[2024-01-24 13:43:27,165] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:43:27,167] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:43:27,167] [INFO] DQC Reference Directory: /var/lib/cwl/stga1875088-8e6e-48b1-8297-d1137c04f661/dqc_reference
[2024-01-24 13:43:28,321] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:43:28,322] [INFO] Task started: Prodigal
[2024-01-24 13:43:28,323] [INFO] Running command: gunzip -c /var/lib/cwl/stg660d88c2-93b3-45f7-80e9-9823c35403a1/GCF_002992955.1_ASM299295v1_genomic.fna.gz | prodigal -d GCF_002992955.1_ASM299295v1_genomic.fna/cds.fna -a GCF_002992955.1_ASM299295v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:43:31,307] [INFO] Task succeeded: Prodigal
[2024-01-24 13:43:31,307] [INFO] Task started: HMMsearch
[2024-01-24 13:43:31,307] [INFO] Running command: hmmsearch --tblout GCF_002992955.1_ASM299295v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1875088-8e6e-48b1-8297-d1137c04f661/dqc_reference/reference_markers.hmm GCF_002992955.1_ASM299295v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:43:31,472] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:43:31,473] [INFO] Found 6/6 markers.
[2024-01-24 13:43:31,495] [INFO] Query marker FASTA was written to GCF_002992955.1_ASM299295v1_genomic.fna/markers.fasta
[2024-01-24 13:43:31,495] [INFO] Task started: Blastn
[2024-01-24 13:43:31,495] [INFO] Running command: blastn -query GCF_002992955.1_ASM299295v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1875088-8e6e-48b1-8297-d1137c04f661/dqc_reference/reference_markers.fasta -out GCF_002992955.1_ASM299295v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:32,105] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:32,108] [INFO] Selected 10 target genomes.
[2024-01-24 13:43:32,108] [INFO] Target genome list was writen to GCF_002992955.1_ASM299295v1_genomic.fna/target_genomes.txt
[2024-01-24 13:43:32,161] [INFO] Task started: fastANI
[2024-01-24 13:43:32,161] [INFO] Running command: fastANI --query /var/lib/cwl/stg660d88c2-93b3-45f7-80e9-9823c35403a1/GCF_002992955.1_ASM299295v1_genomic.fna.gz --refList GCF_002992955.1_ASM299295v1_genomic.fna/target_genomes.txt --output GCF_002992955.1_ASM299295v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:43:36,843] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:36,844] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1875088-8e6e-48b1-8297-d1137c04f661/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:43:36,844] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1875088-8e6e-48b1-8297-d1137c04f661/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:43:36,852] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:43:36,852] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:43:36,853] [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=LMG 24291	GCA_002992955.1	28198	28198	suspected-type	True	100.0	646	649	95	conclusive
Aliarcobacter cryaerophilus	strain=ATCC 43158	GCA_003660105.1	28198	28198	suspected-type	True	99.9972	648	649	95	conclusive
Aliarcobacter cryaerophilus	strain=LMG 9904	GCA_006165035.1	28198	28198	suspected-type	True	99.9964	649	649	95	conclusive
Aliarcobacter trophiarum	strain=LMG 25534	GCA_003355515.1	708186	708186	type	True	86.7345	488	649	95	below_threshold
Aliarcobacter trophiarum	strain=LMG 25534	GCA_024584015.1	708186	708186	type	True	86.6822	485	649	95	below_threshold
Aliarcobacter skirrowii	strain=LMG 6621	GCA_024584055.1	28200	28200	type	True	84.949	463	649	95	below_threshold
Aliarcobacter skirrowii	strain=LMG 6621	GCA_004115735.1	28200	28200	type	True	84.9427	460	649	95	below_threshold
Aliarcobacter faecis	strain=LMG 28519	GCA_024584135.1	1564138	1564138	type	True	83.439	476	649	95	below_threshold
Arcobacter vandammei	strain=LMG 31429	GCA_024583975.1	2782243	2782243	type	True	83.4187	443	649	95	below_threshold
Arcobacter vandammei	strain=R-73987	GCA_016106035.1	2782243	2782243	type	True	83.3612	444	649	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:43:36,854] [INFO] DFAST Taxonomy check result was written to GCF_002992955.1_ASM299295v1_genomic.fna/tc_result.tsv
[2024-01-24 13:43:36,855] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:43:36,855] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:43:36,855] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1875088-8e6e-48b1-8297-d1137c04f661/dqc_reference/checkm_data
[2024-01-24 13:43:36,856] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:43:36,877] [INFO] Task started: CheckM
[2024-01-24 13:43:36,877] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002992955.1_ASM299295v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002992955.1_ASM299295v1_genomic.fna/checkm_input GCF_002992955.1_ASM299295v1_genomic.fna/checkm_result
[2024-01-24 13:43:52,541] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:52,543] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:52,561] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:52,561] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:52,562] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002992955.1_ASM299295v1_genomic.fna/markers.fasta)
[2024-01-24 13:43:52,562] [INFO] Task started: Blastn
[2024-01-24 13:43:52,562] [INFO] Running command: blastn -query GCF_002992955.1_ASM299295v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1875088-8e6e-48b1-8297-d1137c04f661/dqc_reference/reference_markers_gtdb.fasta -out GCF_002992955.1_ASM299295v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:53,564] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:53,568] [INFO] Selected 11 target genomes.
[2024-01-24 13:43:53,568] [INFO] Target genome list was writen to GCF_002992955.1_ASM299295v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:53,577] [INFO] Task started: fastANI
[2024-01-24 13:43:53,577] [INFO] Running command: fastANI --query /var/lib/cwl/stg660d88c2-93b3-45f7-80e9-9823c35403a1/GCF_002992955.1_ASM299295v1_genomic.fna.gz --refList GCF_002992955.1_ASM299295v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002992955.1_ASM299295v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:58,616] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:58,627] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:58,627] [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	99.9972	648	649	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	94.0718	543	649	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	93.6149	223	649	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	92.8159	554	649	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	86.7345	488	649	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	84.8961	456	649	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	83.5372	473	649	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	83.36	444	649	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	82.2882	415	649	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	81.9444	429	649	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	79.8508	349	649	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 13:43:58,629] [INFO] GTDB search result was written to GCF_002992955.1_ASM299295v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:58,629] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:58,633] [INFO] DFAST_QC result json was written to GCF_002992955.1_ASM299295v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:58,633] [INFO] DFAST_QC completed!
[2024-01-24 13:43:58,633] [INFO] Total running time: 0h0m31s