[2024-01-25 18:46:35,668] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:46:35,670] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:46:35,670] [INFO] DQC Reference Directory: /var/lib/cwl/stg8612f7f6-5ec2-44ba-a7b8-195a779c2f12/dqc_reference
[2024-01-25 18:46:36,818] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:46:36,818] [INFO] Task started: Prodigal
[2024-01-25 18:46:36,818] [INFO] Running command: gunzip -c /var/lib/cwl/stg07cdeb38-298a-49d6-8f7d-84b4ce58cfba/GCF_016726985.1_ASM1672698v1_genomic.fna.gz | prodigal -d GCF_016726985.1_ASM1672698v1_genomic.fna/cds.fna -a GCF_016726985.1_ASM1672698v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:46:50,181] [INFO] Task succeeded: Prodigal
[2024-01-25 18:46:50,181] [INFO] Task started: HMMsearch
[2024-01-25 18:46:50,182] [INFO] Running command: hmmsearch --tblout GCF_016726985.1_ASM1672698v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8612f7f6-5ec2-44ba-a7b8-195a779c2f12/dqc_reference/reference_markers.hmm GCF_016726985.1_ASM1672698v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:46:50,465] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:46:50,466] [INFO] Found 6/6 markers.
[2024-01-25 18:46:50,502] [INFO] Query marker FASTA was written to GCF_016726985.1_ASM1672698v1_genomic.fna/markers.fasta
[2024-01-25 18:46:50,503] [INFO] Task started: Blastn
[2024-01-25 18:46:50,503] [INFO] Running command: blastn -query GCF_016726985.1_ASM1672698v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8612f7f6-5ec2-44ba-a7b8-195a779c2f12/dqc_reference/reference_markers.fasta -out GCF_016726985.1_ASM1672698v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:46:51,167] [INFO] Task succeeded: Blastn
[2024-01-25 18:46:51,169] [INFO] Selected 13 target genomes.
[2024-01-25 18:46:51,169] [INFO] Target genome list was writen to GCF_016726985.1_ASM1672698v1_genomic.fna/target_genomes.txt
[2024-01-25 18:46:51,179] [INFO] Task started: fastANI
[2024-01-25 18:46:51,180] [INFO] Running command: fastANI --query /var/lib/cwl/stg07cdeb38-298a-49d6-8f7d-84b4ce58cfba/GCF_016726985.1_ASM1672698v1_genomic.fna.gz --refList GCF_016726985.1_ASM1672698v1_genomic.fna/target_genomes.txt --output GCF_016726985.1_ASM1672698v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:47:02,004] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:02,004] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8612f7f6-5ec2-44ba-a7b8-195a779c2f12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:47:02,005] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8612f7f6-5ec2-44ba-a7b8-195a779c2f12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:47:02,012] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 18:47:02,012] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:47:02,013] [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
Myroides odoratus	strain=FDAARGOS_1131	GCA_016726985.1	256	256	type	True	100.0	1414	1414	95	conclusive
Myroides odoratus	strain=NCTC11036	GCA_900453865.1	256	256	type	True	99.9987	1411	1414	95	conclusive
Myroides odoratus	strain=DSM 2801	GCA_000243275.1	256	256	type	True	99.9769	1395	1414	95	conclusive
Myroides fluvii	strain=CJ210	GCA_009792295.1	2572594	2572594	type	True	85.0174	904	1414	95	below_threshold
Myroides albus	strain=BIT-d1	GCA_009711045.1	2562892	2562892	type	True	79.0336	301	1414	95	below_threshold
Myroides phaeus	strain=DSM 23313	GCA_900099675.1	702745	702745	type	True	78.9936	300	1414	95	below_threshold
Myroides marinus	strain=DSM 23048	GCA_900109075.1	703342	703342	type	True	78.8231	314	1414	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	77.863	122	1414	95	below_threshold
Flavobacterium sediminis	strain=MEBiC07310	GCA_003148385.1	2201181	2201181	type	True	77.1533	102	1414	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	76.512	78	1414	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.3893	71	1414	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:47:02,014] [INFO] DFAST Taxonomy check result was written to GCF_016726985.1_ASM1672698v1_genomic.fna/tc_result.tsv
[2024-01-25 18:47:02,014] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:47:02,014] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:47:02,015] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8612f7f6-5ec2-44ba-a7b8-195a779c2f12/dqc_reference/checkm_data
[2024-01-25 18:47:02,015] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:47:02,057] [INFO] Task started: CheckM
[2024-01-25 18:47:02,057] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016726985.1_ASM1672698v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016726985.1_ASM1672698v1_genomic.fna/checkm_input GCF_016726985.1_ASM1672698v1_genomic.fna/checkm_result
[2024-01-25 18:47:42,777] [INFO] Task succeeded: CheckM
[2024-01-25 18:47:42,778] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:47:42,797] [INFO] ===== Completeness check finished =====
[2024-01-25 18:47:42,797] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:47:42,797] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016726985.1_ASM1672698v1_genomic.fna/markers.fasta)
[2024-01-25 18:47:42,798] [INFO] Task started: Blastn
[2024-01-25 18:47:42,798] [INFO] Running command: blastn -query GCF_016726985.1_ASM1672698v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8612f7f6-5ec2-44ba-a7b8-195a779c2f12/dqc_reference/reference_markers_gtdb.fasta -out GCF_016726985.1_ASM1672698v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:47:43,689] [INFO] Task succeeded: Blastn
[2024-01-25 18:47:43,692] [INFO] Selected 6 target genomes.
[2024-01-25 18:47:43,692] [INFO] Target genome list was writen to GCF_016726985.1_ASM1672698v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:47:43,701] [INFO] Task started: fastANI
[2024-01-25 18:47:43,702] [INFO] Running command: fastANI --query /var/lib/cwl/stg07cdeb38-298a-49d6-8f7d-84b4ce58cfba/GCF_016726985.1_ASM1672698v1_genomic.fna.gz --refList GCF_016726985.1_ASM1672698v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016726985.1_ASM1672698v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:47:50,144] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:50,150] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:47:50,150] [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_000243275.1	s__Flavobacterium odoratum	99.9769	1395	1414	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.25	95.68	0.94	0.87	6	conclusive
GCF_001549985.1	s__Flavobacterium odoratum_A	91.2088	1164	1414	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009792295.1	s__Flavobacterium sp009792295	85.0301	907	1414	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014145635.1	s__Flavobacterium sp014145635	83.4987	807	1414	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014145665.1	s__Flavobacterium sp014145665	82.9674	763	1414	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148385.1	s__Flavobacterium sediminis	77.248	102	1414	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:47:50,151] [INFO] GTDB search result was written to GCF_016726985.1_ASM1672698v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:47:50,152] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:47:50,155] [INFO] DFAST_QC result json was written to GCF_016726985.1_ASM1672698v1_genomic.fna/dqc_result.json
[2024-01-25 18:47:50,155] [INFO] DFAST_QC completed!
[2024-01-25 18:47:50,155] [INFO] Total running time: 0h1m14s