[2024-01-24 13:17:04,887] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:04,889] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:04,889] [INFO] DQC Reference Directory: /var/lib/cwl/stg36f2a043-1867-44b8-954d-54a5e6ded696/dqc_reference
[2024-01-24 13:17:06,240] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:06,241] [INFO] Task started: Prodigal
[2024-01-24 13:17:06,242] [INFO] Running command: gunzip -c /var/lib/cwl/stg53fd15fd-8184-4ceb-9835-24451bb30e71/GCF_000585155.1_Arcobacter_septicus_AF1078_genomic.fna.gz | prodigal -d GCF_000585155.1_Arcobacter_septicus_AF1078_genomic.fna/cds.fna -a GCF_000585155.1_Arcobacter_septicus_AF1078_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:09,843] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:09,844] [INFO] Task started: HMMsearch
[2024-01-24 13:17:09,844] [INFO] Running command: hmmsearch --tblout GCF_000585155.1_Arcobacter_septicus_AF1078_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36f2a043-1867-44b8-954d-54a5e6ded696/dqc_reference/reference_markers.hmm GCF_000585155.1_Arcobacter_septicus_AF1078_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:10,077] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:10,079] [INFO] Found 6/6 markers.
[2024-01-24 13:17:10,104] [INFO] Query marker FASTA was written to GCF_000585155.1_Arcobacter_septicus_AF1078_genomic.fna/markers.fasta
[2024-01-24 13:17:10,105] [INFO] Task started: Blastn
[2024-01-24 13:17:10,105] [INFO] Running command: blastn -query GCF_000585155.1_Arcobacter_septicus_AF1078_genomic.fna/markers.fasta -db /var/lib/cwl/stg36f2a043-1867-44b8-954d-54a5e6ded696/dqc_reference/reference_markers.fasta -out GCF_000585155.1_Arcobacter_septicus_AF1078_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:10,686] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:10,689] [INFO] Selected 10 target genomes.
[2024-01-24 13:17:10,690] [INFO] Target genome list was writen to GCF_000585155.1_Arcobacter_septicus_AF1078_genomic.fna/target_genomes.txt
[2024-01-24 13:17:10,694] [INFO] Task started: fastANI
[2024-01-24 13:17:10,694] [INFO] Running command: fastANI --query /var/lib/cwl/stg53fd15fd-8184-4ceb-9835-24451bb30e71/GCF_000585155.1_Arcobacter_septicus_AF1078_genomic.fna.gz --refList GCF_000585155.1_Arcobacter_septicus_AF1078_genomic.fna/target_genomes.txt --output GCF_000585155.1_Arcobacter_septicus_AF1078_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:16,506] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:16,506] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36f2a043-1867-44b8-954d-54a5e6ded696/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:16,506] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36f2a043-1867-44b8-954d-54a5e6ded696/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:16,516] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:17:16,516] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:16,516] [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 faecis	strain=AF1078	GCA_000585155.1	1564138	1564138	type	True	100.0	797	805	95	conclusive
Aliarcobacter faecis	strain=CCUG 66484	GCA_013201705.1	1564138	1564138	type	True	99.9887	793	805	95	conclusive
Aliarcobacter faecis	strain=LMG 28519	GCA_024584135.1	1564138	1564138	type	True	99.9659	759	805	95	conclusive
Arcobacter vandammei	strain=R-73987	GCA_016106035.1	2782243	2782243	type	True	85.9702	541	805	95	below_threshold
Arcobacter vandammei	strain=LMG 31429	GCA_024583975.1	2782243	2782243	type	True	85.9454	544	805	95	below_threshold
Aliarcobacter cibarius	strain=LMG 21996	GCA_000522465.1	255507	255507	type	True	85.1603	542	805	95	below_threshold
Aliarcobacter cibarius	strain=LMG 21996	GCA_013372265.1	255507	255507	type	True	85.1295	555	805	95	below_threshold
Aliarcobacter cibarius	strain=DSM 17680	GCA_005818875.1	255507	255507	type	True	85.1086	531	805	95	below_threshold
Aliarcobacter vitoriensis	strain=LMG 30050	GCA_024583985.1	2011099	2011099	type	True	83.0746	500	805	95	below_threshold
Aliarcobacter vitoriensis	strain=CECT 9230	GCA_003316695.1	2011099	2011099	type	True	82.9871	507	805	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:16,517] [INFO] DFAST Taxonomy check result was written to GCF_000585155.1_Arcobacter_septicus_AF1078_genomic.fna/tc_result.tsv
