[2024-01-24 13:58:42,150] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:42,155] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:42,155] [INFO] DQC Reference Directory: /var/lib/cwl/stgafd84550-2f58-4b40-828c-24d8f53831f4/dqc_reference
[2024-01-24 13:58:43,486] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:43,488] [INFO] Task started: Prodigal
[2024-01-24 13:58:43,488] [INFO] Running command: gunzip -c /var/lib/cwl/stgefb532d0-8a71-4159-816a-ffc53390d403/GCF_007991255.1_ASM799125v1_genomic.fna.gz | prodigal -d GCF_007991255.1_ASM799125v1_genomic.fna/cds.fna -a GCF_007991255.1_ASM799125v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:51,175] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:51,175] [INFO] Task started: HMMsearch
[2024-01-24 13:58:51,175] [INFO] Running command: hmmsearch --tblout GCF_007991255.1_ASM799125v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgafd84550-2f58-4b40-828c-24d8f53831f4/dqc_reference/reference_markers.hmm GCF_007991255.1_ASM799125v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:51,477] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:51,478] [INFO] Found 6/6 markers.
[2024-01-24 13:58:51,516] [INFO] Query marker FASTA was written to GCF_007991255.1_ASM799125v1_genomic.fna/markers.fasta
[2024-01-24 13:58:51,516] [INFO] Task started: Blastn
[2024-01-24 13:58:51,516] [INFO] Running command: blastn -query GCF_007991255.1_ASM799125v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgafd84550-2f58-4b40-828c-24d8f53831f4/dqc_reference/reference_markers.fasta -out GCF_007991255.1_ASM799125v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:52,250] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:52,254] [INFO] Selected 12 target genomes.
[2024-01-24 13:58:52,255] [INFO] Target genome list was writen to GCF_007991255.1_ASM799125v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:52,262] [INFO] Task started: fastANI
[2024-01-24 13:58:52,262] [INFO] Running command: fastANI --query /var/lib/cwl/stgefb532d0-8a71-4159-816a-ffc53390d403/GCF_007991255.1_ASM799125v1_genomic.fna.gz --refList GCF_007991255.1_ASM799125v1_genomic.fna/target_genomes.txt --output GCF_007991255.1_ASM799125v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:03,202] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:03,203] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgafd84550-2f58-4b40-828c-24d8f53831f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:03,203] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgafd84550-2f58-4b40-828c-24d8f53831f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:03,215] [INFO] Found 11 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:59:03,215] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:59:03,216] [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 nigrifaciens	strain=NBRC 103036	GCA_007991255.1	28109	28109	type	True	100.0	1303	1306	95	inconclusive
Pseudoalteromonas nigrifaciens	strain=KMM 661	GCA_002221505.1	28109	28109	type	True	99.9935	1303	1306	95	inconclusive
Pseudoalteromonas nigrifaciens	strain=NCTC10691	GCA_900455185.1	28109	28109	type	True	99.9852	1304	1306	95	inconclusive
Pseudoalteromonas translucida	strain=KMM 520	GCA_001465295.1	166935	166935	type	True	96.0603	1137	1306	95	inconclusive
Pseudoalteromonas arctica	strain=A 37-1-2	GCA_000238395.4	394751	394751	type	True	83.2408	880	1306	95	below_threshold
Pseudoalteromonas fuliginea	strain=KMM 216	GCA_000690055.1	1872678	1872678	type	True	82.8544	802	1306	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	82.734	831	1306	95	below_threshold
Pseudoalteromonas tetraodonis	strain=GFC	GCA_002310835.1	43659	43659	suspected-type	True	81.7528	770	1306	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	80.4281	629	1306	95	below_threshold
Motilimonas cestriensis	strain=MKS20	GCA_021295315.1	2742685	2742685	type	True	76.7048	58	1306	95	below_threshold
Shewanella marinintestina	strain=LMG 21403	GCA_023283845.1	190305	190305	type	True	76.1389	57	1306	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:03,217] [INFO] DFAST Taxonomy check result was written to GCF_007991255.1_ASM799125v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:03,218] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:03,218] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:03,218] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgafd84550-2f58-4b40-828c-24d8f53831f4/dqc_reference/checkm_data
[2024-01-24 13:59:03,219] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:03,260] [INFO] Task started: CheckM
[2024-01-24 13:59:03,260] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007991255.1_ASM799125v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007991255.1_ASM799125v1_genomic.fna/checkm_input GCF_007991255.1_ASM799125v1_genomic.fna/checkm_result
[2024-01-24 13:59:30,685] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:30,687] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:30,703] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:30,703] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:30,704] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007991255.1_ASM799125v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:30,704] [INFO] Task started: Blastn
[2024-01-24 13:59:30,704] [INFO] Running command: blastn -query GCF_007991255.1_ASM799125v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgafd84550-2f58-4b40-828c-24d8f53831f4/dqc_reference/reference_markers_gtdb.fasta -out GCF_007991255.1_ASM799125v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:31,768] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:31,772] [INFO] Selected 10 target genomes.
[2024-01-24 13:59:31,772] [INFO] Target genome list was writen to GCF_007991255.1_ASM799125v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:31,777] [INFO] Task started: fastANI
[2024-01-24 13:59:31,777] [INFO] Running command: fastANI --query /var/lib/cwl/stgefb532d0-8a71-4159-816a-ffc53390d403/GCF_007991255.1_ASM799125v1_genomic.fna.gz --refList GCF_007991255.1_ASM799125v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007991255.1_ASM799125v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:41,506] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:41,521] [INFO] Found 10 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 13:59:41,521] [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_002221505.1	s__Pseudoalteromonas nigrifaciens	99.9935	1303	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.0242	98.65	98.00	0.90	0.81	15	inconclusive
GCF_001465295.1	s__Pseudoalteromonas translucida	96.0603	1137	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.0242	N/A	N/A	N/A	N/A	1	inconclusive
GCF_000238395.3	s__Pseudoalteromonas arctica	83.2486	878	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.91	96.03	0.87	0.80	33	-
GCF_011378855.1	s__Pseudoalteromonas sp011378855	82.8905	841	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.10	97.06	0.91	0.90	3	-
GCF_000690055.1	s__Pseudoalteromonas fuliginea	82.869	801	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.33	97.88	0.92	0.87	9	-
GCA_000814675.1	s__Pseudoalteromonas distincta	82.7302	832	1306	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	82.6587	831	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.73	97.18	0.90	0.86	5	-
GCF_008370255.1	s__Pseudoalteromonas sp008370255	82.5879	832	1306	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	82.499	794	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.86	97.76	0.88	0.87	3	-
GCA_011050055.1	s__Pseudoalteromonas prydzensis_A	80.0864	538	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:41,523] [INFO] GTDB search result was written to GCF_007991255.1_ASM799125v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:41,523] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:41,526] [INFO] DFAST_QC result json was written to GCF_007991255.1_ASM799125v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:41,526] [INFO] DFAST_QC completed!
[2024-01-24 13:59:41,526] [INFO] Total running time: 0h0m59s