[2024-01-24 12:14:33,852] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:33,857] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:33,857] [INFO] DQC Reference Directory: /var/lib/cwl/stg480156e9-c13e-4b5f-a0b2-b540ced8580e/dqc_reference
[2024-01-24 12:14:35,294] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:35,295] [INFO] Task started: Prodigal
[2024-01-24 12:14:35,295] [INFO] Running command: gunzip -c /var/lib/cwl/stgce25d1b0-a704-4c43-bc9a-045aa5bf8a7e/GCF_024583975.1_ASM2458397v1_genomic.fna.gz | prodigal -d GCF_024583975.1_ASM2458397v1_genomic.fna/cds.fna -a GCF_024583975.1_ASM2458397v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:38,729] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:38,729] [INFO] Task started: HMMsearch
[2024-01-24 12:14:38,730] [INFO] Running command: hmmsearch --tblout GCF_024583975.1_ASM2458397v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg480156e9-c13e-4b5f-a0b2-b540ced8580e/dqc_reference/reference_markers.hmm GCF_024583975.1_ASM2458397v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:38,991] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:38,995] [INFO] Found 6/6 markers.
[2024-01-24 12:14:39,022] [INFO] Query marker FASTA was written to GCF_024583975.1_ASM2458397v1_genomic.fna/markers.fasta
[2024-01-24 12:14:39,022] [INFO] Task started: Blastn
[2024-01-24 12:14:39,023] [INFO] Running command: blastn -query GCF_024583975.1_ASM2458397v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg480156e9-c13e-4b5f-a0b2-b540ced8580e/dqc_reference/reference_markers.fasta -out GCF_024583975.1_ASM2458397v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:39,673] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:39,678] [INFO] Selected 13 target genomes.
[2024-01-24 12:14:39,678] [INFO] Target genome list was writen to GCF_024583975.1_ASM2458397v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:39,685] [INFO] Task started: fastANI
[2024-01-24 12:14:39,685] [INFO] Running command: fastANI --query /var/lib/cwl/stgce25d1b0-a704-4c43-bc9a-045aa5bf8a7e/GCF_024583975.1_ASM2458397v1_genomic.fna.gz --refList GCF_024583975.1_ASM2458397v1_genomic.fna/target_genomes.txt --output GCF_024583975.1_ASM2458397v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:46,312] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:46,312] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg480156e9-c13e-4b5f-a0b2-b540ced8580e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:46,313] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg480156e9-c13e-4b5f-a0b2-b540ced8580e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:46,324] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:14:46,324] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:46,325] [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 vandammei	strain=LMG 31429	GCA_024583975.1	2782243	2782243	type	True	100.0	707	710	95	conclusive
Arcobacter vandammei	strain=R-73987	GCA_016106035.1	2782243	2782243	type	True	99.9993	708	710	95	conclusive
Aliarcobacter faecis	strain=LMG 28519	GCA_024584135.1	1564138	1564138	type	True	86.1643	539	710	95	below_threshold
Aliarcobacter faecis	strain=AF1078	GCA_000585155.1	1564138	1564138	type	True	86.1073	545	710	95	below_threshold
Aliarcobacter faecis	strain=CCUG 66484	GCA_013201705.1	1564138	1564138	type	True	86.0203	545	710	95	below_threshold
Aliarcobacter trophiarum	strain=LMG 25534	GCA_004116585.1	708186	708186	type	True	82.8457	432	710	95	below_threshold
Aliarcobacter trophiarum	strain=LMG 25534	GCA_003355515.1	708186	708186	type	True	82.8077	436	710	95	below_threshold
Aliarcobacter trophiarum	strain=LMG 25534	GCA_024584015.1	708186	708186	type	True	82.7834	439	710	95	below_threshold
Aliarcobacter vitoriensis	strain=CECT 9230	GCA_003316695.1	2011099	2011099	type	True	82.3916	449	710	95	below_threshold
Aliarcobacter vitoriensis	strain=LMG 30050	GCA_024583985.1	2011099	2011099	type	True	82.3816	456	710	95	below_threshold
[Arcobacter] porcinus	strain=LMG 24487	GCA_024584075.1	1935204	1935204	type	True	82.2682	421	710	95	below_threshold
[Arcobacter] porcinus	strain=CCUG 56899	GCA_004299785.2	1935204	1935204	type	True	82.1826	446	710	95	below_threshold
