[2024-01-24 12:14:49,058] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:49,061] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:49,061] [INFO] DQC Reference Directory: /var/lib/cwl/stge9985d99-2945-4c82-9b00-e8c8bbe5c6e7/dqc_reference
[2024-01-24 12:14:50,392] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:50,454] [INFO] Task started: Prodigal
[2024-01-24 12:14:50,454] [INFO] Running command: gunzip -c /var/lib/cwl/stg78a67643-29b3-4d99-a6c0-bed8689d6bea/GCF_013177635.1_ASM1317763v1_genomic.fna.gz | prodigal -d GCF_013177635.1_ASM1317763v1_genomic.fna/cds.fna -a GCF_013177635.1_ASM1317763v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:54,580] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:54,580] [INFO] Task started: HMMsearch
[2024-01-24 12:14:54,580] [INFO] Running command: hmmsearch --tblout GCF_013177635.1_ASM1317763v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9985d99-2945-4c82-9b00-e8c8bbe5c6e7/dqc_reference/reference_markers.hmm GCF_013177635.1_ASM1317763v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:54,815] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:54,817] [INFO] Found 6/6 markers.
[2024-01-24 12:14:54,850] [INFO] Query marker FASTA was written to GCF_013177635.1_ASM1317763v1_genomic.fna/markers.fasta
[2024-01-24 12:14:54,851] [INFO] Task started: Blastn
[2024-01-24 12:14:54,851] [INFO] Running command: blastn -query GCF_013177635.1_ASM1317763v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9985d99-2945-4c82-9b00-e8c8bbe5c6e7/dqc_reference/reference_markers.fasta -out GCF_013177635.1_ASM1317763v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:55,534] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:55,537] [INFO] Selected 9 target genomes.
[2024-01-24 12:14:55,537] [INFO] Target genome list was writen to GCF_013177635.1_ASM1317763v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:55,545] [INFO] Task started: fastANI
[2024-01-24 12:14:55,546] [INFO] Running command: fastANI --query /var/lib/cwl/stg78a67643-29b3-4d99-a6c0-bed8689d6bea/GCF_013177635.1_ASM1317763v1_genomic.fna.gz --refList GCF_013177635.1_ASM1317763v1_genomic.fna/target_genomes.txt --output GCF_013177635.1_ASM1317763v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:01,812] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:01,813] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9985d99-2945-4c82-9b00-e8c8bbe5c6e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:01,813] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9985d99-2945-4c82-9b00-e8c8bbe5c6e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:01,821] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:15:01,821] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:01,822] [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 aquimarinus	strain=W63	GCA_013177635.1	1315211	1315211	type	True	100.0	837	840	95	conclusive
Arcobacter aquimarinus	strain=CECT 8442	GCA_004115795.1	1315211	1315211	type	True	99.9359	783	840	95	conclusive
Arcobacter cloacae	strain=LMG 26153	GCA_013201935.1	1054034	1054034	type	True	93.1758	712	840	95	below_threshold
Arcobacter cloacae	strain=CECT 7834	GCA_004115805.1	1054034	1054034	type	True	92.9035	706	840	95	below_threshold
Arcobacter ellisii	strain=LMG 26155	GCA_003544915.1	913109	913109	type	True	86.2008	651	840	95	below_threshold
Arcobacter defluvii	strain=LMG 25694	GCA_013201725.1	873191	873191	type	True	85.7956	662	840	95	below_threshold
Arcobacter defluvii	strain=CECT 7697	GCA_004115775.1	873191	873191	type	True	85.5842	647	840	95	below_threshold
Arcobacter suis	strain=CECT7833	GCA_004023465.1	1278212	1278212	type	True	84.0238	588	840	95	below_threshold
Arcobacter venerupis	strain=LMG 26156	GCA_013201665.1	1054033	1054033	type	True	83.5206	612	840	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:01,823] [INFO] DFAST Taxonomy check result was written to GCF_013177635.1_ASM1317763v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:01,824] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:01,824] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:01,824] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9985d99-2945-4c82-9b00-e8c8bbe5c6e7/dqc_reference/checkm_data
[2024-01-24 12:15:01,825] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:01,858] [INFO] Task started: CheckM
[2024-01-24 12:15:01,858] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013177635.1_ASM1317763v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013177635.1_ASM1317763v1_genomic.fna/checkm_input GCF_013177635.1_ASM1317763v1_genomic.fna/checkm_result
[2024-01-24 12:15:21,696] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:21,697] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:21,719] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:21,719] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:21,720] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013177635.1_ASM1317763v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:21,720] [INFO] Task started: Blastn
[2024-01-24 12:15:21,720] [INFO] Running command: blastn -query GCF_013177635.1_ASM1317763v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9985d99-2945-4c82-9b00-e8c8bbe5c6e7/dqc_reference/reference_markers_gtdb.fasta -out GCF_013177635.1_ASM1317763v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:22,560] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:22,564] [INFO] Selected 9 target genomes.
[2024-01-24 12:15:22,565] [INFO] Target genome list was writen to GCF_013177635.1_ASM1317763v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:22,572] [INFO] Task started: fastANI
[2024-01-24 12:15:22,573] [INFO] Running command: fastANI --query /var/lib/cwl/stg78a67643-29b3-4d99-a6c0-bed8689d6bea/GCF_013177635.1_ASM1317763v1_genomic.fna.gz --refList GCF_013177635.1_ASM1317763v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013177635.1_ASM1317763v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:28,991] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:29,000] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:29,000] [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_013177635.1	s__Aliarcobacter aquimarinus	100.0	835	840	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_013201935.1	s__Aliarcobacter cloacae	93.2042	711	840	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.96	95.91	0.93	0.87	3	-
GCF_003544915.1	s__Aliarcobacter ellisii	86.1557	649	840	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	85.7932	660	840	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	84.1809	585	840	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	83.6408	548	840	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	83.6184	537	840	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	83.4852	614	840	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	100.00	100.00	0.99	0.99	2	-
GCA_017995775.1	s__Aliarcobacter sp017995775	82.795	504	840	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.13	99.13	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:29,002] [INFO] GTDB search result was written to GCF_013177635.1_ASM1317763v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:29,003] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:29,008] [INFO] DFAST_QC result json was written to GCF_013177635.1_ASM1317763v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:29,008] [INFO] DFAST_QC completed!
[2024-01-24 12:15:29,008] [INFO] Total running time: 0h0m40s