[2023-06-17 14:48:59,061] [INFO] DFAST_QC pipeline started.
[2023-06-17 14:48:59,063] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 14:48:59,064] [INFO] DQC Reference Directory: /var/lib/cwl/stg419609b9-5274-4c06-8c9a-5fee9d0ebf7b/dqc_reference
[2023-06-17 14:49:00,380] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 14:49:00,381] [INFO] Task started: Prodigal
[2023-06-17 14:49:00,381] [INFO] Running command: gunzip -c /var/lib/cwl/stg94eaef48-3b19-4429-a0d6-7dfd1673e93b/GCA_905182295.1_FRAM18_bin216_genomic.fna.gz | prodigal -d GCA_905182295.1_FRAM18_bin216_genomic.fna/cds.fna -a GCA_905182295.1_FRAM18_bin216_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 14:49:05,861] [INFO] Task succeeded: Prodigal
[2023-06-17 14:49:05,861] [INFO] Task started: HMMsearch
[2023-06-17 14:49:05,861] [INFO] Running command: hmmsearch --tblout GCA_905182295.1_FRAM18_bin216_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg419609b9-5274-4c06-8c9a-5fee9d0ebf7b/dqc_reference/reference_markers.hmm GCA_905182295.1_FRAM18_bin216_genomic.fna/protein.faa > /dev/null
[2023-06-17 14:49:06,074] [INFO] Task succeeded: HMMsearch
[2023-06-17 14:49:06,075] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg94eaef48-3b19-4429-a0d6-7dfd1673e93b/GCA_905182295.1_FRAM18_bin216_genomic.fna.gz]
[2023-06-17 14:49:06,096] [INFO] Query marker FASTA was written to GCA_905182295.1_FRAM18_bin216_genomic.fna/markers.fasta
[2023-06-17 14:49:06,096] [INFO] Task started: Blastn
[2023-06-17 14:49:06,096] [INFO] Running command: blastn -query GCA_905182295.1_FRAM18_bin216_genomic.fna/markers.fasta -db /var/lib/cwl/stg419609b9-5274-4c06-8c9a-5fee9d0ebf7b/dqc_reference/reference_markers.fasta -out GCA_905182295.1_FRAM18_bin216_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 14:49:06,799] [INFO] Task succeeded: Blastn
[2023-06-17 14:49:06,803] [INFO] Selected 18 target genomes.
[2023-06-17 14:49:06,804] [INFO] Target genome list was writen to GCA_905182295.1_FRAM18_bin216_genomic.fna/target_genomes.txt
[2023-06-17 14:49:06,811] [INFO] Task started: fastANI
[2023-06-17 14:49:06,811] [INFO] Running command: fastANI --query /var/lib/cwl/stg94eaef48-3b19-4429-a0d6-7dfd1673e93b/GCA_905182295.1_FRAM18_bin216_genomic.fna.gz --refList GCA_905182295.1_FRAM18_bin216_genomic.fna/target_genomes.txt --output GCA_905182295.1_FRAM18_bin216_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 14:49:19,383] [INFO] Task succeeded: fastANI
[2023-06-17 14:49:19,383] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg419609b9-5274-4c06-8c9a-5fee9d0ebf7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 14:49:19,384] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg419609b9-5274-4c06-8c9a-5fee9d0ebf7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 14:49:19,398] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 14:49:19,398] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 14:49:19,398] [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
Cellulophaga lytica	strain=DSM 7489	GCA_000190595.1	979	979	type	True	76.9948	63	449	95	below_threshold
Maribacter vaceletii	strain=DSM 25230	GCA_003634105.1	1206816	1206816	type	True	76.9849	63	449	95	below_threshold
Cellulophaga omnivescoria	strain=W5C	GCA_001999725.1	1888890	1888890	type	True	76.8293	70	449	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001673755.1	1836467	1836467	type	True	76.804	62	449	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001913155.1	1836467	1836467	type	True	76.764	62	449	95	below_threshold
Cellulophaga algicola	strain=DSM 14237	GCA_000186265.1	59600	59600	type	True	76.5887	64	449	95	below_threshold
Cellulophaga baltica	strain=DSM 24729	GCA_900102165.1	76594	76594	type	True	76.5871	67	449	95	below_threshold
Maribacter dokdonensis	strain=DSW-8	GCA_001447995.1	320912	320912	type	True	76.0935	64	449	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 14:49:19,406] [INFO] DFAST Taxonomy check result was written to GCA_905182295.1_FRAM18_bin216_genomic.fna/tc_result.tsv
