[2024-01-24 13:41:41,348] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:41,350] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:41,350] [INFO] DQC Reference Directory: /var/lib/cwl/stgcfe6cd74-dead-4457-a9a3-9198449dbf27/dqc_reference
[2024-01-24 13:41:42,539] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:42,540] [INFO] Task started: Prodigal
[2024-01-24 13:41:42,540] [INFO] Running command: gunzip -c /var/lib/cwl/stg8aedf143-7c49-40ed-9e03-43c7876b7b00/GCF_004115795.1_ASM411579v1_genomic.fna.gz | prodigal -d GCF_004115795.1_ASM411579v1_genomic.fna/cds.fna -a GCF_004115795.1_ASM411579v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:46,144] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:46,145] [INFO] Task started: HMMsearch
[2024-01-24 13:41:46,145] [INFO] Running command: hmmsearch --tblout GCF_004115795.1_ASM411579v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcfe6cd74-dead-4457-a9a3-9198449dbf27/dqc_reference/reference_markers.hmm GCF_004115795.1_ASM411579v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:46,429] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:46,436] [INFO] Found 6/6 markers.
[2024-01-24 13:41:46,476] [INFO] Query marker FASTA was written to GCF_004115795.1_ASM411579v1_genomic.fna/markers.fasta
[2024-01-24 13:41:46,477] [INFO] Task started: Blastn
[2024-01-24 13:41:46,478] [INFO] Running command: blastn -query GCF_004115795.1_ASM411579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfe6cd74-dead-4457-a9a3-9198449dbf27/dqc_reference/reference_markers.fasta -out GCF_004115795.1_ASM411579v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:47,175] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:47,180] [INFO] Selected 9 target genomes.
[2024-01-24 13:41:47,180] [INFO] Target genome list was writen to GCF_004115795.1_ASM411579v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:47,188] [INFO] Task started: fastANI
[2024-01-24 13:41:47,188] [INFO] Running command: fastANI --query /var/lib/cwl/stg8aedf143-7c49-40ed-9e03-43c7876b7b00/GCF_004115795.1_ASM411579v1_genomic.fna.gz --refList GCF_004115795.1_ASM411579v1_genomic.fna/target_genomes.txt --output GCF_004115795.1_ASM411579v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:53,200] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:53,201] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcfe6cd74-dead-4457-a9a3-9198449dbf27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:53,202] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcfe6cd74-dead-4457-a9a3-9198449dbf27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:53,218] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:53,218] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:53,218] [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=CECT 8442	GCA_004115795.1	1315211	1315211	type	True	100.0	788	791	95	conclusive
Arcobacter aquimarinus	strain=W63	GCA_013177635.1	1315211	1315211	type	True	99.9981	790	791	95	conclusive
Arcobacter cloacae	strain=LMG 26153	GCA_013201935.1	1054034	1054034	type	True	93.0241	687	791	95	below_threshold
Arcobacter cloacae	strain=CECT 7834	GCA_004115805.1	1054034	1054034	type	True	93.0206	681	791	95	below_threshold
Arcobacter ellisii	strain=LMG 26155	GCA_003544915.1	913109	913109	type	True	85.9209	632	791	95	below_threshold
Arcobacter defluvii	strain=CECT 7697	GCA_004115775.1	873191	873191	type	True	85.5359	632	791	95	below_threshold
Arcobacter defluvii	strain=LMG 25694	GCA_013201725.1	873191	873191	type	True	85.525	631	791	95	below_threshold
Arcobacter suis	strain=CECT7833	GCA_004023465.1	1278212	1278212	type	True	84.1204	570	791	95	below_threshold
Arcobacter venerupis	strain=LMG 26156	GCA_013201665.1	1054033	1054033	type	True	83.3742	591	791	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:53,221] [INFO] DFAST Taxonomy check result was written to GCF_004115795.1_ASM411579v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:53,222] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:53,222] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:53,223] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcfe6cd74-dead-4457-a9a3-9198449dbf27/dqc_reference/checkm_data
[2024-01-24 13:41:53,225] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:53,274] [INFO] Task started: CheckM
[2024-01-24 13:41:53,275] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004115795.1_ASM411579v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004115795.1_ASM411579v1_genomic.fna/checkm_input GCF_004115795.1_ASM411579v1_genomic.fna/checkm_result
[2024-01-24 13:42:12,590] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:12,591] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:12,620] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:12,621] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:12,621] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004115795.1_ASM411579v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:12,622] [INFO] Task started: Blastn
[2024-01-24 13:42:12,622] [INFO] Running command: blastn -query GCF_004115795.1_ASM411579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfe6cd74-dead-4457-a9a3-9198449dbf27/dqc_reference/reference_markers_gtdb.fasta -out GCF_004115795.1_ASM411579v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:13,459] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:13,464] [INFO] Selected 9 target genomes.
[2024-01-24 13:42:13,464] [INFO] Target genome list was writen to GCF_004115795.1_ASM411579v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:13,473] [INFO] Task started: fastANI
[2024-01-24 13:42:13,474] [INFO] Running command: fastANI --query /var/lib/cwl/stg8aedf143-7c49-40ed-9e03-43c7876b7b00/GCF_004115795.1_ASM411579v1_genomic.fna.gz --refList GCF_004115795.1_ASM411579v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004115795.1_ASM411579v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:19,793] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:19,813] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:19,814] [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	99.9981	790	791	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	93.0511	686	791	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	85.9678	630	791	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	85.525	631	791	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	84.1677	569	791	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	83.6121	535	791	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	83.4099	522	791	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	83.3327	594	791	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	82.866	490	791	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 13:42:19,816] [INFO] GTDB search result was written to GCF_004115795.1_ASM411579v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:19,817] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:19,823] [INFO] DFAST_QC result json was written to GCF_004115795.1_ASM411579v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:19,824] [INFO] DFAST_QC completed!
[2024-01-24 13:42:19,824] [INFO] Total running time: 0h0m38s