[2023-06-27 05:20:21,589] [INFO] DFAST_QC pipeline started.
[2023-06-27 05:20:21,592] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 05:20:21,592] [INFO] DQC Reference Directory: /var/lib/cwl/stg36464b6f-6cbe-4dcd-b8cd-586191d0e345/dqc_reference
[2023-06-27 05:20:22,843] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 05:20:22,844] [INFO] Task started: Prodigal
[2023-06-27 05:20:22,845] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a2c7ea5-c049-485b-8497-89dc427c6ceb/GCA_002341045.1_ASM234104v1_genomic.fna.gz | prodigal -d GCA_002341045.1_ASM234104v1_genomic.fna/cds.fna -a GCA_002341045.1_ASM234104v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 05:20:30,959] [INFO] Task succeeded: Prodigal
[2023-06-27 05:20:30,960] [INFO] Task started: HMMsearch
[2023-06-27 05:20:30,960] [INFO] Running command: hmmsearch --tblout GCA_002341045.1_ASM234104v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36464b6f-6cbe-4dcd-b8cd-586191d0e345/dqc_reference/reference_markers.hmm GCA_002341045.1_ASM234104v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 05:20:31,240] [INFO] Task succeeded: HMMsearch
[2023-06-27 05:20:31,242] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6a2c7ea5-c049-485b-8497-89dc427c6ceb/GCA_002341045.1_ASM234104v1_genomic.fna.gz]
[2023-06-27 05:20:31,289] [INFO] Query marker FASTA was written to GCA_002341045.1_ASM234104v1_genomic.fna/markers.fasta
[2023-06-27 05:20:31,289] [INFO] Task started: Blastn
[2023-06-27 05:20:31,289] [INFO] Running command: blastn -query GCA_002341045.1_ASM234104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36464b6f-6cbe-4dcd-b8cd-586191d0e345/dqc_reference/reference_markers.fasta -out GCA_002341045.1_ASM234104v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:20:31,939] [INFO] Task succeeded: Blastn
[2023-06-27 05:20:31,944] [INFO] Selected 21 target genomes.
[2023-06-27 05:20:31,944] [INFO] Target genome list was writen to GCA_002341045.1_ASM234104v1_genomic.fna/target_genomes.txt
[2023-06-27 05:20:31,949] [INFO] Task started: fastANI
[2023-06-27 05:20:31,949] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a2c7ea5-c049-485b-8497-89dc427c6ceb/GCA_002341045.1_ASM234104v1_genomic.fna.gz --refList GCA_002341045.1_ASM234104v1_genomic.fna/target_genomes.txt --output GCA_002341045.1_ASM234104v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 05:20:45,355] [INFO] Task succeeded: fastANI
[2023-06-27 05:20:45,355] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36464b6f-6cbe-4dcd-b8cd-586191d0e345/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 05:20:45,356] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36464b6f-6cbe-4dcd-b8cd-586191d0e345/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 05:20:45,374] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 05:20:45,374] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 05:20:45,374] [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	79.6225	395	1032	95	below_threshold
Oleibacter marinus	strain=DSM 24913	GCA_900156675.1	484498	484498	type	True	78.4929	167	1032	95	below_threshold
Thalassolituus oleivorans	strain=MIL-1	GCA_000355675.1	187493	187493	type	True	78.381	165	1032	95	below_threshold
Oceanobacter kriegii	strain=DSM 6294	GCA_000422845.1	64972	64972	type	True	78.2092	214	1032	95	below_threshold
Oceanobacter mangrovi	strain=SM2-42	GCA_019740315.1	2862510	2862510	type	True	77.9873	207	1032	95	below_threshold
Bacterioplanes sanyensis	strain=KCTC 32220	GCA_014652515.1	1249553	1249553	type	True	77.4279	186	1032	95	below_threshold
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	76.3662	55	1032	95	below_threshold
Marinobacterium lutimaris	strain=DSM 22012	GCA_900108065.1	568106	568106	type	True	76.219	68	1032	95	below_threshold
Marinobacter shengliensis subsp. alexandrii	strain=LZ-6	GCA_005871095.1	2570350	1389223	type	True	76.1621	53	1032	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 05:20:45,377] [INFO] DFAST Taxonomy check result was written to GCA_002341045.1_ASM234104v1_genomic.fna/tc_result.tsv
[2023-06-27 05:20:45,378] [INFO] ===== Taxonomy check completed =====
[2023-06-27 05:20:45,378] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 05:20:45,378] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36464b6f-6cbe-4dcd-b8cd-586191d0e345/dqc_reference/checkm_data
[2023-06-27 05:20:45,379] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 05:20:45,419] [INFO] Task started: CheckM
[2023-06-27 05:20:45,419] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002341045.1_ASM234104v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002341045.1_ASM234104v1_genomic.fna/checkm_input GCA_002341045.1_ASM234104v1_genomic.fna/checkm_result
[2023-06-27 05:21:14,789] [INFO] Task succeeded: CheckM
[2023-06-27 05:21:14,790] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 05:21:14,813] [INFO] ===== Completeness check finished =====
[2023-06-27 05:21:14,814] [INFO] ===== Start GTDB Search =====
[2023-06-27 05:21:14,814] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002341045.1_ASM234104v1_genomic.fna/markers.fasta)
[2023-06-27 05:21:14,814] [INFO] Task started: Blastn
[2023-06-27 05:21:14,814] [INFO] Running command: blastn -query GCA_002341045.1_ASM234104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36464b6f-6cbe-4dcd-b8cd-586191d0e345/dqc_reference/reference_markers_gtdb.fasta -out GCA_002341045.1_ASM234104v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:21:15,728] [INFO] Task succeeded: Blastn
[2023-06-27 05:21:15,734] [INFO] Selected 10 target genomes.
[2023-06-27 05:21:15,734] [INFO] Target genome list was writen to GCA_002341045.1_ASM234104v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 05:21:15,745] [INFO] Task started: fastANI
[2023-06-27 05:21:15,746] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a2c7ea5-c049-485b-8497-89dc427c6ceb/GCA_002341045.1_ASM234104v1_genomic.fna.gz --refList GCA_002341045.1_ASM234104v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002341045.1_ASM234104v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 05:21:22,748] [INFO] Task succeeded: fastANI
[2023-06-27 05:21:22,761] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 05:21:22,761] [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	97.4799	952	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	97.54	97.44	0.92	0.92	6	conclusive
GCA_002733205.1	s__UBA2009 sp002733205	89.071	792	1032	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	79.8981	413	1032	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	79.2354	356	1032	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	78.7512	383	1032	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_000422845.1	s__Oceanobacter kriegii	78.1936	215	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oceanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006212115.1	s__Oleibacter sp006212115	77.4949	129	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019061305.1	s__Marinobacterium sp019061305	75.8489	52	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 05:21:22,764] [INFO] GTDB search result was written to GCA_002341045.1_ASM234104v1_genomic.fna/result_gtdb.tsv
[2023-06-27 05:21:22,765] [INFO] ===== GTDB Search completed =====
[2023-06-27 05:21:22,793] [INFO] DFAST_QC result json was written to GCA_002341045.1_ASM234104v1_genomic.fna/dqc_result.json
[2023-06-27 05:21:22,794] [INFO] DFAST_QC completed!
[2023-06-27 05:21:22,794] [INFO] Total running time: 0h1m1s