[2024-01-24 15:27:07,899] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:07,901] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:07,901] [INFO] DQC Reference Directory: /var/lib/cwl/stg50b8c721-1949-458e-b6e9-a4b7cfe3abd1/dqc_reference
[2024-01-24 15:27:09,321] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:09,322] [INFO] Task started: Prodigal
[2024-01-24 15:27:09,322] [INFO] Running command: gunzip -c /var/lib/cwl/stg41498c85-02b7-45dd-a3f2-1db600d8b5ff/GCF_900142175.1_IMG-taxon_2622736581_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900142175.1_IMG-taxon_2622736581_annotated_assembly_genomic.fna/cds.fna -a GCF_900142175.1_IMG-taxon_2622736581_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:25,297] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:25,298] [INFO] Task started: HMMsearch
[2024-01-24 15:27:25,298] [INFO] Running command: hmmsearch --tblout GCF_900142175.1_IMG-taxon_2622736581_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50b8c721-1949-458e-b6e9-a4b7cfe3abd1/dqc_reference/reference_markers.hmm GCF_900142175.1_IMG-taxon_2622736581_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:25,661] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:25,663] [INFO] Found 6/6 markers.
[2024-01-24 15:27:25,709] [INFO] Query marker FASTA was written to GCF_900142175.1_IMG-taxon_2622736581_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 15:27:25,709] [INFO] Task started: Blastn
[2024-01-24 15:27:25,709] [INFO] Running command: blastn -query GCF_900142175.1_IMG-taxon_2622736581_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg50b8c721-1949-458e-b6e9-a4b7cfe3abd1/dqc_reference/reference_markers.fasta -out GCF_900142175.1_IMG-taxon_2622736581_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:26,522] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:26,526] [INFO] Selected 11 target genomes.
[2024-01-24 15:27:26,526] [INFO] Target genome list was writen to GCF_900142175.1_IMG-taxon_2622736581_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 15:27:26,539] [INFO] Task started: fastANI
[2024-01-24 15:27:26,539] [INFO] Running command: fastANI --query /var/lib/cwl/stg41498c85-02b7-45dd-a3f2-1db600d8b5ff/GCF_900142175.1_IMG-taxon_2622736581_annotated_assembly_genomic.fna.gz --refList GCF_900142175.1_IMG-taxon_2622736581_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900142175.1_IMG-taxon_2622736581_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:36,488] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:36,489] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50b8c721-1949-458e-b6e9-a4b7cfe3abd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:36,489] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50b8c721-1949-458e-b6e9-a4b7cfe3abd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:36,499] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:36,499] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:36,500] [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
Maribacter aquivivus	strain=DSM 16478	GCA_900142175.1	228958	228958	type	True	100.0	1520	1521	95	conclusive
Maribacter caenipelagi	strain=CECT 8455	GCA_004364175.1	1447781	1447781	type	True	87.4537	1132	1521	95	below_threshold
Maribacter spongiicola	strain=DSM 25233	GCA_004364165.1	1206753	1206753	type	True	87.3418	1192	1521	95	below_threshold
Maribacter stanieri	strain=DSM 19891	GCA_900112245.1	440514	440514	type	True	86.3823	1123	1521	95	below_threshold
Maribacter forsetii	strain=DSM 18668	GCA_000744105.1	444515	444515	type	True	85.1101	1117	1521	95	below_threshold
Maribacter ulvicola	strain=DSM 15366	GCA_900155985.1	228959	228959	type	True	83.259	993	1521	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	76.1864	126	1521	95	below_threshold
Poritiphilus flavus	strain=R33	GCA_009901585.1	2697053	2697053	type	True	76.0902	57	1521	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	75.8571	74	1521	95	below_threshold
Salegentibacter lacus	strain=LM13S	GCA_020164555.1	2873599	2873599	type	True	75.8436	76	1521	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:36,502] [INFO] DFAST Taxonomy check result was written to GCF_900142175.1_IMG-taxon_2622736581_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 15:27:36,503] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:36,503] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:36,504] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50b8c721-1949-458e-b6e9-a4b7cfe3abd1/dqc_reference/checkm_data
[2024-01-24 15:27:36,505] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:36,555] [INFO] Task started: CheckM
[2024-01-24 15:27:36,556] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900142175.1_IMG-taxon_2622736581_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900142175.1_IMG-taxon_2622736581_annotated_assembly_genomic.fna/checkm_input GCF_900142175.1_IMG-taxon_2622736581_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 15:28:23,272] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:23,273] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:23,292] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:23,293] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:23,293] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900142175.1_IMG-taxon_2622736581_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 15:28:23,294] [INFO] Task started: Blastn
[2024-01-24 15:28:23,294] [INFO] Running command: blastn -query GCF_900142175.1_IMG-taxon_2622736581_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg50b8c721-1949-458e-b6e9-a4b7cfe3abd1/dqc_reference/reference_markers_gtdb.fasta -out GCF_900142175.1_IMG-taxon_2622736581_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:24,242] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:24,247] [INFO] Selected 7 target genomes.
[2024-01-24 15:28:24,247] [INFO] Target genome list was writen to GCF_900142175.1_IMG-taxon_2622736581_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:24,256] [INFO] Task started: fastANI
[2024-01-24 15:28:24,256] [INFO] Running command: fastANI --query /var/lib/cwl/stg41498c85-02b7-45dd-a3f2-1db600d8b5ff/GCF_900142175.1_IMG-taxon_2622736581_annotated_assembly_genomic.fna.gz --refList GCF_900142175.1_IMG-taxon_2622736581_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900142175.1_IMG-taxon_2622736581_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:32,098] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:32,112] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:32,112] [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_900142175.1	s__Maribacter aquivivus	100.0	1520	1521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004364175.1	s__Maribacter caenipelagi	87.4651	1131	1521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364165.1	s__Maribacter spongiicola	87.3418	1192	1521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112245.1	s__Maribacter stanieri	86.3719	1124	1521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	98.09	98.09	0.92	0.92	2	-
GCF_000744105.1	s__Maribacter forsetii	85.0832	1120	1521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050675.1	s__Maribacter sp011050675	84.2353	1021	1521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900155985.1	s__Maribacter ulvicola	83.268	992	1521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:32,114] [INFO] GTDB search result was written to GCF_900142175.1_IMG-taxon_2622736581_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:32,115] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:32,118] [INFO] DFAST_QC result json was written to GCF_900142175.1_IMG-taxon_2622736581_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 15:28:32,118] [INFO] DFAST_QC completed!
[2024-01-24 15:28:32,118] [INFO] Total running time: 0h1m24s