[2024-01-24 12:53:56,854] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:56,856] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:56,856] [INFO] DQC Reference Directory: /var/lib/cwl/stg408b3297-fd09-43da-823a-a68e63d77ee7/dqc_reference
[2024-01-24 12:53:58,277] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:58,278] [INFO] Task started: Prodigal
[2024-01-24 12:53:58,278] [INFO] Running command: gunzip -c /var/lib/cwl/stge09cf8ed-e139-48a1-8e1f-cb435e413253/GCF_004115805.1_ASM411580v1_genomic.fna.gz | prodigal -d GCF_004115805.1_ASM411580v1_genomic.fna/cds.fna -a GCF_004115805.1_ASM411580v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:02,583] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:02,584] [INFO] Task started: HMMsearch
[2024-01-24 12:54:02,584] [INFO] Running command: hmmsearch --tblout GCF_004115805.1_ASM411580v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg408b3297-fd09-43da-823a-a68e63d77ee7/dqc_reference/reference_markers.hmm GCF_004115805.1_ASM411580v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:02,882] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:02,884] [INFO] Found 6/6 markers.
[2024-01-24 12:54:02,916] [INFO] Query marker FASTA was written to GCF_004115805.1_ASM411580v1_genomic.fna/markers.fasta
[2024-01-24 12:54:02,916] [INFO] Task started: Blastn
[2024-01-24 12:54:02,917] [INFO] Running command: blastn -query GCF_004115805.1_ASM411580v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg408b3297-fd09-43da-823a-a68e63d77ee7/dqc_reference/reference_markers.fasta -out GCF_004115805.1_ASM411580v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:03,559] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:03,563] [INFO] Selected 11 target genomes.
[2024-01-24 12:54:03,563] [INFO] Target genome list was writen to GCF_004115805.1_ASM411580v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:03,568] [INFO] Task started: fastANI
[2024-01-24 12:54:03,568] [INFO] Running command: fastANI --query /var/lib/cwl/stge09cf8ed-e139-48a1-8e1f-cb435e413253/GCF_004115805.1_ASM411580v1_genomic.fna.gz --refList GCF_004115805.1_ASM411580v1_genomic.fna/target_genomes.txt --output GCF_004115805.1_ASM411580v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:10,942] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:10,942] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg408b3297-fd09-43da-823a-a68e63d77ee7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:10,942] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg408b3297-fd09-43da-823a-a68e63d77ee7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:10,952] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:54:10,952] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:10,953] [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 cloacae	strain=CECT 7834	GCA_004115805.1	1054034	1054034	type	True	100.0	884	886	95	conclusive
Arcobacter cloacae	strain=LMG 26153	GCA_013201935.1	1054034	1054034	type	True	99.9958	885	886	95	conclusive
Arcobacter aquimarinus	strain=CECT 8442	GCA_004115795.1	1315211	1315211	type	True	93.0653	671	886	95	below_threshold
Arcobacter aquimarinus	strain=W63	GCA_013177635.1	1315211	1315211	type	True	93.0264	695	886	95	below_threshold
Arcobacter ellisii	strain=CECT 7837	GCA_004115815.1	913109	913109	type	True	86.3512	652	886	95	below_threshold
Arcobacter ellisii	strain=LMG 26155	GCA_003544915.1	913109	913109	type	True	86.2081	670	886	95	below_threshold
Arcobacter suis	strain=CECT7833	GCA_004023465.1	1278212	1278212	type	True	84.5088	575	886	95	below_threshold
Arcobacter venerupis	strain=LMG 26156	GCA_013201665.1	1054033	1054033	type	True	83.5869	610	886	95	below_threshold
Aliarcobacter faecis	strain=LMG 28519	GCA_024584135.1	1564138	1564138	type	True	80.4131	466	886	95	below_threshold
Arcobacter vandammei	strain=LMG 31429	GCA_024583975.1	2782243	2782243	type	True	80.2357	434	886	95	below_threshold
Arcobacter vandammei	strain=R-73987	GCA_016106035.1	2782243	2782243	type	True	80.193	432	886	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:10,954] [INFO] DFAST Taxonomy check result was written to GCF_004115805.1_ASM411580v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:10,955] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:10,955] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:10,955] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg408b3297-fd09-43da-823a-a68e63d77ee7/dqc_reference/checkm_data
[2024-01-24 12:54:10,956] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:10,984] [INFO] Task started: CheckM
[2024-01-24 12:54:10,984] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004115805.1_ASM411580v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004115805.1_ASM411580v1_genomic.fna/checkm_input GCF_004115805.1_ASM411580v1_genomic.fna/checkm_result
[2024-01-24 12:54:30,674] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:30,675] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:30,697] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:30,697] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:30,698] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004115805.1_ASM411580v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:30,698] [INFO] Task started: Blastn
[2024-01-24 12:54:30,698] [INFO] Running command: blastn -query GCF_004115805.1_ASM411580v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg408b3297-fd09-43da-823a-a68e63d77ee7/dqc_reference/reference_markers_gtdb.fasta -out GCF_004115805.1_ASM411580v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:31,658] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:31,661] [INFO] Selected 12 target genomes.
[2024-01-24 12:54:31,661] [INFO] Target genome list was writen to GCF_004115805.1_ASM411580v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:31,667] [INFO] Task started: fastANI
[2024-01-24 12:54:31,668] [INFO] Running command: fastANI --query /var/lib/cwl/stge09cf8ed-e139-48a1-8e1f-cb435e413253/GCF_004115805.1_ASM411580v1_genomic.fna.gz --refList GCF_004115805.1_ASM411580v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004115805.1_ASM411580v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:39,308] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:39,319] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:39,319] [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_013201935.1	s__Aliarcobacter cloacae	99.9958	885	886	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.96	95.91	0.93	0.87	3	conclusive
GCF_013177635.1	s__Aliarcobacter aquimarinus	92.9819	697	886	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003544915.1	s__Aliarcobacter ellisii	86.1873	671	886	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.73	97.46	0.92	0.84	3	-
GCF_013201725.1	s__Aliarcobacter defluvii	84.8134	657	886	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.85	98.15	0.93	0.88	4	-
GCF_003544815.1	s__Aliarcobacter suis	84.6218	578	886	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003063245.1	s__Aliarcobacter caeni	83.8181	554	886	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013201665.1	s__Aliarcobacter venerupis	83.557	613	886	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	83.0273	520	886	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003660105.1	s__Aliarcobacter cryaerophilus	80.5732	399	886	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.99	99.99	1.00	0.99	3	-
GCF_016106035.1	s__Aliarcobacter sp016106035	80.2002	431	886	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009208075.1	s__Poseidonibacter sp009208075	79.9726	433	886	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	99.63	99.63	0.93	0.93	3	-
GCF_003667345.1	s__Poseidonibacter antarcticus	79.914	444	886	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:54:39,321] [INFO] GTDB search result was written to GCF_004115805.1_ASM411580v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:39,322] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:39,327] [INFO] DFAST_QC result json was written to GCF_004115805.1_ASM411580v1_genomic.fna/dqc_result.json
[2024-01-24 12:54:39,328] [INFO] DFAST_QC completed!
[2024-01-24 12:54:39,328] [INFO] Total running time: 0h0m42s