[2024-01-25 20:06:50,550] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:06:50,551] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:06:50,551] [INFO] DQC Reference Directory: /var/lib/cwl/stgcdbe28b3-9eb6-46ff-a335-dbe4f427fcf7/dqc_reference
[2024-01-25 20:06:51,690] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:06:51,691] [INFO] Task started: Prodigal
[2024-01-25 20:06:51,691] [INFO] Running command: gunzip -c /var/lib/cwl/stg8602dc04-9cb6-445e-b3c8-7b2547601efd/GCF_014925295.1_ASM1492529v1_genomic.fna.gz | prodigal -d GCF_014925295.1_ASM1492529v1_genomic.fna/cds.fna -a GCF_014925295.1_ASM1492529v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:06:59,189] [INFO] Task succeeded: Prodigal
[2024-01-25 20:06:59,189] [INFO] Task started: HMMsearch
[2024-01-25 20:06:59,189] [INFO] Running command: hmmsearch --tblout GCF_014925295.1_ASM1492529v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcdbe28b3-9eb6-46ff-a335-dbe4f427fcf7/dqc_reference/reference_markers.hmm GCF_014925295.1_ASM1492529v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:06:59,466] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:06:59,468] [INFO] Found 6/6 markers.
[2024-01-25 20:06:59,504] [INFO] Query marker FASTA was written to GCF_014925295.1_ASM1492529v1_genomic.fna/markers.fasta
[2024-01-25 20:06:59,505] [INFO] Task started: Blastn
[2024-01-25 20:06:59,505] [INFO] Running command: blastn -query GCF_014925295.1_ASM1492529v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcdbe28b3-9eb6-46ff-a335-dbe4f427fcf7/dqc_reference/reference_markers.fasta -out GCF_014925295.1_ASM1492529v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:00,181] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:00,184] [INFO] Selected 11 target genomes.
[2024-01-25 20:07:00,184] [INFO] Target genome list was writen to GCF_014925295.1_ASM1492529v1_genomic.fna/target_genomes.txt
[2024-01-25 20:07:00,193] [INFO] Task started: fastANI
[2024-01-25 20:07:00,193] [INFO] Running command: fastANI --query /var/lib/cwl/stg8602dc04-9cb6-445e-b3c8-7b2547601efd/GCF_014925295.1_ASM1492529v1_genomic.fna.gz --refList GCF_014925295.1_ASM1492529v1_genomic.fna/target_genomes.txt --output GCF_014925295.1_ASM1492529v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:07:12,103] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:12,104] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcdbe28b3-9eb6-46ff-a335-dbe4f427fcf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:07:12,104] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcdbe28b3-9eb6-46ff-a335-dbe4f427fcf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:07:12,112] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 20:07:12,112] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:07:12,112] [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
Pseudoalteromonas carrageenovora	strain=IAM 12662	GCA_014925295.1	227	227	type	True	100.0	1509	1510	95	conclusive
Pseudoalteromonas carrageenovora	strain=ATCC 43555	GCA_900239935.1	227	227	type	True	99.9756	1503	1510	95	conclusive
Pseudoalteromonas carrageenovora	strain=NBRC 12985	GCA_006539245.1	227	227	type	True	99.9259	1421	1510	95	conclusive
Pseudoalteromonas espejiana	strain=ATCC 29659	GCA_002221525.1	28107	28107	type	True	88.0343	1134	1510	95	below_threshold
Pseudoalteromonas espejiana	strain=NBRC 102222	GCA_007989585.1	28107	28107	type	True	87.8508	1106	1510	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	85.607	1136	1510	95	below_threshold
Pseudoalteromonas marina	strain=DSM 17587	GCA_000238335.4	267375	267375	type	True	84.4098	945	1510	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	80.197	638	1510	95	below_threshold
Motilimonas cestriensis	strain=MKS20	GCA_021295315.1	2742685	2742685	type	True	76.8726	73	1510	95	below_threshold
Shewanella marinintestina	strain=LMG 21403	GCA_023283845.1	190305	190305	type	True	76.5885	65	1510	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:07:12,113] [INFO] DFAST Taxonomy check result was written to GCF_014925295.1_ASM1492529v1_genomic.fna/tc_result.tsv
