[2023-06-17 06:59:23,332] [INFO] DFAST_QC pipeline started.
[2023-06-17 06:59:23,334] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 06:59:23,335] [INFO] DQC Reference Directory: /var/lib/cwl/stgad55e807-783d-4cfe-bccc-0236f7e21f9c/dqc_reference
[2023-06-17 06:59:24,658] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 06:59:24,659] [INFO] Task started: Prodigal
[2023-06-17 06:59:24,659] [INFO] Running command: gunzip -c /var/lib/cwl/stgb7906636-4541-4a43-aec0-719751997b96/GCA_028690015.1_ASM2869001v1_genomic.fna.gz | prodigal -d GCA_028690015.1_ASM2869001v1_genomic.fna/cds.fna -a GCA_028690015.1_ASM2869001v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 06:59:28,335] [INFO] Task succeeded: Prodigal
[2023-06-17 06:59:28,336] [INFO] Task started: HMMsearch
[2023-06-17 06:59:28,336] [INFO] Running command: hmmsearch --tblout GCA_028690015.1_ASM2869001v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad55e807-783d-4cfe-bccc-0236f7e21f9c/dqc_reference/reference_markers.hmm GCA_028690015.1_ASM2869001v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 06:59:28,525] [INFO] Task succeeded: HMMsearch
[2023-06-17 06:59:28,526] [INFO] Found 6/6 markers.
[2023-06-17 06:59:28,550] [INFO] Query marker FASTA was written to GCA_028690015.1_ASM2869001v1_genomic.fna/markers.fasta
[2023-06-17 06:59:28,550] [INFO] Task started: Blastn
[2023-06-17 06:59:28,550] [INFO] Running command: blastn -query GCA_028690015.1_ASM2869001v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad55e807-783d-4cfe-bccc-0236f7e21f9c/dqc_reference/reference_markers.fasta -out GCA_028690015.1_ASM2869001v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 06:59:29,135] [INFO] Task succeeded: Blastn
[2023-06-17 06:59:29,139] [INFO] Selected 9 target genomes.
[2023-06-17 06:59:29,139] [INFO] Target genome list was writen to GCA_028690015.1_ASM2869001v1_genomic.fna/target_genomes.txt
[2023-06-17 06:59:29,142] [INFO] Task started: fastANI
[2023-06-17 06:59:29,143] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7906636-4541-4a43-aec0-719751997b96/GCA_028690015.1_ASM2869001v1_genomic.fna.gz --refList GCA_028690015.1_ASM2869001v1_genomic.fna/target_genomes.txt --output GCA_028690015.1_ASM2869001v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 06:59:34,926] [INFO] Task succeeded: fastANI
[2023-06-17 06:59:34,926] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad55e807-783d-4cfe-bccc-0236f7e21f9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 06:59:34,927] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad55e807-783d-4cfe-bccc-0236f7e21f9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 06:59:34,935] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2023-06-17 06:59:34,935] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-17 06:59:34,935] [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
Arcobacter ellisii	strain=LMG 26155	GCA_003544915.1	913109	913109	type	True	96.7401	688	801	95	conclusive
Arcobacter ellisii	strain=CECT 7837	GCA_004115815.1	913109	913109	type	True	96.7349	681	801	95	conclusive
Arcobacter defluvii	strain=CECT 7697	GCA_004115775.1	873191	873191	type	True	88.2293	645	801	95	below_threshold
Arcobacter defluvii	strain=LMG 25694	GCA_013201725.1	873191	873191	type	True	88.1512	647	801	95	below_threshold
Arcobacter cloacae	strain=LMG 26153	GCA_013201935.1	1054034	1054034	type	True	86.4457	623	801	95	below_threshold
Arcobacter cloacae	strain=CECT 7834	GCA_004115805.1	1054034	1054034	type	True	86.4158	599	801	95	below_threshold
Arcobacter aquimarinus	strain=CECT 8442	GCA_004115795.1	1315211	1315211	type	True	86.3583	600	801	95	below_threshold
Arcobacter suis	strain=CECT7833	GCA_004023465.1	1278212	1278212	type	True	84.6562	583	801	95	below_threshold
Arcobacter venerupis	strain=LMG 26156	GCA_013201665.1	1054033	1054033	type	True	83.7971	623	801	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 06:59:34,937] [INFO] DFAST Taxonomy check result was written to GCA_028690015.1_ASM2869001v1_genomic.fna/tc_result.tsv
