[2024-01-25 19:55:20,898] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:55:20,899] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:55:20,900] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a526abf-09a2-4f30-9954-9372c261df98/dqc_reference
[2024-01-25 19:55:22,062] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:55:22,063] [INFO] Task started: Prodigal
[2024-01-25 19:55:22,063] [INFO] Running command: gunzip -c /var/lib/cwl/stge7993a52-a817-4bba-9631-dab8cdb8e7e4/GCF_025345565.1_ASM2534556v1_genomic.fna.gz | prodigal -d GCF_025345565.1_ASM2534556v1_genomic.fna/cds.fna -a GCF_025345565.1_ASM2534556v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:55:31,573] [INFO] Task succeeded: Prodigal
[2024-01-25 19:55:31,573] [INFO] Task started: HMMsearch
[2024-01-25 19:55:31,573] [INFO] Running command: hmmsearch --tblout GCF_025345565.1_ASM2534556v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a526abf-09a2-4f30-9954-9372c261df98/dqc_reference/reference_markers.hmm GCF_025345565.1_ASM2534556v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:55:31,790] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:55:31,791] [INFO] Found 6/6 markers.
[2024-01-25 19:55:31,821] [INFO] Query marker FASTA was written to GCF_025345565.1_ASM2534556v1_genomic.fna/markers.fasta
[2024-01-25 19:55:31,821] [INFO] Task started: Blastn
[2024-01-25 19:55:31,821] [INFO] Running command: blastn -query GCF_025345565.1_ASM2534556v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a526abf-09a2-4f30-9954-9372c261df98/dqc_reference/reference_markers.fasta -out GCF_025345565.1_ASM2534556v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:55:32,583] [INFO] Task succeeded: Blastn
[2024-01-25 19:55:32,586] [INFO] Selected 19 target genomes.
[2024-01-25 19:55:32,586] [INFO] Target genome list was writen to GCF_025345565.1_ASM2534556v1_genomic.fna/target_genomes.txt
[2024-01-25 19:55:32,597] [INFO] Task started: fastANI
[2024-01-25 19:55:32,598] [INFO] Running command: fastANI --query /var/lib/cwl/stge7993a52-a817-4bba-9631-dab8cdb8e7e4/GCF_025345565.1_ASM2534556v1_genomic.fna.gz --refList GCF_025345565.1_ASM2534556v1_genomic.fna/target_genomes.txt --output GCF_025345565.1_ASM2534556v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:55:45,901] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:45,901] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a526abf-09a2-4f30-9954-9372c261df98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:55:45,901] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a526abf-09a2-4f30-9954-9372c261df98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:55:45,912] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:55:45,912] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:55:45,913] [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
Thalassolituus marinus	strain=IMCC1826	GCA_020320395.1	671053	671053	type	True	79.7323	572	1355	95	below_threshold
Thalassolituus oleivorans	strain=MIL-1	GCA_000355675.1	187493	187493	type	True	78.4853	221	1355	95	below_threshold
Oleibacter marinus	strain=DSM 24913	GCA_900156675.1	484498	484498	type	True	78.3708	228	1355	95	below_threshold
Oceanobacter kriegii	strain=DSM 6294	GCA_000422845.1	64972	64972	type	True	78.3661	282	1355	95	below_threshold
Oceanobacter mangrovi	strain=SM2-42	GCA_019740315.1	2862510	2862510	type	True	78.2593	287	1355	95	below_threshold
Pseudocitrobacter corydidari		GCA_021172065.1	2891570	2891570	type	True	78.0025	59	1355	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	77.8137	68	1355	95	below_threshold
Bacterioplanes sanyensis	strain=KCTC 32220	GCA_014652515.1	1249553	1249553	type	True	77.4959	254	1355	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	76.6919	80	1355	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	76.5804	94	1355	95	below_threshold
Halopseudomonas oceani	strain=CGMCC 1.15195	GCA_014641295.1	1708783	1708783	type	True	76.5248	90	1355	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	76.5083	52	1355	95	below_threshold
Halopseudomonas oceani	strain=DSM 100277	GCA_002903165.1	1708783	1708783	type	True	76.4276	91	1355	95	below_threshold
Marinobacterium halophilum	strain=DSM 17586	GCA_003014615.1	267374	267374	type	True	76.4192	91	1355	95	below_threshold
