[2024-01-24 13:22:30,805] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:30,807] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:30,807] [INFO] DQC Reference Directory: /var/lib/cwl/stg99ac0f05-dddf-4ef2-b229-5d7819105014/dqc_reference
[2024-01-24 13:22:32,157] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:32,168] [INFO] Task started: Prodigal
[2024-01-24 13:22:32,169] [INFO] Running command: gunzip -c /var/lib/cwl/stge882f3d9-5830-40f2-8802-b5ff194e989e/GCF_005818985.1_ASM581898v1_genomic.fna.gz | prodigal -d GCF_005818985.1_ASM581898v1_genomic.fna/cds.fna -a GCF_005818985.1_ASM581898v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:35,004] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:35,005] [INFO] Task started: HMMsearch
[2024-01-24 13:22:35,005] [INFO] Running command: hmmsearch --tblout GCF_005818985.1_ASM581898v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99ac0f05-dddf-4ef2-b229-5d7819105014/dqc_reference/reference_markers.hmm GCF_005818985.1_ASM581898v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:35,243] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:35,245] [INFO] Found 6/6 markers.
[2024-01-24 13:22:35,272] [INFO] Query marker FASTA was written to GCF_005818985.1_ASM581898v1_genomic.fna/markers.fasta
[2024-01-24 13:22:35,634] [INFO] Task started: Blastn
[2024-01-24 13:22:35,635] [INFO] Running command: blastn -query GCF_005818985.1_ASM581898v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99ac0f05-dddf-4ef2-b229-5d7819105014/dqc_reference/reference_markers.fasta -out GCF_005818985.1_ASM581898v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:36,517] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:36,520] [INFO] Selected 6 target genomes.
[2024-01-24 13:22:36,521] [INFO] Target genome list was writen to GCF_005818985.1_ASM581898v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:36,805] [INFO] Task started: fastANI
[2024-01-24 13:22:36,805] [INFO] Running command: fastANI --query /var/lib/cwl/stge882f3d9-5830-40f2-8802-b5ff194e989e/GCF_005818985.1_ASM581898v1_genomic.fna.gz --refList GCF_005818985.1_ASM581898v1_genomic.fna/target_genomes.txt --output GCF_005818985.1_ASM581898v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:39,742] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:39,743] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99ac0f05-dddf-4ef2-b229-5d7819105014/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:39,743] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99ac0f05-dddf-4ef2-b229-5d7819105014/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:40,065] [INFO] Found 6 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:22:40,065] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:40,065] [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 thereius	strain=DSM 23385	GCA_005818985.1	544718	544718	type	True	100.0	621	623	95	conclusive
Aliarcobacter thereius	strain=LMG 24486	GCA_004214815.1	544718	544718	type	True	99.9994	622	623	95	conclusive
Aliarcobacter thereius	strain=LMG 24486	GCA_001695395.1	544718	544718	type	True	99.9976	623	623	95	conclusive
Aliarcobacter thereius	strain=LMG 24486	GCA_024584025.1	544718	544718	type	True	99.9893	622	623	95	conclusive
[Arcobacter] porcinus	strain=LMG 24487	GCA_024584075.1	1935204	1935204	type	True	93.5104	521	623	95	below_threshold
[Arcobacter] porcinus	strain=CCUG 56899	GCA_004299785.2	1935204	1935204	type	True	93.026	543	623	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:40,067] [INFO] DFAST Taxonomy check result was written to GCF_005818985.1_ASM581898v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:40,067] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:40,067] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:40,068] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99ac0f05-dddf-4ef2-b229-5d7819105014/dqc_reference/checkm_data
[2024-01-24 13:22:40,072] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:40,094] [INFO] Task started: CheckM
[2024-01-24 13:22:40,094] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005818985.1_ASM581898v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005818985.1_ASM581898v1_genomic.fna/checkm_input GCF_005818985.1_ASM581898v1_genomic.fna/checkm_result
[2024-01-24 13:22:59,875] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:59,877] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:59,903] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:59,904] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:59,904] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005818985.1_ASM581898v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:59,918] [INFO] Task started: Blastn
[2024-01-24 13:22:59,919] [INFO] Running command: blastn -query GCF_005818985.1_ASM581898v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99ac0f05-dddf-4ef2-b229-5d7819105014/dqc_reference/reference_markers_gtdb.fasta -out GCF_005818985.1_ASM581898v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:01,342] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:01,347] [INFO] Selected 13 target genomes.
[2024-01-24 13:23:01,347] [INFO] Target genome list was writen to GCF_005818985.1_ASM581898v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:01,883] [INFO] Task started: fastANI
[2024-01-24 13:23:01,883] [INFO] Running command: fastANI --query /var/lib/cwl/stge882f3d9-5830-40f2-8802-b5ff194e989e/GCF_005818985.1_ASM581898v1_genomic.fna.gz --refList GCF_005818985.1_ASM581898v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005818985.1_ASM581898v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:08,212] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:08,250] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:08,250] [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_004214815.1	s__Aliarcobacter thereius	99.9994	622	623	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.14	98.62	0.93	0.89	8	conclusive
GCF_004299785.2	s__Aliarcobacter porcinus	93.026	543	623	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.76	98.06	0.91	0.88	6	-
GCF_003544835.1	s__Aliarcobacter skirrowii	83.6005	453	623	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.32	95.07	0.91	0.85	16	-
GCF_014352935.1	s__Aliarcobacter cryaerophilus_A	82.5614	421	623	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	82.1786	411	623	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.76	99.53	0.96	0.92	3	-
GCF_002993025.1	s__Aliarcobacter cryaerophilus_B	82.0068	415	623	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.88	97.88	0.90	0.90	2	-
GCF_003660105.1	s__Aliarcobacter cryaerophilus	82.0028	424	623	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.99	99.99	1.00	0.99	3	-
GCF_013201705.1	s__Aliarcobacter faecis	81.9401	429	623	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	81.8534	429	623	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003316695.1	s__Aliarcobacter sp003316695	81.6176	425	623	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.67	97.67	0.88	0.88	2	-
GCF_013201625.1	s__Aliarcobacter lanthieri	81.5554	428	623	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.15	95.77	0.93	0.89	6	-
GCF_900187115.1	s__Aliarcobacter butzleri	80.8516	398	623	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.53	96.98	0.89	0.81	50	-
GCF_003063295.1	s__Aliarcobacter lacus	80.8515	374	623	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:08,252] [INFO] GTDB search result was written to GCF_005818985.1_ASM581898v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:08,253] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:08,256] [INFO] DFAST_QC result json was written to GCF_005818985.1_ASM581898v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:08,257] [INFO] DFAST_QC completed!
[2024-01-24 13:23:08,257] [INFO] Total running time: 0h0m37s