[2024-01-25 20:25:50,422] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:25:50,424] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:25:50,424] [INFO] DQC Reference Directory: /var/lib/cwl/stgca375987-d0c4-450e-bfcf-57d049e28ca1/dqc_reference
[2024-01-25 20:25:51,559] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:25:51,560] [INFO] Task started: Prodigal
[2024-01-25 20:25:51,560] [INFO] Running command: gunzip -c /var/lib/cwl/stg964981d8-e538-4428-b0f0-424800bf2cd2/GCF_009711405.1_ASM971140v1_genomic.fna.gz | prodigal -d GCF_009711405.1_ASM971140v1_genomic.fna/cds.fna -a GCF_009711405.1_ASM971140v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:26:17,986] [INFO] Task succeeded: Prodigal
[2024-01-25 20:26:17,987] [INFO] Task started: HMMsearch
[2024-01-25 20:26:17,987] [INFO] Running command: hmmsearch --tblout GCF_009711405.1_ASM971140v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca375987-d0c4-450e-bfcf-57d049e28ca1/dqc_reference/reference_markers.hmm GCF_009711405.1_ASM971140v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:26:18,277] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:26:18,278] [INFO] Found 6/6 markers.
[2024-01-25 20:26:18,331] [INFO] Query marker FASTA was written to GCF_009711405.1_ASM971140v1_genomic.fna/markers.fasta
[2024-01-25 20:26:18,332] [INFO] Task started: Blastn
[2024-01-25 20:26:18,332] [INFO] Running command: blastn -query GCF_009711405.1_ASM971140v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca375987-d0c4-450e-bfcf-57d049e28ca1/dqc_reference/reference_markers.fasta -out GCF_009711405.1_ASM971140v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:26:18,888] [INFO] Task succeeded: Blastn
[2024-01-25 20:26:18,895] [INFO] Selected 17 target genomes.
[2024-01-25 20:26:18,895] [INFO] Target genome list was writen to GCF_009711405.1_ASM971140v1_genomic.fna/target_genomes.txt
[2024-01-25 20:26:18,914] [INFO] Task started: fastANI
[2024-01-25 20:26:18,914] [INFO] Running command: fastANI --query /var/lib/cwl/stg964981d8-e538-4428-b0f0-424800bf2cd2/GCF_009711405.1_ASM971140v1_genomic.fna.gz --refList GCF_009711405.1_ASM971140v1_genomic.fna/target_genomes.txt --output GCF_009711405.1_ASM971140v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:26:34,903] [INFO] Task succeeded: fastANI
[2024-01-25 20:26:34,903] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca375987-d0c4-450e-bfcf-57d049e28ca1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:26:34,903] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca375987-d0c4-450e-bfcf-57d049e28ca1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:26:34,909] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:26:34,909] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:26:34,909] [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 kasyanovii	strain=JCM 16186	GCA_009711405.1	396812	396812	type	True	100.0	2077	2092	95	conclusive
Fulvivirga marina	strain=29W222	GCA_016775155.1	2494733	2494733	type	True	80.1365	983	2092	95	below_threshold
Fulvivirga aurantia	strain=RKSG066	GCA_009711475.1	2529383	2529383	type	True	78.089	88	2092	95	below_threshold
Fulvivirga imtechensis	strain=AK7	GCA_000331535.1	881893	881893	type	True	77.8688	296	2092	95	below_threshold
Fulvivirga sediminis	strain=2943	GCA_016757215.1	2803949	2803949	type	True	77.0534	111	2092	95	below_threshold
Fulvivirga lutea	strain=S481	GCA_017068455.1	2810512	2810512	type	True	76.7198	77	2092	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:26:34,910] [INFO] DFAST Taxonomy check result was written to GCF_009711405.1_ASM971140v1_genomic.fna/tc_result.tsv
[2024-01-25 20:26:34,910] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:26:34,911] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:26:34,911] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca375987-d0c4-450e-bfcf-57d049e28ca1/dqc_reference/checkm_data
[2024-01-25 20:26:34,912] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:26:34,989] [INFO] Task started: CheckM
[2024-01-25 20:26:34,989] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009711405.1_ASM971140v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009711405.1_ASM971140v1_genomic.fna/checkm_input GCF_009711405.1_ASM971140v1_genomic.fna/checkm_result
[2024-01-25 20:27:50,330] [INFO] Task succeeded: CheckM
[2024-01-25 20:27:50,331] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:27:50,371] [INFO] ===== Completeness check finished =====
[2024-01-25 20:27:50,371] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:27:50,372] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009711405.1_ASM971140v1_genomic.fna/markers.fasta)
[2024-01-25 20:27:50,372] [INFO] Task started: Blastn
[2024-01-25 20:27:50,372] [INFO] Running command: blastn -query GCF_009711405.1_ASM971140v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca375987-d0c4-450e-bfcf-57d049e28ca1/dqc_reference/reference_markers_gtdb.fasta -out GCF_009711405.1_ASM971140v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:27:51,181] [INFO] Task succeeded: Blastn
[2024-01-25 20:27:51,184] [INFO] Selected 20 target genomes.
[2024-01-25 20:27:51,184] [INFO] Target genome list was writen to GCF_009711405.1_ASM971140v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:27:51,210] [INFO] Task started: fastANI
[2024-01-25 20:27:51,210] [INFO] Running command: fastANI --query /var/lib/cwl/stg964981d8-e538-4428-b0f0-424800bf2cd2/GCF_009711405.1_ASM971140v1_genomic.fna.gz --refList GCF_009711405.1_ASM971140v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009711405.1_ASM971140v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:28:09,665] [INFO] Task succeeded: fastANI
[2024-01-25 20:28:09,671] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:28:09,671] [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_009711405.1	s__Fulvivirga kasyanovii	100.0	2077	2092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002338655.1	s__Fulvivirga sp002338655	83.0717	109	2092	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	80.1311	984	2092	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	78.089	88	2092	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	77.8716	297	2092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016757215.1	s__Fulvivirga sp016757215	77.0303	112	2092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097395.1	s__Fulvivirga sp007097395	76.1193	71	2092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:28:09,672] [INFO] GTDB search result was written to GCF_009711405.1_ASM971140v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:28:09,673] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:28:09,675] [INFO] DFAST_QC result json was written to GCF_009711405.1_ASM971140v1_genomic.fna/dqc_result.json
[2024-01-25 20:28:09,675] [INFO] DFAST_QC completed!
[2024-01-25 20:28:09,675] [INFO] Total running time: 0h2m19s