[2024-01-24 14:07:14,983] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:07:14,986] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:07:14,987] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d4ccce2-143f-451d-a3e8-1f30999bbb41/dqc_reference
[2024-01-24 14:07:16,237] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:07:16,238] [INFO] Task started: Prodigal
[2024-01-24 14:07:16,238] [INFO] Running command: gunzip -c /var/lib/cwl/stgc1ea14d7-d76f-45f3-b75b-79a331bf4d2b/GCF_024584055.1_ASM2458405v1_genomic.fna.gz | prodigal -d GCF_024584055.1_ASM2458405v1_genomic.fna/cds.fna -a GCF_024584055.1_ASM2458405v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:07:19,574] [INFO] Task succeeded: Prodigal
[2024-01-24 14:07:19,575] [INFO] Task started: HMMsearch
[2024-01-24 14:07:19,575] [INFO] Running command: hmmsearch --tblout GCF_024584055.1_ASM2458405v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d4ccce2-143f-451d-a3e8-1f30999bbb41/dqc_reference/reference_markers.hmm GCF_024584055.1_ASM2458405v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:07:19,820] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:07:19,821] [INFO] Found 6/6 markers.
[2024-01-24 14:07:19,844] [INFO] Query marker FASTA was written to GCF_024584055.1_ASM2458405v1_genomic.fna/markers.fasta
[2024-01-24 14:07:19,845] [INFO] Task started: Blastn
[2024-01-24 14:07:19,845] [INFO] Running command: blastn -query GCF_024584055.1_ASM2458405v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d4ccce2-143f-451d-a3e8-1f30999bbb41/dqc_reference/reference_markers.fasta -out GCF_024584055.1_ASM2458405v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:20,516] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:20,520] [INFO] Selected 5 target genomes.
[2024-01-24 14:07:20,521] [INFO] Target genome list was writen to GCF_024584055.1_ASM2458405v1_genomic.fna/target_genomes.txt
[2024-01-24 14:07:20,525] [INFO] Task started: fastANI
[2024-01-24 14:07:20,526] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1ea14d7-d76f-45f3-b75b-79a331bf4d2b/GCF_024584055.1_ASM2458405v1_genomic.fna.gz --refList GCF_024584055.1_ASM2458405v1_genomic.fna/target_genomes.txt --output GCF_024584055.1_ASM2458405v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:23,191] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:23,192] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d4ccce2-143f-451d-a3e8-1f30999bbb41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:23,192] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d4ccce2-143f-451d-a3e8-1f30999bbb41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:23,199] [INFO] Found 5 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 14:07:23,199] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:23,199] [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
Aliarcobacter skirrowii	strain=LMG 6621	GCA_024584055.1	28200	28200	type	True	100.0	641	641	95	conclusive
Aliarcobacter skirrowii	strain=LMG 6621	GCA_004115735.1	28200	28200	type	True	99.9979	640	641	95	conclusive
Aliarcobacter skirrowii	strain=CCUG 10374	GCA_008802155.1	28200	28200	type	True	99.9974	636	641	95	conclusive
Aliarcobacter skirrowii	strain=CCUG 10374	GCA_003544835.1	28200	28200	type	True	99.9974	640	641	95	conclusive
Aliarcobacter skirrowii	strain=NCTC12713	GCA_900445295.1	28200	28200	type	True	99.9936	639	641	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 14:07:23,201] [INFO] DFAST Taxonomy check result was written to GCF_024584055.1_ASM2458405v1_genomic.fna/tc_result.tsv
[2024-01-24 14:07:23,202] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:23,202] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:23,202] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d4ccce2-143f-451d-a3e8-1f30999bbb41/dqc_reference/checkm_data
[2024-01-24 14:07:23,204] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:23,233] [INFO] Task started: CheckM
[2024-01-24 14:07:23,234] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024584055.1_ASM2458405v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024584055.1_ASM2458405v1_genomic.fna/checkm_input GCF_024584055.1_ASM2458405v1_genomic.fna/checkm_result
[2024-01-24 14:07:41,400] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:41,401] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:41,428] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:41,428] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:41,429] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024584055.1_ASM2458405v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:41,429] [INFO] Task started: Blastn
[2024-01-24 14:07:41,429] [INFO] Running command: blastn -query GCF_024584055.1_ASM2458405v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d4ccce2-143f-451d-a3e8-1f30999bbb41/dqc_reference/reference_markers_gtdb.fasta -out GCF_024584055.1_ASM2458405v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:42,314] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:42,317] [INFO] Selected 8 target genomes.
[2024-01-24 14:07:42,317] [INFO] Target genome list was writen to GCF_024584055.1_ASM2458405v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:42,325] [INFO] Task started: fastANI
[2024-01-24 14:07:42,325] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1ea14d7-d76f-45f3-b75b-79a331bf4d2b/GCF_024584055.1_ASM2458405v1_genomic.fna.gz --refList GCF_024584055.1_ASM2458405v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024584055.1_ASM2458405v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:46,554] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:46,562] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:46,563] [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_003544835.1	s__Aliarcobacter skirrowii	99.9974	640	641	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.32	95.07	0.91	0.85	16	conclusive
GCF_014352935.1	s__Aliarcobacter cryaerophilus_A	86.6908	475	641	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.54	96.41	0.86	0.82	23	-
GCA_017996075.1	s__Aliarcobacter sp017996075	85.82	206	641	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.83	97.42	0.84	0.83	6	-
GCF_002993025.1	s__Aliarcobacter cryaerophilus_B	85.6969	455	641	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.88	97.88	0.90	0.90	2	-
GCF_003660105.1	s__Aliarcobacter cryaerophilus	84.665	477	641	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.99	99.99	1.00	0.99	3	-
GCF_004299785.2	s__Aliarcobacter porcinus	83.4593	474	641	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.76	98.06	0.91	0.88	6	-
GCF_004214815.1	s__Aliarcobacter thereius	83.3606	461	641	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.14	98.62	0.93	0.89	8	-
GCF_013201705.1	s__Aliarcobacter faecis	82.5548	457	641	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.88	99.77	0.97	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:46,566] [INFO] GTDB search result was written to GCF_024584055.1_ASM2458405v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:46,567] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:46,570] [INFO] DFAST_QC result json was written to GCF_024584055.1_ASM2458405v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:46,570] [INFO] DFAST_QC completed!
[2024-01-24 14:07:46,571] [INFO] Total running time: 0h0m32s