[2024-01-24 15:02:46,687] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:46,689] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:46,689] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd11ebc4-720e-4362-ba51-0511aecbf446/dqc_reference
[2024-01-24 15:02:48,008] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:48,008] [INFO] Task started: Prodigal
[2024-01-24 15:02:48,009] [INFO] Running command: gunzip -c /var/lib/cwl/stg1dc8ebe6-cd01-4836-82d0-cdb9e8c3cdfd/GCF_014905615.1_ASM1490561v1_genomic.fna.gz | prodigal -d GCF_014905615.1_ASM1490561v1_genomic.fna/cds.fna -a GCF_014905615.1_ASM1490561v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:57,282] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:57,283] [INFO] Task started: HMMsearch
[2024-01-24 15:02:57,283] [INFO] Running command: hmmsearch --tblout GCF_014905615.1_ASM1490561v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd11ebc4-720e-4362-ba51-0511aecbf446/dqc_reference/reference_markers.hmm GCF_014905615.1_ASM1490561v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:57,648] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:57,650] [INFO] Found 6/6 markers.
[2024-01-24 15:02:57,708] [INFO] Query marker FASTA was written to GCF_014905615.1_ASM1490561v1_genomic.fna/markers.fasta
[2024-01-24 15:02:57,709] [INFO] Task started: Blastn
[2024-01-24 15:02:57,709] [INFO] Running command: blastn -query GCF_014905615.1_ASM1490561v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd11ebc4-720e-4362-ba51-0511aecbf446/dqc_reference/reference_markers.fasta -out GCF_014905615.1_ASM1490561v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:58,545] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:58,549] [INFO] Selected 16 target genomes.
[2024-01-24 15:02:58,550] [INFO] Target genome list was writen to GCF_014905615.1_ASM1490561v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:58,556] [INFO] Task started: fastANI
[2024-01-24 15:02:58,556] [INFO] Running command: fastANI --query /var/lib/cwl/stg1dc8ebe6-cd01-4836-82d0-cdb9e8c3cdfd/GCF_014905615.1_ASM1490561v1_genomic.fna.gz --refList GCF_014905615.1_ASM1490561v1_genomic.fna/target_genomes.txt --output GCF_014905615.1_ASM1490561v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:19,151] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:19,152] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd11ebc4-720e-4362-ba51-0511aecbf446/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:19,152] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd11ebc4-720e-4362-ba51-0511aecbf446/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:19,164] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:03:19,164] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:19,165] [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 aliena	strain=SW19	GCA_014905615.1	247523	247523	type	True	100.0	1484	1485	95	conclusive
Pseudoalteromonas fuliginea	strain=KMM 216	GCA_000690055.1	1872678	1872678	type	True	88.0488	1036	1485	95	below_threshold
Pseudoalteromonas arctica	strain=A 37-1-2	GCA_000238395.4	394751	394751	type	True	87.5906	997	1485	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	87.1815	1011	1485	95	below_threshold
Pseudoalteromonas carrageenovora	strain=NBRC 12985	GCA_006539245.1	227	227	type	True	83.2929	872	1485	95	below_threshold
Pseudoalteromonas nigrifaciens	strain=NCTC10691	GCA_900455185.1	28109	28109	type	True	82.5306	787	1485	95	below_threshold
Pseudoalteromonas nigrifaciens	strain=KMM 661	GCA_002221505.1	28109	28109	type	True	82.4444	799	1485	95	below_threshold
Pseudoalteromonas translucida	strain=KMM 520	GCA_001465295.1	166935	166935	type	True	82.4199	803	1485	95	below_threshold
Pseudoalteromonas nigrifaciens	strain=NBRC 103036	GCA_007991255.1	28109	28109	type	True	82.3132	759	1485	95	below_threshold
Pseudoalteromonas issachenkonii	strain=KMM 3549	GCA_002310795.1	152297	152297	suspected-type	True	81.3972	774	1485	95	below_threshold
Pseudoalteromonas tetraodonis	strain=GFC	GCA_002310835.1	43659	43659	suspected-type	True	81.3682	795	1485	95	below_threshold
Pseudoalteromonas tetraodonis	strain=NBRC 103034	GCA_007991235.1	43659	43659	suspected-type	True	81.1381	779	1485	95	below_threshold
Photobacterium swingsii	strain=CECT 7576	GCA_024346715.1	680026	680026	type	True	77.5658	73	1485	95	below_threshold