Aliarcobacter lanthieri	strain=LMG 28516	GCA_013201625.1	1355374	1355374	type	True	82.1536	446	710	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:46,328] [INFO] DFAST Taxonomy check result was written to GCF_024583975.1_ASM2458397v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:46,328] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:46,329] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:46,329] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg480156e9-c13e-4b5f-a0b2-b540ced8580e/dqc_reference/checkm_data
[2024-01-24 12:14:46,330] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:46,361] [INFO] Task started: CheckM
[2024-01-24 12:14:46,361] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024583975.1_ASM2458397v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024583975.1_ASM2458397v1_genomic.fna/checkm_input GCF_024583975.1_ASM2458397v1_genomic.fna/checkm_result
[2024-01-24 12:15:05,466] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:05,467] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:05,496] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:05,497] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:05,497] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024583975.1_ASM2458397v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:05,498] [INFO] Task started: Blastn
[2024-01-24 12:15:05,498] [INFO] Running command: blastn -query GCF_024583975.1_ASM2458397v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg480156e9-c13e-4b5f-a0b2-b540ced8580e/dqc_reference/reference_markers_gtdb.fasta -out GCF_024583975.1_ASM2458397v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:06,513] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:06,519] [INFO] Selected 14 target genomes.
[2024-01-24 12:15:06,519] [INFO] Target genome list was writen to GCF_024583975.1_ASM2458397v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:06,528] [INFO] Task started: fastANI
[2024-01-24 12:15:06,529] [INFO] Running command: fastANI --query /var/lib/cwl/stgce25d1b0-a704-4c43-bc9a-045aa5bf8a7e/GCF_024583975.1_ASM2458397v1_genomic.fna.gz --refList GCF_024583975.1_ASM2458397v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024583975.1_ASM2458397v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:13,934] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:13,948] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:13,949] [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_016106035.1	s__Aliarcobacter sp016106035	99.9993	708	710	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013201705.1	s__Aliarcobacter faecis	86.0203	545	710	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.88	99.77	0.97	0.95	3	-
GCF_013372265.1	s__Aliarcobacter cibarius	83.9243	500	710	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.17	98.67	0.91	0.84	6	-
GCA_017996075.1	s__Aliarcobacter sp017996075	83.6193	211	710	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	83.5483	460	710	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.54	96.41	0.86	0.82	23	-
GCF_003660105.1	s__Aliarcobacter cryaerophilus	83.3467	455	710	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.99	99.99	1.00	0.99	3	-
GCF_003355515.1	s__Aliarcobacter trophiarum	82.7893	437	710	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	82.3852	448	710	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	82.2169	444	710	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.76	98.06	0.91	0.88	6	-
GCF_013201625.1	s__Aliarcobacter lanthieri	82.1511	447	710	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.15	95.77	0.93	0.89	6	-
GCF_004214815.1	s__Aliarcobacter thereius	82.1487	422	710	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.14	98.62	0.93	0.89	8	-
GCF_013201935.1	s__Aliarcobacter cloacae	80.3444	423	710	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.96	95.91	0.93	0.87	3	-
GCA_017995775.1	s__Aliarcobacter sp017995775	79.6024	353	710	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.13	99.13	0.84	0.84	2	-
GCF_013201665.1	s__Aliarcobacter venerupis	79.4982	404	710	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:13,952] [INFO] GTDB search result was written to GCF_024583975.1_ASM2458397v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:13,953] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:13,959] [INFO] DFAST_QC result json was written to GCF_024583975.1_ASM2458397v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:13,960] [INFO] DFAST_QC completed!
[2024-01-24 12:15:13,960] [INFO] Total running time: 0h0m40s