[2024-01-25 20:07:12,114] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:07:12,114] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:07:12,114] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcdbe28b3-9eb6-46ff-a335-dbe4f427fcf7/dqc_reference/checkm_data
[2024-01-25 20:07:12,115] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:07:12,157] [INFO] Task started: CheckM
[2024-01-25 20:07:12,157] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014925295.1_ASM1492529v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014925295.1_ASM1492529v1_genomic.fna/checkm_input GCF_014925295.1_ASM1492529v1_genomic.fna/checkm_result
[2024-01-25 20:07:38,930] [INFO] Task succeeded: CheckM
[2024-01-25 20:07:38,931] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:07:38,947] [INFO] ===== Completeness check finished =====
[2024-01-25 20:07:38,947] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:07:38,947] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014925295.1_ASM1492529v1_genomic.fna/markers.fasta)
[2024-01-25 20:07:38,948] [INFO] Task started: Blastn
[2024-01-25 20:07:38,948] [INFO] Running command: blastn -query GCF_014925295.1_ASM1492529v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcdbe28b3-9eb6-46ff-a335-dbe4f427fcf7/dqc_reference/reference_markers_gtdb.fasta -out GCF_014925295.1_ASM1492529v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:40,060] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:40,062] [INFO] Selected 11 target genomes.
[2024-01-25 20:07:40,063] [INFO] Target genome list was writen to GCF_014925295.1_ASM1492529v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:07:40,072] [INFO] Task started: fastANI
[2024-01-25 20:07:40,072] [INFO] Running command: fastANI --query /var/lib/cwl/stg8602dc04-9cb6-445e-b3c8-7b2547601efd/GCF_014925295.1_ASM1492529v1_genomic.fna.gz --refList GCF_014925295.1_ASM1492529v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014925295.1_ASM1492529v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:07:52,647] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:52,655] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:07:52,656] [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_900239935.1	s__Pseudoalteromonas carrageenovora	99.9756	1503	1510	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.00	96.44	0.97	0.91	6	conclusive
GCF_018100985.1	s__Pseudoalteromonas sp018100985	92.4506	1186	1510	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.38	98.38	0.93	0.93	2	-
GCF_002221525.1	s__Pseudoalteromonas espejiana	88.0386	1133	1510	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_007988745.1	s__Pseudoalteromonas atlantica	86.1194	1096	1510	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.93	97.66	0.89	0.85	29	-
GCF_008370255.1	s__Pseudoalteromonas sp008370255	85.9477	1125	1510	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000814675.1	s__Pseudoalteromonas distincta	85.5836	1141	1510	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	95.34	0.88	0.77	38	-
GCF_011378855.1	s__Pseudoalteromonas sp011378855	85.1729	1084	1510	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.10	97.06	0.91	0.90	3	-
GCF_000238335.3	s__Pseudoalteromonas marina	84.4202	944	1510	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.76	97.57	0.91	0.88	12	-
GCF_001468485.1	s__Pseudoalteromonas sp001468485	84.3962	948	1510	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.31	96.95	0.95	0.92	8	-
GCF_000690055.1	s__Pseudoalteromonas fuliginea	84.2023	1022	1510	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.33	97.88	0.92	0.87	9	-
GCF_002310835.1	s__Pseudoalteromonas tetraodonis	81.7952	803	1510	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.76	96.28	0.91	0.84	28	-
--------------------------------------------------------------------------------
[2024-01-25 20:07:52,657] [INFO] GTDB search result was written to GCF_014925295.1_ASM1492529v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:07:52,658] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:07:52,660] [INFO] DFAST_QC result json was written to GCF_014925295.1_ASM1492529v1_genomic.fna/dqc_result.json
[2024-01-25 20:07:52,661] [INFO] DFAST_QC completed!
[2024-01-25 20:07:52,661] [INFO] Total running time: 0h1m2s