[2023-06-17 06:59:34,938] [INFO] ===== Taxonomy check completed =====
[2023-06-17 06:59:34,938] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 06:59:34,938] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad55e807-783d-4cfe-bccc-0236f7e21f9c/dqc_reference/checkm_data
[2023-06-17 06:59:34,939] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 06:59:34,964] [INFO] Task started: CheckM
[2023-06-17 06:59:34,964] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028690015.1_ASM2869001v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028690015.1_ASM2869001v1_genomic.fna/checkm_input GCA_028690015.1_ASM2869001v1_genomic.fna/checkm_result
[2023-06-17 06:59:52,986] [INFO] Task succeeded: CheckM
[2023-06-17 06:59:52,987] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.42%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 06:59:53,003] [INFO] ===== Completeness check finished =====
[2023-06-17 06:59:53,003] [INFO] ===== Start GTDB Search =====
[2023-06-17 06:59:53,004] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028690015.1_ASM2869001v1_genomic.fna/markers.fasta)
[2023-06-17 06:59:53,004] [INFO] Task started: Blastn
[2023-06-17 06:59:53,004] [INFO] Running command: blastn -query GCA_028690015.1_ASM2869001v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad55e807-783d-4cfe-bccc-0236f7e21f9c/dqc_reference/reference_markers_gtdb.fasta -out GCA_028690015.1_ASM2869001v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 06:59:53,818] [INFO] Task succeeded: Blastn
[2023-06-17 06:59:53,822] [INFO] Selected 10 target genomes.
[2023-06-17 06:59:53,822] [INFO] Target genome list was writen to GCA_028690015.1_ASM2869001v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 06:59:53,830] [INFO] Task started: fastANI
[2023-06-17 06:59:53,830] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7906636-4541-4a43-aec0-719751997b96/GCA_028690015.1_ASM2869001v1_genomic.fna.gz --refList GCA_028690015.1_ASM2869001v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028690015.1_ASM2869001v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 07:00:00,292] [INFO] Task succeeded: fastANI
[2023-06-17 07:00:00,303] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 07:00:00,303] [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_003544915.1	s__Aliarcobacter ellisii	96.7665	687	801	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.73	97.46	0.92	0.84	3	conclusive
GCF_013201725.1	s__Aliarcobacter defluvii	88.1512	647	801	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.85	98.15	0.93	0.88	4	-
GCF_013201935.1	s__Aliarcobacter cloacae	86.4014	626	801	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.96	95.91	0.93	0.87	3	-
GCF_013177635.1	s__Aliarcobacter aquimarinus	86.2798	610	801	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003544815.1	s__Aliarcobacter suis	84.5577	600	801	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003063295.1	s__Aliarcobacter lacus	84.2724	488	801	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187115.1	s__Aliarcobacter butzleri	84.1088	526	801	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.53	96.98	0.89	0.81	50	-
GCF_013201665.1	s__Aliarcobacter venerupis	83.7808	623	801	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	100.00	100.00	0.99	0.99	2	-
GCA_018816105.1	s__Aliarcobacter sp018816105	83.2229	519	801	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013201625.1	s__Aliarcobacter lanthieri	80.5262	423	801	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.15	95.77	0.93	0.89	6	-
--------------------------------------------------------------------------------
[2023-06-17 07:00:00,305] [INFO] GTDB search result was written to GCA_028690015.1_ASM2869001v1_genomic.fna/result_gtdb.tsv
[2023-06-17 07:00:00,306] [INFO] ===== GTDB Search completed =====
[2023-06-17 07:00:00,309] [INFO] DFAST_QC result json was written to GCA_028690015.1_ASM2869001v1_genomic.fna/dqc_result.json
[2023-06-17 07:00:00,309] [INFO] DFAST_QC completed!
[2023-06-17 07:00:00,309] [INFO] Total running time: 0h0m37s