:23,723] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:23,726] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:23,726] [INFO] DQC Reference Directory: /var/lib/cwl/stgc24a7902-7cfd-4667-b720-336a163f4dd1/dqc_reference
[2024-01-24 13:13:25,106] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:25,107] [INFO] Task started: Prodigal
[2024-01-24 13:13:25,107] [INFO] Running command: gunzip -c /var/lib/cwl/stge24ee6e0-6f1b-4068-ba55-190f1fb6548f/GCF_000422845.1_ASM42284v1_genomic.fna.gz | prodigal -d GCF_000422845.1_ASM42284v1_genomic.fna/cds.fna -a GCF_000422845.1_ASM42284v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:39,831] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:39,832] [INFO] Task started: HMMsearch
[2024-01-24 13:13:39,832] [INFO] Running command: hmmsearch --tblout GCF_000422845.1_ASM42284v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc24a7902-7cfd-4667-b720-336a163f4dd1/dqc_reference/reference_markers.hmm GCF_000422845.1_ASM42284v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:40,205] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:40,206] [INFO] Found 6/6 markers.
[2024-01-24 13:13:40,262] [INFO] Query marker FASTA was written to GCF_000422845.1_ASM42284v1_genomic.fna/markers.fasta
[2024-01-24 13:13:40,262] [INFO] Task started: Blastn
[2024-01-24 13:13:40,262] [INFO] Running command: blastn -query GCF_000422845.1_ASM42284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc24a7902-7cfd-4667-b720-336a163f4dd1/dqc_reference/reference_markers.fasta -out GCF_000422845.1_ASM42284v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:41,212] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:41,216] [INFO] Selected 17 target genomes.
[2024-01-24 13:13:41,216] [INFO] Target genome list was writen to GCF_000422845.1_ASM42284v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:41,239] [INFO] Task started: fastANI
[2024-01-24 13:13:41,239] [INFO] Running command: fastANI --query /var/lib/cwl/stge24ee6e0-6f1b-4068-ba55-190f1fb6548f/GCF_000422845.1_ASM42284v1_genomic.fna.gz --refList GCF_000422845.1_ASM42284v1_genomic.fna/target_genomes.txt --output GCF_000422845.1_ASM42284v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:55,589] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:55,590] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc24a7902-7cfd-4667-b720-336a163f4dd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:55,590] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc24a7902-7cfd-4667-b720-336a163f4dd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:55,604] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:55,604] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:55,604] [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
Oceanobacter kriegii	strain=DSM 6294	GCA_000422845.1	64972	64972	type	True	100.0	1482	1485	95	conclusive
Oceanobacter mangrovi	strain=SM2-42	GCA_019740315.1	2862510	2862510	type	True	80.2296	728	1485	95	below_threshold
Thalassolituus marinus	strain=IMCC1826	GCA_020320395.1	671053	671053	type	True	78.4881	258	1485	95	below_threshold
Oleibacter marinus	strain=DSM 24913	GCA_900156675.1	484498	484498	type	True	78.2053	169	1485	95	below_threshold
Thalassolituus oleivorans	strain=MIL-1	GCA_000355675.1	187493	187493	type	True	77.5719	106	1485	95	below_threshold
Bacterioplanes sanyensis	strain=KCTC 32220	GCA_014652515.1	1249553	1249553	type	True	77.2266	175	1485	95	below_threshold
Marinobacter zhejiangensis	strain=CGMCC 1.7061	GCA_900114775.1	488535	488535	type	True	76.4902	87	1485	95	below_threshold
Marinobacterium lutimaris	strain=DSM 22012	GCA_900108065.1	568106	568106	type	True	76.4543	139	1485	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	76.399	128	1485	95	below_threshold
Marinobacterium stanieri	strain=DSM 7027	GCA_900155945.1	49186	49186	type	True	76.388	136	1485	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_021165935.1	86173	86173	type	True	76.3755	75	1485	95	below_threshold
Pseudomonas oryzicola	strain=RD9SR1	GCA_014269185.2	485876	485876	type	True	76.2091	105	1485	95	below_threshold
Marinobacter santoriniensis	strain=NKSG1	GCA_000347775.1	523742	523742	type	True	76.1362	68	1485	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	76.1046	100	1485	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	76.0782	107	1485	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	75.6533	55	1485	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	75.5031	92	1485	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:55,606] [INFO] DFAST Taxonomy check result was written to GCF_000422845.1_ASM42284v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:55,606] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:55,607] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:55,607] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc24a7902-7cfd-4667-b720-336a163f4dd1/dqc_reference/checkm_data
[2024-01-24 13:13:55,608] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:55,651] [INFO] Task started: CheckM
[2024-01-24 13:13:55,652] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000422845.1_ASM42284v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000422845.1_ASM42284v1_genomic.fna/checkm_input GCF_000422845.1_ASM42284v1_genomic.fna/checkm_result
[2024-01-24 13:14:40,921] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:40,922] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:40,940] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:40,941] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:40,941] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000422845.1_ASM42284v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:40,941] [INFO] Task started: Blastn
[2024-01-24 13:14:40,942] [INFO] Running command: blastn -query GCF_000422845.1_ASM42284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc24a7902-7cfd-4667-b720-336a163f4dd1/dqc_reference/reference_markers_gtdb.fasta -out GCF_000422845.1_ASM42284v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:42,334] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:42,338] [INFO] Selected 8 target genomes.
[2024-01-24 13:14:42,338] [INFO] Target genome list was writen to GCF_000422845.1_ASM42284v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:42,350] [INFO] Task started: fastANI
[2024-01-24 13:14:42,351] [INFO] Running command: fastANI --query /var/lib/cwl/stge24ee6e0-6f1b-4068-ba55-190f1fb6548f/GCF_000422845.1_ASM42284v1_genomic.fna.gz --refList GCF_000422845.1_ASM42284v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000422845.1_ASM42284v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:50,211] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:50,219] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:50,219] [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_000422845.1	s__Oceanobacter kriegii	100.0	1482	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oceanobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002723385.1	s__Oceanobacter sp002723385	78.4231	235	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oceanobacter	95.0	99.82	99.82	0.84	0.84	2	-
GCF_007785795.1	s__UBA2009 sp002335285	78.1779	286	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	97.54	97.44	0.92	0.92	6	-
GCA_002706025.1	s__UBA2009 sp002706025	78.1727	261	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	98.78	97.86	0.91	0.85	7	-
GCA_002733205.1	s__UBA2009 sp002733205	77.9587	246	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	96.83	96.83	0.84	0.84	2	-
GCA_016132445.1	s__UBA2009 sp016132445	77.9268	262	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	97.98	97.98	0.94	0.94	2	-
GCA_002314145.1	s__UBA2009 sp002314145	77.6948	239	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	99.98	99.96	0.95	0.88	5	-
GCF_014652515.1	s__Bacterioplanes sanyensis	77.2234	176	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Bacterioplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:50,222] [INFO] GTDB search result was written to GCF_000422845.1_ASM42284v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:50,222] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:50,226] [INFO] DFAST_QC result json was written to GCF_000422845.1_ASM42284v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:50,226] [INFO] DFAST_QC completed!
[2024-01-24 13:14:50,226] [INFO] Total running time: 0h1m27s