[2024-01-24 12:47:12,215] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:12,217] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:12,218] [INFO] DQC Reference Directory: /var/lib/cwl/stgf8edb689-5e48-4560-9300-dc71e10a2b0d/dqc_reference
[2024-01-24 12:47:13,623] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:13,624] [INFO] Task started: Prodigal
[2024-01-24 12:47:13,625] [INFO] Running command: gunzip -c /var/lib/cwl/stgc98dd534-98ee-4656-a62d-8b03463535f4/GCF_021389955.1_ASM2138995v1_genomic.fna.gz | prodigal -d GCF_021389955.1_ASM2138995v1_genomic.fna/cds.fna -a GCF_021389955.1_ASM2138995v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:37,587] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:37,588] [INFO] Task started: HMMsearch
[2024-01-24 12:47:37,588] [INFO] Running command: hmmsearch --tblout GCF_021389955.1_ASM2138995v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf8edb689-5e48-4560-9300-dc71e10a2b0d/dqc_reference/reference_markers.hmm GCF_021389955.1_ASM2138995v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:37,919] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:37,920] [INFO] Found 6/6 markers.
[2024-01-24 12:47:37,996] [INFO] Query marker FASTA was written to GCF_021389955.1_ASM2138995v1_genomic.fna/markers.fasta
[2024-01-24 12:47:37,996] [INFO] Task started: Blastn
[2024-01-24 12:47:37,996] [INFO] Running command: blastn -query GCF_021389955.1_ASM2138995v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8edb689-5e48-4560-9300-dc71e10a2b0d/dqc_reference/reference_markers.fasta -out GCF_021389955.1_ASM2138995v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:38,660] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:38,663] [INFO] Selected 20 target genomes.
[2024-01-24 12:47:38,664] [INFO] Target genome list was writen to GCF_021389955.1_ASM2138995v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:38,672] [INFO] Task started: fastANI
[2024-01-24 12:47:38,673] [INFO] Running command: fastANI --query /var/lib/cwl/stgc98dd534-98ee-4656-a62d-8b03463535f4/GCF_021389955.1_ASM2138995v1_genomic.fna.gz --refList GCF_021389955.1_ASM2138995v1_genomic.fna/target_genomes.txt --output GCF_021389955.1_ASM2138995v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:55,746] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:55,747] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf8edb689-5e48-4560-9300-dc71e10a2b0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:55,747] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf8edb689-5e48-4560-9300-dc71e10a2b0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:55,762] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:47:55,763] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:47:55,763] [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
Fulvivirga sediminis	strain=2943	GCA_016757215.1	2803949	2803949	type	True	85.3009	1383	2130	95	below_threshold
Fulvivirga lutimaris	strain=KCTC 42720	GCA_009711525.1	1819566	1819566	type	True	77.0751	102	2130	95	below_threshold
Roseivirga pacifica	strain=DSM 100771	GCA_003633845.1	1267423	1267423	type	True	76.9924	51	2130	95	below_threshold
Fulvivirga marina	strain=29W222	GCA_016775155.1	2494733	2494733	type	True	76.7571	172	2130	95	below_threshold
Fulvivirga kasyanovii	strain=JCM 16186	GCA_009711405.1	396812	396812	type	True	76.7491	143	2130	95	below_threshold
Fulvivirga imtechensis	strain=AK7	GCA_000331535.1	881893	881893	type	True	76.6163	139	2130	95	below_threshold
Fulvivirga aurantia	strain=RKSG066	GCA_009711475.1	2529383	2529383	type	True	76.4757	90	2130	95	below_threshold
Marivirga tractuosa	strain=DSM 4126	GCA_000183425.1	1006	1006	type	True	76.3855	57	2130	95	below_threshold
Marivirga sericea	strain=DSM 4125	GCA_900177665.1	1028	1028	type	True	76.2194	58	2130	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:55,765] [INFO] DFAST Taxonomy check result was written to GCF_021389955.1_ASM2138995v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:55,766] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:55,766] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:55,766] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf8edb689-5e48-4560-9300-dc71e10a2b0d/dqc_reference/checkm_data
[2024-01-24 12:47:55,768] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:55,832] [INFO] Task started: CheckM
[2024-01-24 12:47:55,832] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021389955.1_ASM2138995v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021389955.1_ASM2138995v1_genomic.fna/checkm_input GCF_021389955.1_ASM2138995v1_genomic.fna/checkm_result
[2024-01-24 12:49:00,295] [INFO] Task succeeded: CheckM
[2024-01-24 12:49:00,297] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:49:00,324] [INFO] ===== Completeness check finished =====
[2024-01-24 12:49:00,324] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:49:00,325] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021389955.1_ASM2138995v1_genomic.fna/markers.fasta)
[2024-01-24 12:49:00,325] [INFO] Task started: Blastn
[2024-01-24 12:49:00,326] [INFO] Running command: blastn -query GCF_021389955.1_ASM2138995v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8edb689-5e48-4560-9300-dc71e10a2b0d/dqc_reference/reference_markers_gtdb.fasta -out GCF_021389955.1_ASM2138995v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:49:01,116] [INFO] Task succeeded: Blastn
[2024-01-24 12:49:01,120] [INFO] Selected 21 target genomes.
[2024-01-24 12:49:01,121] [INFO] Target genome list was writen to GCF_021389955.1_ASM2138995v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:49:01,136] [INFO] Task started: fastANI
[2024-01-24 12:49:01,136] [INFO] Running command: fastANI --query /var/lib/cwl/stgc98dd534-98ee-4656-a62d-8b03463535f4/GCF_021389955.1_ASM2138995v1_genomic.fna.gz --refList GCF_021389955.1_ASM2138995v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021389955.1_ASM2138995v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:49:17,270] [INFO] Task succeeded: fastANI
[2024-01-24 12:49:17,281] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:49:17,281] [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_016757215.1	s__Fulvivirga sp016757215	85.2965	1384	2130	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111145.1	s__Fabibacter pacificus	77.3276	52	2130	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009711525.1	s__Fulvivirga lutimaris	77.0751	102	2130	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016775155.1	s__Fulvivirga sp016775155	76.7571	172	2130	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711405.1	s__Fulvivirga kasyanovii	76.7491	143	2130	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331535.1	s__Fulvivirga imtechensis	76.6163	139	2130	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711475.1	s__Fulvivirga aurantia	76.4757	90	2130	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177665.1	s__Marivirga sericea	76.4589	58	2130	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Marivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000183425.1	s__Marivirga tractuosa	76.3656	57	2130	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Marivirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:49:17,283] [INFO] GTDB search result was written to GCF_021389955.1_ASM2138995v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:49:17,283] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:49:17,287] [INFO] DFAST_QC result json was written to GCF_021389955.1_ASM2138995v1_genomic.fna/dqc_result.json
[2024-01-24 12:49:17,287] [INFO] DFAST_QC completed!
[2024-01-24 12:49:17,287] [INFO] Total running time: 0h2m5s