[2024-01-24 13:40:55,996] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:55,998] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:55,999] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a41b824-a229-424e-8828-0443ef7ebe02/dqc_reference
[2024-01-24 13:40:57,146] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:57,147] [INFO] Task started: Prodigal
[2024-01-24 13:40:57,147] [INFO] Running command: gunzip -c /var/lib/cwl/stg104809be-4824-4df4-80d5-86d7ce755334/GCF_003344925.1_ASM334492v1_genomic.fna.gz | prodigal -d GCF_003344925.1_ASM334492v1_genomic.fna/cds.fna -a GCF_003344925.1_ASM334492v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:05,153] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:05,154] [INFO] Task started: HMMsearch
[2024-01-24 13:41:05,154] [INFO] Running command: hmmsearch --tblout GCF_003344925.1_ASM334492v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a41b824-a229-424e-8828-0443ef7ebe02/dqc_reference/reference_markers.hmm GCF_003344925.1_ASM334492v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:05,440] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:05,441] [INFO] Found 6/6 markers.
[2024-01-24 13:41:05,466] [INFO] Query marker FASTA was written to GCF_003344925.1_ASM334492v1_genomic.fna/markers.fasta
[2024-01-24 13:41:05,466] [INFO] Task started: Blastn
[2024-01-24 13:41:05,466] [INFO] Running command: blastn -query GCF_003344925.1_ASM334492v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a41b824-a229-424e-8828-0443ef7ebe02/dqc_reference/reference_markers.fasta -out GCF_003344925.1_ASM334492v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:06,126] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:06,131] [INFO] Selected 10 target genomes.
[2024-01-24 13:41:06,131] [INFO] Target genome list was writen to GCF_003344925.1_ASM334492v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:06,136] [INFO] Task started: fastANI
[2024-01-24 13:41:06,136] [INFO] Running command: fastANI --query /var/lib/cwl/stg104809be-4824-4df4-80d5-86d7ce755334/GCF_003344925.1_ASM334492v1_genomic.fna.gz --refList GCF_003344925.1_ASM334492v1_genomic.fna/target_genomes.txt --output GCF_003344925.1_ASM334492v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:12,693] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:12,693] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a41b824-a229-424e-8828-0443ef7ebe02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:12,694] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a41b824-a229-424e-8828-0443ef7ebe02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:12,700] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:12,700] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:12,700] [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
Flavobacterium arcticum	strain=SM1502	GCA_003344925.1	1784713	1784713	type	True	100.0	989	990	95	conclusive
Flavobacterium arcticum	strain=KCTC 42668	GCA_004634185.1	1784713	1784713	type	True	99.9852	976	990	95	conclusive
Flavobacterium salilacus subsp. altitudinum	strain=LaA7.5	GCA_010078225.1	2691899	2898423	type	True	82.9737	757	990	95	below_threshold
Flavobacterium salilacus subsp. salilacus	strain=SaA2.12	GCA_004634195.1	2545633	2898423	type	True	82.9431	739	990	95	below_threshold
Flavobacterium litorale	strain=WSW3-B6	GCA_019613795.1	2856519	2856519	type	True	80.3172	575	990	95	below_threshold
Flavobacterium alkalisoli	strain=XS-5	GCA_008000935.1	2602769	2602769	type	True	78.2691	295	990	95	below_threshold
Flavobacterium coralii	strain=D11R37	GCA_019891545.1	2838017	2838017	type	True	77.8583	322	990	95	below_threshold
Flavobacterium solisilvae	strain=SE-s27	GCA_012911605.1	1852019	1852019	type	True	76.788	96	990	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:12,701] [INFO] DFAST Taxonomy check result was written to GCF_003344925.1_ASM334492v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:12,702] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:12,702] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:12,702] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a41b824-a229-424e-8828-0443ef7ebe02/dqc_reference/checkm_data
[2024-01-24 13:41:12,703] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:12,742] [INFO] Task started: CheckM
[2024-01-24 13:41:12,742] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003344925.1_ASM334492v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003344925.1_ASM334492v1_genomic.fna/checkm_input GCF_003344925.1_ASM334492v1_genomic.fna/checkm_result
[2024-01-24 13:41:38,968] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:38,968] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:38,979] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:38,980] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:38,980] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003344925.1_ASM334492v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:38,980] [INFO] Task started: Blastn
[2024-01-24 13:41:38,980] [INFO] Running command: blastn -query GCF_003344925.1_ASM334492v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a41b824-a229-424e-8828-0443ef7ebe02/dqc_reference/reference_markers_gtdb.fasta -out GCF_003344925.1_ASM334492v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:39,883] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:39,885] [INFO] Selected 13 target genomes.
[2024-01-24 13:41:39,886] [INFO] Target genome list was writen to GCF_003344925.1_ASM334492v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:39,907] [INFO] Task started: fastANI
[2024-01-24 13:41:39,907] [INFO] Running command: fastANI --query /var/lib/cwl/stg104809be-4824-4df4-80d5-86d7ce755334/GCF_003344925.1_ASM334492v1_genomic.fna.gz --refList GCF_003344925.1_ASM334492v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003344925.1_ASM334492v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:48,552] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:48,561] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:48,562] [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_003344925.1	s__Flavobacterium arcticum	100.0	989	990	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_004634195.1	s__Flavobacterium sp004634195	82.9431	739	990	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.56	97.13	0.95	0.91	3	-
GCA_001874325.1	s__Flavobacterium sp001874325	80.7525	536	990	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014642915.1	s__Flavobacterium suaedae	79.0777	472	990	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008000935.1	s__Flavobacterium alkalisoli	78.2421	299	990	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002714575.1	s__Flavobacterium sp002714575	77.8977	328	990	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009848495.1	s__Flavobacterium sp009848495	77.8327	259	990	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009741375.1	s__Flavobacterium rakeshii	77.777	300	990	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350375.1	s__Flavobacterium sp003350375	77.7531	245	990	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932585.1	s__Flavobacterium sp012932585	77.7082	259	990	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003243255.1	s__Flavobacterium psychrophilum_B	77.5211	227	990	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422725.1	s__Flavobacterium subsaxonicum	77.4983	230	990	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002862805.1	s__Flavobacterium sp002862805	76.7765	132	990	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:48,563] [INFO] GTDB search result was written to GCF_003344925.1_ASM334492v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:48,564] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:48,566] [INFO] DFAST_QC result json was written to GCF_003344925.1_ASM334492v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:48,566] [INFO] DFAST_QC completed!
[2024-01-24 13:41:48,566] [INFO] Total running time: 0h0m53s