[2024-01-24 13:17:16,518] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:16,518] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:16,518] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36f2a043-1867-44b8-954d-54a5e6ded696/dqc_reference/checkm_data
[2024-01-24 13:17:16,519] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:16,557] [INFO] Task started: CheckM
[2024-01-24 13:17:16,557] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000585155.1_Arcobacter_septicus_AF1078_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000585155.1_Arcobacter_septicus_AF1078_genomic.fna/checkm_input GCF_000585155.1_Arcobacter_septicus_AF1078_genomic.fna/checkm_result
[2024-01-24 13:17:36,274] [INFO] Task succeeded: CheckM
[2024-01-24 13:17:36,276] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:17:36,294] [INFO] ===== Completeness check finished =====
[2024-01-24 13:17:36,294] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:17:36,295] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000585155.1_Arcobacter_septicus_AF1078_genomic.fna/markers.fasta)
[2024-01-24 13:17:36,295] [INFO] Task started: Blastn
[2024-01-24 13:17:36,295] [INFO] Running command: blastn -query GCF_000585155.1_Arcobacter_septicus_AF1078_genomic.fna/markers.fasta -db /var/lib/cwl/stg36f2a043-1867-44b8-954d-54a5e6ded696/dqc_reference/reference_markers_gtdb.fasta -out GCF_000585155.1_Arcobacter_septicus_AF1078_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:37,058] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:37,061] [INFO] Selected 14 target genomes.
[2024-01-24 13:17:37,061] [INFO] Target genome list was writen to GCF_000585155.1_Arcobacter_septicus_AF1078_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:17:37,070] [INFO] Task started: fastANI
[2024-01-24 13:17:37,070] [INFO] Running command: fastANI --query /var/lib/cwl/stg53fd15fd-8184-4ceb-9835-24451bb30e71/GCF_000585155.1_Arcobacter_septicus_AF1078_genomic.fna.gz --refList GCF_000585155.1_Arcobacter_septicus_AF1078_genomic.fna/target_genomes_gtdb.txt --output GCF_000585155.1_Arcobacter_septicus_AF1078_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:17:44,411] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:44,426] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:17:44,426] [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_013201705.1	s__Aliarcobacter faecis	99.9887	795	805	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.88	99.77	0.97	0.95	3	conclusive
GCF_016106035.1	s__Aliarcobacter sp016106035	85.9538	542	805	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013372265.1	s__Aliarcobacter cibarius	85.0488	555	805	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.17	98.67	0.91	0.84	6	-
GCF_003660105.1	s__Aliarcobacter cryaerophilus	83.7138	497	805	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.99	99.99	1.00	0.99	3	-
GCA_017996075.1	s__Aliarcobacter sp017996075	83.6358	220	805	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.83	97.42	0.84	0.83	6	-
GCF_013201625.1	s__Aliarcobacter lanthieri	83.2767	509	805	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.15	95.77	0.93	0.89	6	-
GCF_002993025.1	s__Aliarcobacter cryaerophilus_B	83.2212	470	805	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.88	97.88	0.90	0.90	2	-
GCF_003355515.1	s__Aliarcobacter trophiarum	83.2037	464	805	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.76	99.53	0.96	0.92	3	-
GCA_003316695.1	s__Aliarcobacter sp003316695	82.9503	510	805	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.67	97.67	0.88	0.88	2	-
GCF_004299785.2	s__Aliarcobacter porcinus	82.3315	433	805	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	82.2983	435	805	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.14	98.62	0.93	0.89	8	-
GCF_900187115.1	s__Aliarcobacter butzleri	82.1137	493	805	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	82.0631	455	805	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017995775.1	s__Aliarcobacter sp017995775	80.2651	376	805	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 13:17:44,428] [INFO] GTDB search result was written to GCF_000585155.1_Arcobacter_septicus_AF1078_genomic.fna/result_gtdb.tsv
[2024-01-24 13:17:44,429] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:17:44,432] [INFO] DFAST_QC result json was written to GCF_000585155.1_Arcobacter_septicus_AF1078_genomic.fna/dqc_result.json
[2024-01-24 13:17:44,432] [INFO] DFAST_QC completed!
[2024-01-24 13:17:44,432] [INFO] Total running time: 0h0m40s