[2024-01-24 15:02:59,585] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:59,590] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:59,590] [INFO] DQC Reference Directory: /var/lib/cwl/stg10c6fe7c-6273-4c39-ab58-100a11252841/dqc_reference
[2024-01-24 15:03:00,986] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:03:00,987] [INFO] Task started: Prodigal
[2024-01-24 15:03:00,988] [INFO] Running command: gunzip -c /var/lib/cwl/stgca2f4725-e472-48cb-9dc4-b4359896dbe6/GCF_004634185.1_ASM463418v1_genomic.fna.gz | prodigal -d GCF_004634185.1_ASM463418v1_genomic.fna/cds.fna -a GCF_004634185.1_ASM463418v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:03:10,553] [INFO] Task succeeded: Prodigal
[2024-01-24 15:03:10,554] [INFO] Task started: HMMsearch
[2024-01-24 15:03:10,554] [INFO] Running command: hmmsearch --tblout GCF_004634185.1_ASM463418v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10c6fe7c-6273-4c39-ab58-100a11252841/dqc_reference/reference_markers.hmm GCF_004634185.1_ASM463418v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:10,836] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:10,837] [INFO] Found 6/6 markers.
[2024-01-24 15:03:10,864] [INFO] Query marker FASTA was written to GCF_004634185.1_ASM463418v1_genomic.fna/markers.fasta
[2024-01-24 15:03:10,864] [INFO] Task started: Blastn
[2024-01-24 15:03:10,864] [INFO] Running command: blastn -query GCF_004634185.1_ASM463418v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10c6fe7c-6273-4c39-ab58-100a11252841/dqc_reference/reference_markers.fasta -out GCF_004634185.1_ASM463418v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:11,584] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:11,587] [INFO] Selected 10 target genomes.
[2024-01-24 15:03:11,587] [INFO] Target genome list was writen to GCF_004634185.1_ASM463418v1_genomic.fna/target_genomes.txt
[2024-01-24 15:03:11,591] [INFO] Task started: fastANI
[2024-01-24 15:03:11,591] [INFO] Running command: fastANI --query /var/lib/cwl/stgca2f4725-e472-48cb-9dc4-b4359896dbe6/GCF_004634185.1_ASM463418v1_genomic.fna.gz --refList GCF_004634185.1_ASM463418v1_genomic.fna/target_genomes.txt --output GCF_004634185.1_ASM463418v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:18,191] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:18,191] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10c6fe7c-6273-4c39-ab58-100a11252841/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:18,192] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10c6fe7c-6273-4c39-ab58-100a11252841/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:18,200] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:03:18,201] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:18,201] [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=KCTC 42668	GCA_004634185.1	1784713	1784713	type	True	100.0	976	976	95	conclusive
Flavobacterium arcticum	strain=SM1502	GCA_003344925.1	1784713	1784713	type	True	99.9997	975	976	95	conclusive
Flavobacterium salilacus subsp. altitudinum	strain=LaA7.5	GCA_010078225.1	2691899	2898423	type	True	83.0316	731	976	95	below_threshold
Flavobacterium salilacus subsp. salilacus	strain=SaA2.12	GCA_004634195.1	2545633	2898423	type	True	82.9267	736	976	95	below_threshold
Flavobacterium litorale	strain=WSW3-B6	GCA_019613795.1	2856519	2856519	type	True	80.2248	553	976	95	below_threshold
Flavobacterium coralii	strain=D11R37	GCA_019891545.1	2838017	2838017	type	True	78.0109	313	976	95	below_threshold
Flavobacterium alkalisoli	strain=XS-5	GCA_008000935.1	2602769	2602769	type	True	78.0009	294	976	95	below_threshold
Flavobacterium solisilvae	strain=SE-s27	GCA_012911605.1	1852019	1852019	type	True	76.5582	98	976	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:18,206] [INFO] DFAST Taxonomy check result was written to GCF_004634185.1_ASM463418v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:18,207] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:18,207] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:18,207] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10c6fe7c-6273-4c39-ab58-100a11252841/dqc_reference/checkm_data
[2024-01-24 15:03:18,208] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:18,257] [INFO] Task started: CheckM
[2024-01-24 15:03:18,258] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004634185.1_ASM463418v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004634185.1_ASM463418v1_genomic.fna/checkm_input GCF_004634185.1_ASM463418v1_genomic.fna/checkm_result
[2024-01-24 15:03:50,686] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:50,688] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:50,709] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:50,710] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:50,710] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004634185.1_ASM463418v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:50,710] [INFO] Task started: Blastn
[2024-01-24 15:03:50,711] [INFO] Running command: blastn -query GCF_004634185.1_ASM463418v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10c6fe7c-6273-4c39-ab58-100a11252841/dqc_reference/reference_markers_gtdb.fasta -out GCF_004634185.1_ASM463418v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:51,705] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:51,709] [INFO] Selected 13 target genomes.
[2024-01-24 15:03:51,709] [INFO] Target genome list was writen to GCF_004634185.1_ASM463418v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:51,717] [INFO] Task started: fastANI
[2024-01-24 15:03:51,717] [INFO] Running command: fastANI --query /var/lib/cwl/stgca2f4725-e472-48cb-9dc4-b4359896dbe6/GCF_004634185.1_ASM463418v1_genomic.fna.gz --refList GCF_004634185.1_ASM463418v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004634185.1_ASM463418v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:00,797] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:00,808] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:00,808] [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	99.9997	975	976	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	82.9153	737	976	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	80.8102	537	976	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	79.2785	468	976	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	78.0736	322	976	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	77.9937	293	976	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	77.8537	254	976	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	77.7302	307	976	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	77.6759	240	976	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	77.6585	218	976	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003350375.1	s__Flavobacterium sp003350375	77.6413	248	976	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	77.6103	232	976	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862805.1	s__Flavobacterium sp002862805	76.6516	137	976	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 15:04:00,818] [INFO] GTDB search result was written to GCF_004634185.1_ASM463418v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:00,818] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:00,825] [INFO] DFAST_QC result json was written to GCF_004634185.1_ASM463418v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:00,826] [INFO] DFAST_QC completed!
[2024-01-24 15:04:00,826] [INFO] Total running time: 0h1m1s