Marinobacterium litorale	strain=DSM 23545	GCA_000428985.1	404770	404770	type	True	76.4169	71	1355	95	below_threshold
Marinobacter shengliensis subsp. alexandrii	strain=LZ-6	GCA_005871095.1	2570350	1389223	type	True	76.1519	84	1355	95	below_threshold
Marinobacter daepoensis	strain=DSM 16072	GCA_000421165.1	262077	262077	type	True	75.9987	65	1355	95	below_threshold
Marinobacterium nitratireducens	strain=CGMCC 1.7286	GCA_014645375.1	518897	518897	type	True	75.9526	69	1355	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:55:45,914] [INFO] DFAST Taxonomy check result was written to GCF_025345565.1_ASM2534556v1_genomic.fna/tc_result.tsv
[2024-01-25 19:55:45,914] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:55:45,914] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:55:45,915] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a526abf-09a2-4f30-9954-9372c261df98/dqc_reference/checkm_data
[2024-01-25 19:55:45,915] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:55:45,957] [INFO] Task started: CheckM
[2024-01-25 19:55:45,957] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025345565.1_ASM2534556v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025345565.1_ASM2534556v1_genomic.fna/checkm_input GCF_025345565.1_ASM2534556v1_genomic.fna/checkm_result
[2024-01-25 19:56:17,874] [INFO] Task succeeded: CheckM
[2024-01-25 19:56:17,877] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:56:17,895] [INFO] ===== Completeness check finished =====
[2024-01-25 19:56:17,896] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:56:17,897] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025345565.1_ASM2534556v1_genomic.fna/markers.fasta)
[2024-01-25 19:56:17,897] [INFO] Task started: Blastn
[2024-01-25 19:56:17,897] [INFO] Running command: blastn -query GCF_025345565.1_ASM2534556v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a526abf-09a2-4f30-9954-9372c261df98/dqc_reference/reference_markers_gtdb.fasta -out GCF_025345565.1_ASM2534556v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:19,211] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:19,214] [INFO] Selected 8 target genomes.
[2024-01-25 19:56:19,214] [INFO] Target genome list was writen to GCF_025345565.1_ASM2534556v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:56:19,225] [INFO] Task started: fastANI
[2024-01-25 19:56:19,225] [INFO] Running command: fastANI --query /var/lib/cwl/stge7993a52-a817-4bba-9631-dab8cdb8e7e4/GCF_025345565.1_ASM2534556v1_genomic.fna.gz --refList GCF_025345565.1_ASM2534556v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025345565.1_ASM2534556v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:56:26,299] [INFO] Task succeeded: fastANI
[2024-01-25 19:56:26,305] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:56:26,305] [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_007785795.1	s__UBA2009 sp002335285	92.9082	1203	1355	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_002733205.1	s__UBA2009 sp002733205	88.8545	1018	1355	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	80.0726	557	1355	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_002706025.1	s__UBA2009 sp002706025	79.438	488	1355	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_002314145.1	s__UBA2009 sp002314145	78.9992	490	1355	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_900156675.1	s__Oleibacter marinus	78.3694	227	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	98.96	98.96	0.99	0.99	2	-
GCA_002724925.1	s__Oleibacter sp002724925	78.3574	231	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	98.64	97.85	0.94	0.89	5	-
GCF_000422845.1	s__Oceanobacter kriegii	78.3395	284	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oceanobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:56:26,307] [INFO] GTDB search result was written to GCF_025345565.1_ASM2534556v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:56:26,307] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:56:26,310] [INFO] DFAST_QC result json was written to GCF_025345565.1_ASM2534556v1_genomic.fna/dqc_result.json
[2024-01-25 19:56:26,310] [INFO] DFAST_QC completed!
[2024-01-25 19:56:26,311] [INFO] Total running time: 0h1m5s