[2023-06-19 05:51:59,118] [INFO] DFAST_QC pipeline started.
[2023-06-19 05:51:59,120] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 05:51:59,120] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ebea0e4-8045-4a2b-885e-486a62103d0d/dqc_reference
[2023-06-19 05:52:00,381] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 05:52:00,381] [INFO] Task started: Prodigal
[2023-06-19 05:52:00,382] [INFO] Running command: gunzip -c /var/lib/cwl/stg89d526ba-16ef-43ff-a575-c4dbc95812d2/GCA_013042365.1_ASM1304236v1_genomic.fna.gz | prodigal -d GCA_013042365.1_ASM1304236v1_genomic.fna/cds.fna -a GCA_013042365.1_ASM1304236v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 05:52:10,364] [INFO] Task succeeded: Prodigal
[2023-06-19 05:52:10,365] [INFO] Task started: HMMsearch
[2023-06-19 05:52:10,365] [INFO] Running command: hmmsearch --tblout GCA_013042365.1_ASM1304236v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ebea0e4-8045-4a2b-885e-486a62103d0d/dqc_reference/reference_markers.hmm GCA_013042365.1_ASM1304236v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 05:52:10,569] [INFO] Task succeeded: HMMsearch
[2023-06-19 05:52:10,570] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg89d526ba-16ef-43ff-a575-c4dbc95812d2/GCA_013042365.1_ASM1304236v1_genomic.fna.gz]
[2023-06-19 05:52:10,594] [INFO] Query marker FASTA was written to GCA_013042365.1_ASM1304236v1_genomic.fna/markers.fasta
[2023-06-19 05:52:10,594] [INFO] Task started: Blastn
[2023-06-19 05:52:10,594] [INFO] Running command: blastn -query GCA_013042365.1_ASM1304236v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ebea0e4-8045-4a2b-885e-486a62103d0d/dqc_reference/reference_markers.fasta -out GCA_013042365.1_ASM1304236v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:52:11,204] [INFO] Task succeeded: Blastn
[2023-06-19 05:52:11,228] [INFO] Selected 20 target genomes.
[2023-06-19 05:52:11,228] [INFO] Target genome list was writen to GCA_013042365.1_ASM1304236v1_genomic.fna/target_genomes.txt
[2023-06-19 05:52:11,234] [INFO] Task started: fastANI
[2023-06-19 05:52:11,235] [INFO] Running command: fastANI --query /var/lib/cwl/stg89d526ba-16ef-43ff-a575-c4dbc95812d2/GCA_013042365.1_ASM1304236v1_genomic.fna.gz --refList GCA_013042365.1_ASM1304236v1_genomic.fna/target_genomes.txt --output GCA_013042365.1_ASM1304236v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 05:52:22,645] [INFO] Task succeeded: fastANI
[2023-06-19 05:52:22,646] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ebea0e4-8045-4a2b-885e-486a62103d0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 05:52:22,646] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ebea0e4-8045-4a2b-885e-486a62103d0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 05:52:22,658] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 05:52:22,658] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 05:52:22,658] [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
Muriicola soli	strain=MMS17-SY002	GCA_004139715.1	2507538	2507538	type	True	76.5886	61	576	95	below_threshold
Eudoraea adriatica	strain=DSM 19308	GCA_000382125.1	446681	446681	type	True	76.5579	65	576	95	below_threshold
Poritiphilus flavus	strain=R33	GCA_009901585.1	2697053	2697053	type	True	76.4466	73	576	95	below_threshold
Muriicola jejuensis	strain=KCTC 22299	GCA_010671595.1	504488	504488	type	True	76.2898	66	576	95	below_threshold
Muriicola marianensis	strain=CGMCC 1.12606	GCA_014638095.1	1324801	1324801	type	True	76.2183	71	576	95	below_threshold
Zeaxanthinibacter enoshimensis	strain=DSM 18435	GCA_004362865.1	392009	392009	type	True	76.1211	59	576	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 05:52:22,661] [INFO] DFAST Taxonomy check result was written to GCA_013042365.1_ASM1304236v1_genomic.fna/tc_result.tsv
[2023-06-19 05:52:22,662] [INFO] ===== Taxonomy check completed =====
[2023-06-19 05:52:22,662] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 05:52:22,662] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ebea0e4-8045-4a2b-885e-486a62103d0d/dqc_reference/checkm_data
[2023-06-19 05:52:22,663] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 05:52:22,693] [INFO] Task started: CheckM
[2023-06-19 05:52:22,693] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013042365.1_ASM1304236v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013042365.1_ASM1304236v1_genomic.fna/checkm_input GCA_013042365.1_ASM1304236v1_genomic.fna/checkm_result
[2023-06-19 05:52:56,247] [INFO] Task succeeded: CheckM
[2023-06-19 05:52:56,249] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.86%
Contamintation: 8.71%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-19 05:52:56,300] [INFO] ===== Completeness check finished =====
[2023-06-19 05:52:56,300] [INFO] ===== Start GTDB Search =====
[2023-06-19 05:52:56,301] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013042365.1_ASM1304236v1_genomic.fna/markers.fasta)
[2023-06-19 05:52:56,301] [INFO] Task started: Blastn
[2023-06-19 05:52:56,301] [INFO] Running command: blastn -query GCA_013042365.1_ASM1304236v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ebea0e4-8045-4a2b-885e-486a62103d0d/dqc_reference/reference_markers_gtdb.fasta -out GCA_013042365.1_ASM1304236v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:52:57,158] [INFO] Task succeeded: Blastn
[2023-06-19 05:52:57,164] [INFO] Selected 18 target genomes.
[2023-06-19 05:52:57,164] [INFO] Target genome list was writen to GCA_013042365.1_ASM1304236v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 05:52:57,175] [INFO] Task started: fastANI
[2023-06-19 05:52:57,175] [INFO] Running command: fastANI --query /var/lib/cwl/stg89d526ba-16ef-43ff-a575-c4dbc95812d2/GCA_013042365.1_ASM1304236v1_genomic.fna.gz --refList GCA_013042365.1_ASM1304236v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013042365.1_ASM1304236v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 05:53:09,095] [INFO] Task succeeded: fastANI
[2023-06-19 05:53:09,109] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 05:53:09,110] [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
GCA_013041785.1	s__Eudoraea sp013041785	95.6254	359	576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Eudoraea	95.0	97.28	95.79	0.83	0.71	4	conclusive
GCF_004139715.1	s__Muriicola sp004139715	76.5886	61	576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382125.1	s__Eudoraea adriatica	76.5579	65	576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Eudoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009901585.1	s__R33 sp009901585	76.4466	73	576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__R33	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010671595.1	s__Muriicola jejuensis	76.2898	66	576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638095.1	s__Muriicola marianensis	76.2183	71	576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042315.1	s__Muriicola sp013042315	76.0827	61	576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	99.31	99.31	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2023-06-19 05:53:09,151] [INFO] GTDB search result was written to GCA_013042365.1_ASM1304236v1_genomic.fna/result_gtdb.tsv
[2023-06-19 05:53:09,152] [INFO] ===== GTDB Search completed =====
[2023-06-19 05:53:09,155] [INFO] DFAST_QC result json was written to GCA_013042365.1_ASM1304236v1_genomic.fna/dqc_result.json
[2023-06-19 05:53:09,155] [INFO] DFAST_QC completed!
[2023-06-19 05:53:09,156] [INFO] Total running time: 0h1m10s