[2023-06-17 14:49:19,407] [INFO] ===== Taxonomy check completed =====
[2023-06-17 14:49:19,407] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 14:49:19,408] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg419609b9-5274-4c06-8c9a-5fee9d0ebf7b/dqc_reference/checkm_data
[2023-06-17 14:49:19,409] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 14:49:19,427] [INFO] Task started: CheckM
[2023-06-17 14:49:19,427] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905182295.1_FRAM18_bin216_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905182295.1_FRAM18_bin216_genomic.fna/checkm_input GCA_905182295.1_FRAM18_bin216_genomic.fna/checkm_result
[2023-06-17 14:49:42,289] [INFO] Task succeeded: CheckM
[2023-06-17 14:49:42,291] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 14:49:42,313] [INFO] ===== Completeness check finished =====
[2023-06-17 14:49:42,313] [INFO] ===== Start GTDB Search =====
[2023-06-17 14:49:42,314] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905182295.1_FRAM18_bin216_genomic.fna/markers.fasta)
[2023-06-17 14:49:42,314] [INFO] Task started: Blastn
[2023-06-17 14:49:42,314] [INFO] Running command: blastn -query GCA_905182295.1_FRAM18_bin216_genomic.fna/markers.fasta -db /var/lib/cwl/stg419609b9-5274-4c06-8c9a-5fee9d0ebf7b/dqc_reference/reference_markers_gtdb.fasta -out GCA_905182295.1_FRAM18_bin216_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 14:49:43,227] [INFO] Task succeeded: Blastn
[2023-06-17 14:49:43,232] [INFO] Selected 11 target genomes.
[2023-06-17 14:49:43,233] [INFO] Target genome list was writen to GCA_905182295.1_FRAM18_bin216_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 14:49:43,241] [INFO] Task started: fastANI
[2023-06-17 14:49:43,241] [INFO] Running command: fastANI --query /var/lib/cwl/stg94eaef48-3b19-4429-a0d6-7dfd1673e93b/GCA_905182295.1_FRAM18_bin216_genomic.fna.gz --refList GCA_905182295.1_FRAM18_bin216_genomic.fna/target_genomes_gtdb.txt --output GCA_905182295.1_FRAM18_bin216_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 14:49:49,548] [INFO] Task succeeded: fastANI
[2023-06-17 14:49:49,561] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 14:49:49,561] [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_905182295.1	s__MAG-120531 sp905182295	100.0	449	449	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-120531	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000173115.1	s__MAG-120531 sp000173115	91.3249	269	449	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-120531	95.0	99.02	98.72	0.73	0.67	33	-
GCA_018401115.1	s__MAG-120531 sp018401115	87.2486	411	449	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-120531	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018500065.1	s__MAG-120531 sp018500065	78.2699	153	449	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-120531	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000190595.1	s__Cellulophaga lytica	76.9948	63	449	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	99.01	98.71	0.94	0.93	6	-
GCF_003634105.1	s__Maribacter_B vaceletii	76.9849	63	449	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000186265.1	s__Cellulophaga algicola	76.6203	63	449	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	98.35	98.34	0.88	0.87	3	-
GCF_900102165.1	s__Cellulophaga baltica	76.5871	67	449	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	97.62	97.40	0.90	0.89	7	-
GCF_004364175.1	s__Maribacter caenipelagi	76.2088	66	449	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 14:49:49,563] [INFO] GTDB search result was written to GCA_905182295.1_FRAM18_bin216_genomic.fna/result_gtdb.tsv
[2023-06-17 14:49:49,564] [INFO] ===== GTDB Search completed =====
[2023-06-17 14:49:49,568] [INFO] DFAST_QC result json was written to GCA_905182295.1_FRAM18_bin216_genomic.fna/dqc_result.json
[2023-06-17 14:49:49,568] [INFO] DFAST_QC completed!
[2023-06-17 14:49:49,568] [INFO] Total running time: 0h0m51s