[2024-01-24 12:15:04,104] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:04,106] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:04,107] [INFO] DQC Reference Directory: /var/lib/cwl/stg374e5b9e-a55a-4688-8160-71090563ec33/dqc_reference
[2024-01-24 12:15:05,542] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:05,543] [INFO] Task started: Prodigal
[2024-01-24 12:15:05,543] [INFO] Running command: gunzip -c /var/lib/cwl/stg669c145f-9c9f-43f7-96ec-33f21def1c3d/GCF_015209785.1_ASM1520978v1_genomic.fna.gz | prodigal -d GCF_015209785.1_ASM1520978v1_genomic.fna/cds.fna -a GCF_015209785.1_ASM1520978v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:13,734] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:13,735] [INFO] Task started: HMMsearch
[2024-01-24 12:15:13,735] [INFO] Running command: hmmsearch --tblout GCF_015209785.1_ASM1520978v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg374e5b9e-a55a-4688-8160-71090563ec33/dqc_reference/reference_markers.hmm GCF_015209785.1_ASM1520978v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:14,019] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:14,021] [INFO] Found 6/6 markers.
[2024-01-24 12:15:14,054] [INFO] Query marker FASTA was written to GCF_015209785.1_ASM1520978v1_genomic.fna/markers.fasta
[2024-01-24 12:15:14,054] [INFO] Task started: Blastn
[2024-01-24 12:15:14,054] [INFO] Running command: blastn -query GCF_015209785.1_ASM1520978v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg374e5b9e-a55a-4688-8160-71090563ec33/dqc_reference/reference_markers.fasta -out GCF_015209785.1_ASM1520978v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:14,875] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:14,881] [INFO] Selected 11 target genomes.
[2024-01-24 12:15:14,882] [INFO] Target genome list was writen to GCF_015209785.1_ASM1520978v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:14,887] [INFO] Task started: fastANI
[2024-01-24 12:15:14,888] [INFO] Running command: fastANI --query /var/lib/cwl/stg669c145f-9c9f-43f7-96ec-33f21def1c3d/GCF_015209785.1_ASM1520978v1_genomic.fna.gz --refList GCF_015209785.1_ASM1520978v1_genomic.fna/target_genomes.txt --output GCF_015209785.1_ASM1520978v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:25,030] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:25,031] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg374e5b9e-a55a-4688-8160-71090563ec33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:25,031] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg374e5b9e-a55a-4688-8160-71090563ec33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:25,043] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:25,043] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:25,044] [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 arabiensis	strain=JCM 17292	GCA_001550155.1	874454	874454	type	True	99.0949	1102	1192	95	conclusive
Pseudoalteromonas shioyasakiensis	strain=JCM 18891	GCA_001550135.1	1190813	1190813	suspected-type	True	86.7231	876	1192	95	below_threshold
Pseudoalteromonas gelatinilytica	strain=NH153	GCA_001641615.1	1703256	1703256	type	True	86.6627	862	1192	95	below_threshold
Pseudoalteromonas profundi	strain=CGMCC 1.15394	GCA_014642695.1	1774956	1774956	type	True	86.4876	883	1192	95	below_threshold
Pseudoalteromonas lipolytica	strain=CGMCC 1.8499	GCA_900116435.1	570156	570156	suspected-type	True	83.7121	809	1192	95	below_threshold
Pseudoalteromonas lipolytica	strain=LMEB 39	GCA_014925285.1	570156	570156	suspected-type	True	83.6949	810	1192	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	79.7743	456	1192	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_024347355.1	170679	170679	suspected-type	True	79.4274	79	1192	95	below_threshold
Vibrio porteresiae	strain=MSSRF30	GCA_024347055.1	435912	435912	type	True	78.9512	61	1192	95	below_threshold
Motilimonas cestriensis	strain=MKS20	GCA_021295315.1	2742685	2742685	type	True	77.2641	50	1192	95	below_threshold
Photobacterium phosphoreum	strain=ATCC 11040	GCA_000949955.1	659	659	type	True	76.6733	60	1192	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:25,045] [INFO] DFAST Taxonomy check result was written to GCF_015209785.1_ASM1520978v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:25,046] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:25,046] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:25,046] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg374e5b9e-a55a-4688-8160-71090563ec33/dqc_reference/checkm_data
[2024-01-24 12:15:25,047] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:25,083] [INFO] Task started: CheckM
[2024-01-24 12:15:25,083] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015209785.1_ASM1520978v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015209785.1_ASM1520978v1_genomic.fna/checkm_input GCF_015209785.1_ASM1520978v1_genomic.fna/checkm_result
[2024-01-24 12:15:53,747] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:53,748] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:53,768] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:53,768] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:53,769] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015209785.1_ASM1520978v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:53,769] [INFO] Task started: Blastn
[2024-01-24 12:15:53,769] [INFO] Running command: blastn -query GCF_015209785.1_ASM1520978v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg374e5b9e-a55a-4688-8160-71090563ec33/dqc_reference/reference_markers_gtdb.fasta -out GCF_015209785.1_ASM1520978v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:54,891] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:54,896] [INFO] Selected 10 target genomes.
[2024-01-24 12:15:54,896] [INFO] Target genome list was writen to GCF_015209785.1_ASM1520978v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:54,904] [INFO] Task started: fastANI
[2024-01-24 12:15:54,904] [INFO] Running command: fastANI --query /var/lib/cwl/stg669c145f-9c9f-43f7-96ec-33f21def1c3d/GCF_015209785.1_ASM1520978v1_genomic.fna.gz --refList GCF_015209785.1_ASM1520978v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015209785.1_ASM1520978v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:04,643] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:04,655] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:04,655] [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_001550155.1	s__Pseudoalteromonas arabiensis	99.0949	1102	1192	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.77	95.60	0.91	0.90	4	conclusive
GCF_019134595.1	s__Pseudoalteromonas shioyasakiensis_A	86.9614	880	1192	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.6918	N/A	N/A	N/A	N/A	1	-
GCF_001469895.1	s__Pseudoalteromonas sp001469895	86.7992	868	1192	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.7314	N/A	N/A	N/A	N/A	1	-
GCF_013349995.1	s__Pseudoalteromonas sp013349995	86.7387	832	1192	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.6093	97.46	97.37	0.85	0.84	6	-
GCF_001550135.1	s__Pseudoalteromonas shioyasakiensis	86.7051	878	1192	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	97.0029	98.58	98.56	0.94	0.92	4	-
GCF_001641615.1	s__Pseudoalteromonas gelatinilytica	86.6627	862	1192	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.27	97.45	0.92	0.88	6	-
GCF_001306915.1	s__Pseudoalteromonas lipolytica_A	86.5668	872	1192	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.22	97.66	0.91	0.90	9	-
GCF_013391845.1	s__Pseudoalteromonas sp002685175	86.5264	889	1192	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.05	98.96	0.91	0.83	5	-
GCF_004792295.1	s__Pseudoalteromonas lipolytica_C	86.0591	878	1192	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.42	98.24	0.87	0.68	9	-
GCF_900116435.1	s__Pseudoalteromonas lipolytica	83.7008	810	1192	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.07	98.83	0.92	0.86	12	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:04,657] [INFO] GTDB search result was written to GCF_015209785.1_ASM1520978v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:04,658] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:04,662] [INFO] DFAST_QC result json was written to GCF_015209785.1_ASM1520978v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:04,662] [INFO] DFAST_QC completed!
[2024-01-24 12:16:04,662] [INFO] Total running time: 0h1m1s