[2024-01-24 12:46:35,319] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:46:35,322] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:46:35,322] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e52eb65-8b7c-442a-a124-e33aeb2985a3/dqc_reference
[2024-01-24 12:46:36,489] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:46:36,490] [INFO] Task started: Prodigal
[2024-01-24 12:46:36,490] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c7a09b4-173f-475c-a686-d3b3c03a7f9d/GCF_019916085.1_ASM1991608v1_genomic.fna.gz | prodigal -d GCF_019916085.1_ASM1991608v1_genomic.fna/cds.fna -a GCF_019916085.1_ASM1991608v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:46:47,051] [INFO] Task succeeded: Prodigal
[2024-01-24 12:46:47,052] [INFO] Task started: HMMsearch
[2024-01-24 12:46:47,052] [INFO] Running command: hmmsearch --tblout GCF_019916085.1_ASM1991608v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e52eb65-8b7c-442a-a124-e33aeb2985a3/dqc_reference/reference_markers.hmm GCF_019916085.1_ASM1991608v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:46:47,251] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:46:47,253] [INFO] Found 6/6 markers.
[2024-01-24 12:46:47,277] [INFO] Query marker FASTA was written to GCF_019916085.1_ASM1991608v1_genomic.fna/markers.fasta
[2024-01-24 12:46:47,277] [INFO] Task started: Blastn
[2024-01-24 12:46:47,277] [INFO] Running command: blastn -query GCF_019916085.1_ASM1991608v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e52eb65-8b7c-442a-a124-e33aeb2985a3/dqc_reference/reference_markers.fasta -out GCF_019916085.1_ASM1991608v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:47,833] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:47,836] [INFO] Selected 13 target genomes.
[2024-01-24 12:46:47,837] [INFO] Target genome list was writen to GCF_019916085.1_ASM1991608v1_genomic.fna/target_genomes.txt
[2024-01-24 12:46:47,847] [INFO] Task started: fastANI
[2024-01-24 12:46:47,848] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c7a09b4-173f-475c-a686-d3b3c03a7f9d/GCF_019916085.1_ASM1991608v1_genomic.fna.gz --refList GCF_019916085.1_ASM1991608v1_genomic.fna/target_genomes.txt --output GCF_019916085.1_ASM1991608v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:46:55,978] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:55,978] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e52eb65-8b7c-442a-a124-e33aeb2985a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:46:55,978] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e52eb65-8b7c-442a-a124-e33aeb2985a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:46:55,985] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:46:55,985] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:46:55,986] [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
Aquirufa lenticrescens	strain=9H-EGSE	GCA_019916085.1	2696560	2696560	type	True	100.0	835	835	95	conclusive
Aquirufa antheringensis	strain=30S-ANTBAC	GCA_004307425.1	2516559	2516559	type	True	89.6004	714	835	95	below_threshold
Aquirufa aurantiipilula	strain=15D-MOB	GCA_019923745.1	2696561	2696561	type	True	78.5278	177	835	95	below_threshold
Aquirufa nivalisilvae	strain=59G-WUEMPEL	GCA_004307455.1	2516557	2516557	type	True	78.1494	181	835	95	below_threshold
Aquirufa beregesia	strain=50C-KIRBA	GCA_011090385.1	2516556	2516556	type	True	77.8867	168	835	95	below_threshold
Aquirufa ecclesiirivi	strain=50A-KIRBA	GCA_011250515.1	2715124	2715124	type	True	77.8802	173	835	95	below_threshold
Aquirufa rosea	strain=CAR-16	GCA_004118285.1	2509241	2509241	type	True	77.4895	145	835	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:46:55,987] [INFO] DFAST Taxonomy check result was written to GCF_019916085.1_ASM1991608v1_genomic.fna/tc_result.tsv
[2024-01-24 12:46:55,987] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:46:55,988] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:46:55,988] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e52eb65-8b7c-442a-a124-e33aeb2985a3/dqc_reference/checkm_data
[2024-01-24 12:46:55,989] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:46:56,013] [INFO] Task started: CheckM
[2024-01-24 12:46:56,013] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019916085.1_ASM1991608v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019916085.1_ASM1991608v1_genomic.fna/checkm_input GCF_019916085.1_ASM1991608v1_genomic.fna/checkm_result
[2024-01-24 12:47:30,282] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:30,283] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:30,303] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:30,303] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:30,304] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019916085.1_ASM1991608v1_genomic.fna/markers.fasta)
[2024-01-24 12:47:30,304] [INFO] Task started: Blastn
[2024-01-24 12:47:30,304] [INFO] Running command: blastn -query GCF_019916085.1_ASM1991608v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e52eb65-8b7c-442a-a124-e33aeb2985a3/dqc_reference/reference_markers_gtdb.fasta -out GCF_019916085.1_ASM1991608v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:31,089] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:31,093] [INFO] Selected 12 target genomes.
[2024-01-24 12:47:31,094] [INFO] Target genome list was writen to GCF_019916085.1_ASM1991608v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:31,105] [INFO] Task started: fastANI
[2024-01-24 12:47:31,106] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c7a09b4-173f-475c-a686-d3b3c03a7f9d/GCF_019916085.1_ASM1991608v1_genomic.fna.gz --refList GCF_019916085.1_ASM1991608v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019916085.1_ASM1991608v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:37,515] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:37,525] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:47:37,526] [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_004307425.1	s__Aquirufa antheringensis	89.6004	714	835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Aquirufa	95.0	97.17	97.17	0.93	0.93	2	-
GCA_002479785.1	s__Aquirufa sp002479785	88.3798	562	835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Aquirufa	95.0	99.96	99.96	0.93	0.93	2	-
GCA_903837305.1	s__Aquirufa sp903837305	85.941	482	835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Aquirufa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903960725.1	s__Aquirufa sp903960725	84.6658	402	835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Aquirufa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903907915.1	s__Aquirufa sp903907915	83.858	461	835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Aquirufa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017984215.1	s__Aquirufa sp017984215	79.3546	246	835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Aquirufa	95.0	99.80	99.80	0.94	0.94	2	-
GCA_903898715.1	s__Aquirufa sp903898715	78.9549	205	835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Aquirufa	95.0	99.63	99.56	0.90	0.88	3	-
GCA_002454335.1	s__Aquirufa sp002454335	78.5873	224	835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Aquirufa	95.0	99.80	99.80	0.91	0.91	2	-
GCA_004307455.1	s__Allopseudarcicella nivalisilvae	78.1597	181	835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Allopseudarcicella	95.0	97.41	97.41	0.94	0.94	2	-
GCA_903907745.1	s__Aquirufa sp903907745	78.0086	179	835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Aquirufa	95.0	98.69	97.99	0.91	0.88	6	-
GCF_011090385.1	s__Allopseudarcicella beregesia	77.8867	168	835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Allopseudarcicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004118285.1	s__Allopseudarcicella rosea	77.5092	144	835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Allopseudarcicella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:47:37,527] [INFO] GTDB search result was written to GCF_019916085.1_ASM1991608v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:37,528] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:37,531] [INFO] DFAST_QC result json was written to GCF_019916085.1_ASM1991608v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:37,531] [INFO] DFAST_QC completed!
[2024-01-24 12:47:37,531] [INFO] Total running time: 0h1m2s