[2024-01-24 13:46:44,049] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:44,051] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:44,051] [INFO] DQC Reference Directory: /var/lib/cwl/stg850e9bea-b7a2-4eab-98bc-388b25116927/dqc_reference
[2024-01-24 13:46:45,418] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:45,420] [INFO] Task started: Prodigal
[2024-01-24 13:46:45,421] [INFO] Running command: gunzip -c /var/lib/cwl/stg86bb5365-00c6-4f64-aa2f-21fe31bea559/GCF_000019185.1_ASM1918v1_genomic.fna.gz | prodigal -d GCF_000019185.1_ASM1918v1_genomic.fna/cds.fna -a GCF_000019185.1_ASM1918v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:56,968] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:56,968] [INFO] Task started: HMMsearch
[2024-01-24 13:46:56,968] [INFO] Running command: hmmsearch --tblout GCF_000019185.1_ASM1918v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg850e9bea-b7a2-4eab-98bc-388b25116927/dqc_reference/reference_markers.hmm GCF_000019185.1_ASM1918v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:57,278] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:57,279] [INFO] Found 6/6 markers.
[2024-01-24 13:46:57,323] [INFO] Query marker FASTA was written to GCF_000019185.1_ASM1918v1_genomic.fna/markers.fasta
[2024-01-24 13:46:57,323] [INFO] Task started: Blastn
[2024-01-24 13:46:57,324] [INFO] Running command: blastn -query GCF_000019185.1_ASM1918v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg850e9bea-b7a2-4eab-98bc-388b25116927/dqc_reference/reference_markers.fasta -out GCF_000019185.1_ASM1918v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:58,190] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:58,194] [INFO] Selected 10 target genomes.
[2024-01-24 13:46:58,194] [INFO] Target genome list was writen to GCF_000019185.1_ASM1918v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:58,203] [INFO] Task started: fastANI
[2024-01-24 13:46:58,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg86bb5365-00c6-4f64-aa2f-21fe31bea559/GCF_000019185.1_ASM1918v1_genomic.fna.gz --refList GCF_000019185.1_ASM1918v1_genomic.fna/target_genomes.txt --output GCF_000019185.1_ASM1918v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:10,039] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:10,039] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg850e9bea-b7a2-4eab-98bc-388b25116927/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:10,040] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg850e9bea-b7a2-4eab-98bc-388b25116927/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:10,048] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:10,048] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:10,049] [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
Shewanella halifaxensis	strain=HAW-EB4	GCA_000019185.1	271098	271098	type	True	100.0	1742	1742	95	conclusive
Shewanella schlegeliana	strain=LMG 21406	GCA_023283605.1	190308	190308	type	True	86.3445	1312	1742	95	below_threshold
Shewanella schlegeliana	strain=JCM 11561	GCA_019654995.1	190308	190308	type	True	86.3027	1315	1742	95	below_threshold
Shewanella schlegeliana	strain=JCM 11561	GCA_016765635.1	190308	190308	type	True	86.2561	1344	1742	95	below_threshold
Shewanella pealeana	strain=ATCC 700345	GCA_000018285.1	70864	70864	type	True	84.3361	1283	1742	95	below_threshold
Shewanella marinintestina	strain=LMG 21403	GCA_023283845.1	190305	190305	type	True	82.2421	949	1742	95	below_threshold
Shewanella sairae	strain=JCM 11563	GCA_019655015.1	190310	190310	type	True	82.1463	926	1742	95	below_threshold
Shewanella sairae	strain=LMG 21408	GCA_023283535.1	190310	190310	type	True	82.1144	933	1742	95	below_threshold
Shewanella kaireitica	strain=DSM 17170	GCA_023284045.1	212021	212021	type	True	80.1318	615	1742	95	below_threshold
Shewanella glacialipiscicola	strain=LMG 23744	GCA_023283485.1	614069	614069	type	True	77.8447	262	1742	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:10,050] [INFO] DFAST Taxonomy check result was written to GCF_000019185.1_ASM1918v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:10,051] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:10,051] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:10,051] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg850e9bea-b7a2-4eab-98bc-388b25116927/dqc_reference/checkm_data
[2024-01-24 13:47:10,052] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:10,100] [INFO] Task started: CheckM
[2024-01-24 13:47:10,100] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000019185.1_ASM1918v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000019185.1_ASM1918v1_genomic.fna/checkm_input GCF_000019185.1_ASM1918v1_genomic.fna/checkm_result
[2024-01-24 13:47:47,685] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:47,686] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:47,707] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:47,707] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:47,708] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000019185.1_ASM1918v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:47,708] [INFO] Task started: Blastn
[2024-01-24 13:47:47,708] [INFO] Running command: blastn -query GCF_000019185.1_ASM1918v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg850e9bea-b7a2-4eab-98bc-388b25116927/dqc_reference/reference_markers_gtdb.fasta -out GCF_000019185.1_ASM1918v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:48,935] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:48,939] [INFO] Selected 9 target genomes.
[2024-01-24 13:47:48,939] [INFO] Target genome list was writen to GCF_000019185.1_ASM1918v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:48,951] [INFO] Task started: fastANI
[2024-01-24 13:47:48,951] [INFO] Running command: fastANI --query /var/lib/cwl/stg86bb5365-00c6-4f64-aa2f-21fe31bea559/GCF_000019185.1_ASM1918v1_genomic.fna.gz --refList GCF_000019185.1_ASM1918v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000019185.1_ASM1918v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:59,730] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:59,738] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:59,739] [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_000019185.1	s__Shewanella halifaxensis	100.0	1742	1742	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016765635.1	s__Shewanella schlegeliana	86.2431	1345	1742	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000018285.1	s__Shewanella pealeana	84.3173	1282	1742	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518605.1	s__Shewanella fidelis	81.3212	869	1742	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.11	97.11	0.90	0.90	2	-
GCF_000014885.1	s__Shewanella piezotolerans	80.5039	630	1742	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016757755.1	s__Shewanella sp016757755	80.0672	683	1742	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836205.1	s__Shewanella sp002836205	79.8035	647	1742	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.46	99.13	0.96	0.92	4	-
GCF_003605125.1	s__Shewanella algidipiscicola	78.3014	371	1742	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.64	98.64	0.92	0.92	2	-
GCF_000614975.1	s__Shewanella marina	78.2125	230	1742	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:59,740] [INFO] GTDB search result was written to GCF_000019185.1_ASM1918v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:59,747] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:59,751] [INFO] DFAST_QC result json was written to GCF_000019185.1_ASM1918v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:59,751] [INFO] DFAST_QC completed!
[2024-01-24 13:47:59,752] [INFO] Total running time: 0h1m16s