[2024-01-24 11:12:58,071] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:58,073] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:58,073] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a08bf43-df41-4732-bc15-8cc9bcc32d06/dqc_reference
[2024-01-24 11:12:59,521] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:59,521] [INFO] Task started: Prodigal
[2024-01-24 11:12:59,522] [INFO] Running command: gunzip -c /var/lib/cwl/stga1fa3cb4-fa03-4b0a-a95d-9c1ab1691d18/GCF_002157225.2_ASM215722v2_genomic.fna.gz | prodigal -d GCF_002157225.2_ASM215722v2_genomic.fna/cds.fna -a GCF_002157225.2_ASM215722v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:15,696] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:15,697] [INFO] Task started: HMMsearch
[2024-01-24 11:13:15,697] [INFO] Running command: hmmsearch --tblout GCF_002157225.2_ASM215722v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a08bf43-df41-4732-bc15-8cc9bcc32d06/dqc_reference/reference_markers.hmm GCF_002157225.2_ASM215722v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:16,172] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:16,173] [INFO] Found 6/6 markers.
[2024-01-24 11:13:16,230] [INFO] Query marker FASTA was written to GCF_002157225.2_ASM215722v2_genomic.fna/markers.fasta
[2024-01-24 11:13:16,231] [INFO] Task started: Blastn
[2024-01-24 11:13:16,231] [INFO] Running command: blastn -query GCF_002157225.2_ASM215722v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a08bf43-df41-4732-bc15-8cc9bcc32d06/dqc_reference/reference_markers.fasta -out GCF_002157225.2_ASM215722v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:16,937] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:16,940] [INFO] Selected 24 target genomes.
[2024-01-24 11:13:16,940] [INFO] Target genome list was writen to GCF_002157225.2_ASM215722v2_genomic.fna/target_genomes.txt
[2024-01-24 11:13:16,977] [INFO] Task started: fastANI
[2024-01-24 11:13:16,977] [INFO] Running command: fastANI --query /var/lib/cwl/stga1fa3cb4-fa03-4b0a-a95d-9c1ab1691d18/GCF_002157225.2_ASM215722v2_genomic.fna.gz --refList GCF_002157225.2_ASM215722v2_genomic.fna/target_genomes.txt --output GCF_002157225.2_ASM215722v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:36,476] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:36,476] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a08bf43-df41-4732-bc15-8cc9bcc32d06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:36,477] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a08bf43-df41-4732-bc15-8cc9bcc32d06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:36,484] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:36,484] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:36,484] [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
Agarilytica rhodophyticola	strain=017	GCA_002157225.2	1737490	1737490	type	True	100.0	2366	2368	95	conclusive
Teredinibacter franksiae	strain=Bsc2	GCA_014218805.1	2761453	2761453	type	True	77.8507	52	2368	95	below_threshold
Saccharophagus degradans	strain=2-40	GCA_000013665.1	86304	86304	type	True	77.6874	62	2368	95	below_threshold
Teredinibacter haidensis	strain=Bs08	GCA_014211975.1	2731755	2731755	type	True	77.3344	59	2368	95	below_threshold
Teredinibacter waterburyi	strain=Bs02	GCA_001922985.1	1500538	1500538	type	True	76.3216	51	2368	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:36,486] [INFO] DFAST Taxonomy check result was written to GCF_002157225.2_ASM215722v2_genomic.fna/tc_result.tsv
[2024-01-24 11:13:36,486] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:36,487] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:36,487] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a08bf43-df41-4732-bc15-8cc9bcc32d06/dqc_reference/checkm_data
[2024-01-24 11:13:36,488] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:36,561] [INFO] Task started: CheckM
[2024-01-24 11:13:36,562] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002157225.2_ASM215722v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002157225.2_ASM215722v2_genomic.fna/checkm_input GCF_002157225.2_ASM215722v2_genomic.fna/checkm_result
[2024-01-24 11:14:28,176] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:28,178] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:28,198] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:28,198] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:28,198] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002157225.2_ASM215722v2_genomic.fna/markers.fasta)
[2024-01-24 11:14:28,199] [INFO] Task started: Blastn
[2024-01-24 11:14:28,199] [INFO] Running command: blastn -query GCF_002157225.2_ASM215722v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a08bf43-df41-4732-bc15-8cc9bcc32d06/dqc_reference/reference_markers_gtdb.fasta -out GCF_002157225.2_ASM215722v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:29,012] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:29,016] [INFO] Selected 27 target genomes.
[2024-01-24 11:14:29,016] [INFO] Target genome list was writen to GCF_002157225.2_ASM215722v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:29,036] [INFO] Task started: fastANI
[2024-01-24 11:14:29,037] [INFO] Running command: fastANI --query /var/lib/cwl/stga1fa3cb4-fa03-4b0a-a95d-9c1ab1691d18/GCF_002157225.2_ASM215722v2_genomic.fna.gz --refList GCF_002157225.2_ASM215722v2_genomic.fna/target_genomes_gtdb.txt --output GCF_002157225.2_ASM215722v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:48,097] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:48,107] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:48,108] [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_002157225.2	s__Agarilytica rhodophyticola	100.0	2365	2368	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Agarilytica	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000013665.1	s__Saccharophagus degradans	77.4803	62	2368	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Saccharophagus	95.0	96.22	96.22	0.89	0.89	2	-
GCF_014211975.1	s__Teredinibacter haidensis	77.3388	58	2368	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_902141825.1	s__Thalassocella blandensis	76.6042	91	2368	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Thalassocella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002746115.1	s__GCA-2746115 sp002746115	76.5311	55	2368	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__GCA-2746115	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001922985.1	s__Teredinibacter waterburyi	76.2818	51	2368	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:48,109] [INFO] GTDB search result was written to GCF_002157225.2_ASM215722v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:48,110] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:48,112] [INFO] DFAST_QC result json was written to GCF_002157225.2_ASM215722v2_genomic.fna/dqc_result.json
[2024-01-24 11:14:48,112] [INFO] DFAST_QC completed!
[2024-01-24 11:14:48,112] [INFO] Total running time: 0h1m50s