[2024-01-24 11:13:04,545] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:13:04,547] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:13:04,547] [INFO] DQC Reference Directory: /var/lib/cwl/stg34c7b4b0-8eb3-4006-9598-5caf195e8c11/dqc_reference
[2024-01-24 11:13:05,801] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:13:05,802] [INFO] Task started: Prodigal
[2024-01-24 11:13:05,802] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3ef00a3-7dff-4737-8b02-f4a38c2dcb0f/GCF_003660105.1_ASM366010v1_genomic.fna.gz | prodigal -d GCF_003660105.1_ASM366010v1_genomic.fna/cds.fna -a GCF_003660105.1_ASM366010v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:09,116] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:09,116] [INFO] Task started: HMMsearch
[2024-01-24 11:13:09,117] [INFO] Running command: hmmsearch --tblout GCF_003660105.1_ASM366010v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34c7b4b0-8eb3-4006-9598-5caf195e8c11/dqc_reference/reference_markers.hmm GCF_003660105.1_ASM366010v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:09,362] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:09,364] [INFO] Found 6/6 markers.
[2024-01-24 11:13:09,389] [INFO] Query marker FASTA was written to GCF_003660105.1_ASM366010v1_genomic.fna/markers.fasta
[2024-01-24 11:13:09,390] [INFO] Task started: Blastn
[2024-01-24 11:13:09,390] [INFO] Running command: blastn -query GCF_003660105.1_ASM366010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34c7b4b0-8eb3-4006-9598-5caf195e8c11/dqc_reference/reference_markers.fasta -out GCF_003660105.1_ASM366010v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:10,024] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:10,028] [INFO] Selected 10 target genomes.
[2024-01-24 11:13:10,028] [INFO] Target genome list was writen to GCF_003660105.1_ASM366010v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:10,331] [INFO] Task started: fastANI
[2024-01-24 11:13:10,331] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3ef00a3-7dff-4737-8b02-f4a38c2dcb0f/GCF_003660105.1_ASM366010v1_genomic.fna.gz --refList GCF_003660105.1_ASM366010v1_genomic.fna/target_genomes.txt --output GCF_003660105.1_ASM366010v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:15,301] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:15,302] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34c7b4b0-8eb3-4006-9598-5caf195e8c11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:15,302] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34c7b4b0-8eb3-4006-9598-5caf195e8c11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:15,315] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:13:15,315] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:15,315] [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 cryaerophilus	strain=ATCC 43158	GCA_003660105.1	28198	28198	suspected-type	True	100.0	699	701	95	conclusive
Aliarcobacter cryaerophilus	strain=LMG 9904	GCA_006165035.1	28198	28198	suspected-type	True	99.9918	695	701	95	conclusive
Aliarcobacter cryaerophilus	strain=LMG 24291	GCA_002992955.1	28198	28198	suspected-type	True	99.9105	646	701	95	conclusive
Aliarcobacter trophiarum	strain=LMG 25534	GCA_003355515.1	708186	708186	type	True	86.7961	517	701	95	below_threshold
Aliarcobacter trophiarum	strain=LMG 25534	GCA_024584015.1	708186	708186	type	True	86.5646	500	701	95	below_threshold
Aliarcobacter skirrowii	strain=LMG 6621	GCA_024584055.1	28200	28200	type	True	84.7551	473	701	95	below_threshold
Aliarcobacter skirrowii	strain=LMG 6621	GCA_004115735.1	28200	28200	type	True	84.7537	470	701	95	below_threshold
Aliarcobacter faecis	strain=LMG 28519	GCA_024584135.1	1564138	1564138	type	True	83.5899	481	701	95	below_threshold
Arcobacter vandammei	strain=LMG 31429	GCA_024583975.1	2782243	2782243	type	True	83.3547	442	701	95	below_threshold
Arcobacter vandammei	strain=R-73987	GCA_016106035.1	2782243	2782243	type	True	83.3501	436	701	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:15,317] [INFO] DFAST Taxonomy check result was written to GCF_003660105.1_ASM366010v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:15,318] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:15,318] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:15,318] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34c7b4b0-8eb3-4006-9598-5caf195e8c11/dqc_reference/checkm_data
[2024-01-24 11:13:15,319] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:15,341] [INFO] Task started: CheckM
[2024-01-24 11:13:15,342] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003660105.1_ASM366010v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003660105.1_ASM366010v1_genomic.fna/checkm_input GCF_003660105.1_ASM366010v1_genomic.fna/checkm_result
[2024-01-24 11:13:35,615] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:35,617] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:35,641] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:35,641] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:35,641] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003660105.1_ASM366010v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:35,642] [INFO] Task started: Blastn
[2024-01-24 11:13:35,642] [INFO] Running command: blastn -query GCF_003660105.1_ASM366010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34c7b4b0-8eb3-4006-9598-5caf195e8c11/dqc_reference/reference_markers_gtdb.fasta -out GCF_003660105.1_ASM366010v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:36,622] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:36,626] [INFO] Selected 11 target genomes.
[2024-01-24 11:13:36,627] [INFO] Target genome list was writen to GCF_003660105.1_ASM366010v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:36,637] [INFO] Task started: fastANI
[2024-01-24 11:13:36,637] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3ef00a3-7dff-4737-8b02-f4a38c2dcb0f/GCF_003660105.1_ASM366010v1_genomic.fna.gz --refList GCF_003660105.1_ASM366010v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003660105.1_ASM366010v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:42,228] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:42,249] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:42,249] [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_003660105.1	s__Aliarcobacter cryaerophilus	100.0	699	701	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.99	99.99	1.00	0.99	3	conclusive
GCF_002993025.1	s__Aliarcobacter cryaerophilus_B	94.0558	557	701	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.88	97.88	0.90	0.90	2	-
GCA_017996075.1	s__Aliarcobacter sp017996075	93.5013	228	701	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.83	97.42	0.84	0.83	6	-
GCF_014352935.1	s__Aliarcobacter cryaerophilus_A	92.9301	579	701	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.54	96.41	0.86	0.82	23	-
GCF_003355515.1	s__Aliarcobacter trophiarum	86.7644	517	701	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.76	99.53	0.96	0.92	3	-
GCF_003544835.1	s__Aliarcobacter skirrowii	84.9406	487	701	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.32	95.07	0.91	0.85	16	-
GCF_013201705.1	s__Aliarcobacter faecis	83.8671	487	701	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.88	99.77	0.97	0.95	3	-
GCF_016106035.1	s__Aliarcobacter sp016106035	83.3163	439	701	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004299785.2	s__Aliarcobacter porcinus	82.5991	432	701	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	82.2212	434	701	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.14	98.62	0.93	0.89	8	-
GCA_017995775.1	s__Aliarcobacter sp017995775	79.8944	351	701	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 11:13:42,251] [INFO] GTDB search result was written to GCF_003660105.1_ASM366010v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:42,252] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:42,255] [INFO] DFAST_QC result json was written to GCF_003660105.1_ASM366010v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:42,255] [INFO] DFAST_QC completed!
[2024-01-24 11:13:42,255] [INFO] Total running time: 0h0m38s