[2024-01-24 11:22:49,179] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:22:49,180] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:22:49,181] [INFO] DQC Reference Directory: /var/lib/cwl/stg240096a5-b2f0-47df-9801-1098fe65dd99/dqc_reference
[2024-01-24 11:22:50,415] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:22:50,416] [INFO] Task started: Prodigal
[2024-01-24 11:22:50,416] [INFO] Running command: gunzip -c /var/lib/cwl/stgc25a31a9-52b0-4f4e-b821-903a18246414/GCF_015356755.1_ASM1535675v1_genomic.fna.gz | prodigal -d GCF_015356755.1_ASM1535675v1_genomic.fna/cds.fna -a GCF_015356755.1_ASM1535675v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:23:03,054] [INFO] Task succeeded: Prodigal
[2024-01-24 11:23:03,055] [INFO] Task started: HMMsearch
[2024-01-24 11:23:03,055] [INFO] Running command: hmmsearch --tblout GCF_015356755.1_ASM1535675v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg240096a5-b2f0-47df-9801-1098fe65dd99/dqc_reference/reference_markers.hmm GCF_015356755.1_ASM1535675v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:23:03,300] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:23:03,302] [INFO] Found 6/6 markers.
[2024-01-24 11:23:03,332] [INFO] Query marker FASTA was written to GCF_015356755.1_ASM1535675v1_genomic.fna/markers.fasta
[2024-01-24 11:23:03,333] [INFO] Task started: Blastn
[2024-01-24 11:23:03,333] [INFO] Running command: blastn -query GCF_015356755.1_ASM1535675v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg240096a5-b2f0-47df-9801-1098fe65dd99/dqc_reference/reference_markers.fasta -out GCF_015356755.1_ASM1535675v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:23:03,966] [INFO] Task succeeded: Blastn
[2024-01-24 11:23:03,970] [INFO] Selected 19 target genomes.
[2024-01-24 11:23:03,971] [INFO] Target genome list was writen to GCF_015356755.1_ASM1535675v1_genomic.fna/target_genomes.txt
[2024-01-24 11:23:03,978] [INFO] Task started: fastANI
[2024-01-24 11:23:03,979] [INFO] Running command: fastANI --query /var/lib/cwl/stgc25a31a9-52b0-4f4e-b821-903a18246414/GCF_015356755.1_ASM1535675v1_genomic.fna.gz --refList GCF_015356755.1_ASM1535675v1_genomic.fna/target_genomes.txt --output GCF_015356755.1_ASM1535675v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:23:15,889] [INFO] Task succeeded: fastANI
[2024-01-24 11:23:15,889] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg240096a5-b2f0-47df-9801-1098fe65dd99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:23:15,890] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg240096a5-b2f0-47df-9801-1098fe65dd99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:23:15,898] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:23:15,898] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:23:15,898] [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
Nonlabens antarcticus	strain=JCM 14068	GCA_015356755.1	392714	392714	type	True	100.0	1076	1076	95	conclusive
Leeuwenhoekiella marinoflava	strain=DSM 3653	GCA_900129005.1	988	988	type	True	81.2375	72	1076	95	below_threshold
Nonlabens marinus	strain=S1-08	GCA_000831385.1	930802	930802	type	True	78.7621	412	1076	95	below_threshold
Nonlabens agnitus	strain=JCM 17109	GCA_002994045.1	870484	870484	type	True	78.3941	324	1076	95	below_threshold
Nonlabens spongiae	strain=JCM 13191	GCA_002117125.1	331648	331648	type	True	77.8244	143	1076	95	below_threshold
Nonlabens ponticola	strain=MJ115	GCA_003966335.1	2496866	2496866	type	True	77.5397	215	1076	95	below_threshold
Nonlabens xiamenensis	strain=1Q3	GCA_003865345.1	2341043	2341043	type	True	77.3049	83	1076	95	below_threshold
Nonlabens dokdonensis	strain=DSW-6	GCA_000332115.1	328515	328515	type	True	77.0514	175	1076	95	below_threshold
Nonlabens dokdonensis	strain=DSM 17205	GCA_003254015.1	328515	328515	type	True	77.0225	174	1076	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:23:15,900] [INFO] DFAST Taxonomy check result was written to GCF_015356755.1_ASM1535675v1_genomic.fna/tc_result.tsv
[2024-01-24 11:23:15,900] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:23:15,901] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:23:15,901] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg240096a5-b2f0-47df-9801-1098fe65dd99/dqc_reference/checkm_data
[2024-01-24 11:23:15,902] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:23:15,934] [INFO] Task started: CheckM
[2024-01-24 11:23:15,934] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015356755.1_ASM1535675v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015356755.1_ASM1535675v1_genomic.fna/checkm_input GCF_015356755.1_ASM1535675v1_genomic.fna/checkm_result
[2024-01-24 11:23:56,226] [INFO] Task succeeded: CheckM
[2024-01-24 11:23:56,228] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:23:56,247] [INFO] ===== Completeness check finished =====
[2024-01-24 11:23:56,247] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:23:56,247] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015356755.1_ASM1535675v1_genomic.fna/markers.fasta)
[2024-01-24 11:23:56,248] [INFO] Task started: Blastn
[2024-01-24 11:23:56,248] [INFO] Running command: blastn -query GCF_015356755.1_ASM1535675v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg240096a5-b2f0-47df-9801-1098fe65dd99/dqc_reference/reference_markers_gtdb.fasta -out GCF_015356755.1_ASM1535675v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:23:57,058] [INFO] Task succeeded: Blastn
[2024-01-24 11:23:57,062] [INFO] Selected 13 target genomes.
[2024-01-24 11:23:57,063] [INFO] Target genome list was writen to GCF_015356755.1_ASM1535675v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:23:57,074] [INFO] Task started: fastANI
[2024-01-24 11:23:57,074] [INFO] Running command: fastANI --query /var/lib/cwl/stgc25a31a9-52b0-4f4e-b821-903a18246414/GCF_015356755.1_ASM1535675v1_genomic.fna.gz --refList GCF_015356755.1_ASM1535675v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015356755.1_ASM1535675v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:24:04,767] [INFO] Task succeeded: fastANI
[2024-01-24 11:24:04,776] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:24:04,777] [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_015356755.1	s__Nonlabens antarcticus	100.0	1076	1076	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000831385.1	s__Nonlabens marinus	78.7621	412	1076	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002994045.1	s__Nonlabens agnitus	78.3941	324	1076	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001413925.1	s__Nonlabens sp001413925	78.1816	323	1076	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101765.1	s__Nonlabens sp900101765	78.0205	323	1076	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002117125.1	s__Nonlabens spongiae	77.8475	142	1076	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966335.1	s__Nonlabens ponticola	77.5397	215	1076	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934445.1	s__Nonlabens xylanidelens	77.5033	148	1076	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	99.99	99.99	1.00	1.00	2	-
GCF_012974865.1	s__Nonlabens sp012974865	77.3066	154	1076	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002831625.1	s__Nonlabens sp002831625	77.2148	159	1076	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:24:04,778] [INFO] GTDB search result was written to GCF_015356755.1_ASM1535675v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:24:04,779] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:24:04,782] [INFO] DFAST_QC result json was written to GCF_015356755.1_ASM1535675v1_genomic.fna/dqc_result.json
[2024-01-24 11:24:04,782] [INFO] DFAST_QC completed!
[2024-01-24 11:24:04,782] [INFO] Total running time: 0h1m16s