[2024-01-24 14:42:02,929] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:42:02,931] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:42:02,931] [INFO] DQC Reference Directory: /var/lib/cwl/stg195f589a-34bb-4120-8ed3-1f0b0ae4407b/dqc_reference
[2024-01-24 14:42:04,233] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:42:04,234] [INFO] Task started: Prodigal
[2024-01-24 14:42:04,234] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb3e9607-f2cc-4cf6-a754-6e18de6acf01/GCF_019613795.1_ASM1961379v1_genomic.fna.gz | prodigal -d GCF_019613795.1_ASM1961379v1_genomic.fna/cds.fna -a GCF_019613795.1_ASM1961379v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:42:14,788] [INFO] Task succeeded: Prodigal
[2024-01-24 14:42:14,788] [INFO] Task started: HMMsearch
[2024-01-24 14:42:14,789] [INFO] Running command: hmmsearch --tblout GCF_019613795.1_ASM1961379v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg195f589a-34bb-4120-8ed3-1f0b0ae4407b/dqc_reference/reference_markers.hmm GCF_019613795.1_ASM1961379v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:42:15,116] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:42:15,117] [INFO] Found 6/6 markers.
[2024-01-24 14:42:15,154] [INFO] Query marker FASTA was written to GCF_019613795.1_ASM1961379v1_genomic.fna/markers.fasta
[2024-01-24 14:42:15,154] [INFO] Task started: Blastn
[2024-01-24 14:42:15,154] [INFO] Running command: blastn -query GCF_019613795.1_ASM1961379v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg195f589a-34bb-4120-8ed3-1f0b0ae4407b/dqc_reference/reference_markers.fasta -out GCF_019613795.1_ASM1961379v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:42:15,937] [INFO] Task succeeded: Blastn
[2024-01-24 14:42:15,942] [INFO] Selected 12 target genomes.
[2024-01-24 14:42:15,942] [INFO] Target genome list was writen to GCF_019613795.1_ASM1961379v1_genomic.fna/target_genomes.txt
[2024-01-24 14:42:15,948] [INFO] Task started: fastANI
[2024-01-24 14:42:15,949] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb3e9607-f2cc-4cf6-a754-6e18de6acf01/GCF_019613795.1_ASM1961379v1_genomic.fna.gz --refList GCF_019613795.1_ASM1961379v1_genomic.fna/target_genomes.txt --output GCF_019613795.1_ASM1961379v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:42:24,074] [INFO] Task succeeded: fastANI
[2024-01-24 14:42:24,075] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg195f589a-34bb-4120-8ed3-1f0b0ae4407b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:42:24,076] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg195f589a-34bb-4120-8ed3-1f0b0ae4407b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:42:24,089] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:42:24,089] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:42:24,089] [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 litorale	strain=WSW3-B6	GCA_019613795.1	2856519	2856519	type	True	100.0	906	908	95	conclusive
Flavobacterium arcticum	strain=SM1502	GCA_003344925.1	1784713	1784713	type	True	80.165	571	908	95	below_threshold
Flavobacterium arcticum	strain=KCTC 42668	GCA_004634185.1	1784713	1784713	type	True	80.0509	569	908	95	below_threshold
Flavobacterium salilacus subsp. altitudinum	strain=LaA7.5	GCA_010078225.1	2691899	2898423	type	True	79.8847	574	908	95	below_threshold
Flavobacterium salilacus subsp. salilacus	strain=SaA2.12	GCA_004634195.1	2545633	2898423	type	True	79.8291	551	908	95	below_threshold
Flavobacterium suaedae	strain=CGMCC 1.15461	GCA_014642915.1	1767027	1767027	type	True	78.376	402	908	95	below_threshold
Flavobacterium coralii	strain=D11R37	GCA_019891545.1	2838017	2838017	type	True	77.4914	289	908	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.4221	61	908	95	below_threshold
Flavobacterium tibetense	strain=YH5	GCA_003293845.1	2233533	2233533	type	True	77.2306	95	908	95	below_threshold
Flavobacterium psychrotolerans	strain=RB1R5	GCA_003097635.1	2169410	2169410	type	True	77.0215	79	908	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.6158	72	908	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:42:24,091] [INFO] DFAST Taxonomy check result was written to GCF_019613795.1_ASM1961379v1_genomic.fna/tc_result.tsv
[2024-01-24 14:42:24,092] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:42:24,092] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:42:24,092] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg195f589a-34bb-4120-8ed3-1f0b0ae4407b/dqc_reference/checkm_data
[2024-01-24 14:42:24,094] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:42:24,123] [INFO] Task started: CheckM
[2024-01-24 14:42:24,123] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019613795.1_ASM1961379v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019613795.1_ASM1961379v1_genomic.fna/checkm_input GCF_019613795.1_ASM1961379v1_genomic.fna/checkm_result
[2024-01-24 14:42:56,652] [INFO] Task succeeded: CheckM
[2024-01-24 14:42:56,653] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:42:56,678] [INFO] ===== Completeness check finished =====
[2024-01-24 14:42:56,678] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:42:56,678] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019613795.1_ASM1961379v1_genomic.fna/markers.fasta)
[2024-01-24 14:42:56,679] [INFO] Task started: Blastn
[2024-01-24 14:42:56,679] [INFO] Running command: blastn -query GCF_019613795.1_ASM1961379v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg195f589a-34bb-4120-8ed3-1f0b0ae4407b/dqc_reference/reference_markers_gtdb.fasta -out GCF_019613795.1_ASM1961379v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:42:57,512] [INFO] Task succeeded: Blastn
[2024-01-24 14:42:57,516] [INFO] Selected 13 target genomes.
[2024-01-24 14:42:57,516] [INFO] Target genome list was writen to GCF_019613795.1_ASM1961379v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:42:57,525] [INFO] Task started: fastANI
[2024-01-24 14:42:57,526] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb3e9607-f2cc-4cf6-a754-6e18de6acf01/GCF_019613795.1_ASM1961379v1_genomic.fna.gz --refList GCF_019613795.1_ASM1961379v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019613795.1_ASM1961379v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:43:05,676] [INFO] Task succeeded: fastANI
[2024-01-24 14:43:05,689] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:43:05,689] [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	80.1854	569	908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004634195.1	s__Flavobacterium sp004634195	79.8291	551	908	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	79.2165	418	908	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	78.3752	402	908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001708385.1	s__Flavobacterium psychrophilum_A	78.025	216	908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002714575.1	s__Flavobacterium sp002714575	77.664	274	908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378485.1	s__Flavobacterium rivuli	77.5908	205	908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000769915.1	s__Flavobacterium beibuense	77.5385	245	908	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	77.508	221	908	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	77.4665	183	908	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	77.4183	177	908	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	77.248	250	908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017984495.1	s__Flavobacterium sp017984495	76.048	56	908	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 14:43:05,691] [INFO] GTDB search result was written to GCF_019613795.1_ASM1961379v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:43:05,692] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:43:05,695] [INFO] DFAST_QC result json was written to GCF_019613795.1_ASM1961379v1_genomic.fna/dqc_result.json
[2024-01-24 14:43:05,695] [INFO] DFAST_QC completed!
[2024-01-24 14:43:05,695] [INFO] Total running time: 0h1m3s