Vibrio crassostreae	strain=LMG 22240	GCA_024347415.1	246167	246167	type	True	77.5617	55	1485	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:19,167] [INFO] DFAST Taxonomy check result was written to GCF_014905615.1_ASM1490561v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:19,167] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:19,168] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:19,168] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd11ebc4-720e-4362-ba51-0511aecbf446/dqc_reference/checkm_data
[2024-01-24 15:03:19,169] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:19,218] [INFO] Task started: CheckM
[2024-01-24 15:03:19,218] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014905615.1_ASM1490561v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014905615.1_ASM1490561v1_genomic.fna/checkm_input GCF_014905615.1_ASM1490561v1_genomic.fna/checkm_result
[2024-01-24 15:03:51,362] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:51,364] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:51,380] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:51,380] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:51,381] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014905615.1_ASM1490561v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:51,381] [INFO] Task started: Blastn
[2024-01-24 15:03:51,381] [INFO] Running command: blastn -query GCF_014905615.1_ASM1490561v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd11ebc4-720e-4362-ba51-0511aecbf446/dqc_reference/reference_markers_gtdb.fasta -out GCF_014905615.1_ASM1490561v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:52,514] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:52,518] [INFO] Selected 10 target genomes.
[2024-01-24 15:03:52,518] [INFO] Target genome list was writen to GCF_014905615.1_ASM1490561v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:52,526] [INFO] Task started: fastANI
[2024-01-24 15:03:52,526] [INFO] Running command: fastANI --query /var/lib/cwl/stg1dc8ebe6-cd01-4836-82d0-cdb9e8c3cdfd/GCF_014905615.1_ASM1490561v1_genomic.fna.gz --refList GCF_014905615.1_ASM1490561v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014905615.1_ASM1490561v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:10,540] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:10,556] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:10,557] [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_014905615.1	s__Pseudoalteromonas aliena	100.0	1484	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.51	97.10	0.91	0.88	7	conclusive
GCF_000690055.1	s__Pseudoalteromonas fuliginea	88.0276	1039	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.33	97.88	0.92	0.87	9	-
GCF_000238395.3	s__Pseudoalteromonas arctica	87.5649	1002	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.91	96.03	0.87	0.80	33	-
GCA_000814675.1	s__Pseudoalteromonas distincta	87.1963	1010	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	95.34	0.88	0.77	38	-
GCF_001974875.1	s__Pseudoalteromonas sp001974875	87.129	1006	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.73	97.18	0.90	0.86	5	-
GCF_011378855.1	s__Pseudoalteromonas sp011378855	86.9547	956	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.10	97.06	0.91	0.90	3	-
GCF_000239855.1	s__Pseudoalteromonas sp000239855	86.6227	927	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000498095.1	s__Pseudoalteromonas sp000498095	85.8231	952	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.86	97.76	0.88	0.87	3	-
GCF_004328665.1	s__Pseudoalteromonas sp001974855	81.3771	749	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.16	95.35	0.86	0.83	5	-
GCF_002310835.1	s__Pseudoalteromonas tetraodonis	81.3708	797	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.76	96.28	0.91	0.84	28	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:10,561] [INFO] GTDB search result was written to GCF_014905615.1_ASM1490561v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:10,562] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:10,566] [INFO] DFAST_QC result json was written to GCF_014905615.1_ASM1490561v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:10,566] [INFO] DFAST_QC completed!
[2024-01-24 15:04:10,566] [INFO] Total running time: 0h1m24s