[2024-01-24 11:02:48,583] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:02:48,585] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:02:48,585] [INFO] DQC Reference Directory: /var/lib/cwl/stgd703049f-2198-4040-9fc8-d10a7ed0289a/dqc_reference
[2024-01-24 11:02:49,805] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:02:49,806] [INFO] Task started: Prodigal
[2024-01-24 11:02:49,806] [INFO] Running command: gunzip -c /var/lib/cwl/stg8adc54d9-6c6d-4131-95eb-cf32119164eb/GCF_024584015.1_ASM2458401v1_genomic.fna.gz | prodigal -d GCF_024584015.1_ASM2458401v1_genomic.fna/cds.fna -a GCF_024584015.1_ASM2458401v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:02:52,631] [INFO] Task succeeded: Prodigal
[2024-01-24 11:02:52,632] [INFO] Task started: HMMsearch
[2024-01-24 11:02:52,632] [INFO] Running command: hmmsearch --tblout GCF_024584015.1_ASM2458401v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd703049f-2198-4040-9fc8-d10a7ed0289a/dqc_reference/reference_markers.hmm GCF_024584015.1_ASM2458401v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:02:52,850] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:02:52,852] [INFO] Found 6/6 markers.
[2024-01-24 11:02:52,877] [INFO] Query marker FASTA was written to GCF_024584015.1_ASM2458401v1_genomic.fna/markers.fasta
[2024-01-24 11:02:52,877] [INFO] Task started: Blastn
[2024-01-24 11:02:52,877] [INFO] Running command: blastn -query GCF_024584015.1_ASM2458401v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd703049f-2198-4040-9fc8-d10a7ed0289a/dqc_reference/reference_markers.fasta -out GCF_024584015.1_ASM2458401v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:02:53,478] [INFO] Task succeeded: Blastn
[2024-01-24 11:02:53,483] [INFO] Selected 10 target genomes.
[2024-01-24 11:02:53,483] [INFO] Target genome list was writen to GCF_024584015.1_ASM2458401v1_genomic.fna/target_genomes.txt
[2024-01-24 11:02:53,509] [INFO] Task started: fastANI
[2024-01-24 11:02:53,510] [INFO] Running command: fastANI --query /var/lib/cwl/stg8adc54d9-6c6d-4131-95eb-cf32119164eb/GCF_024584015.1_ASM2458401v1_genomic.fna.gz --refList GCF_024584015.1_ASM2458401v1_genomic.fna/target_genomes.txt --output GCF_024584015.1_ASM2458401v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:02:58,495] [INFO] Task succeeded: fastANI
[2024-01-24 11:02:58,496] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd703049f-2198-4040-9fc8-d10a7ed0289a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:02:58,496] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd703049f-2198-4040-9fc8-d10a7ed0289a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:02:58,510] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:02:58,510] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:02:58,511] [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 trophiarum	strain=LMG 25534	GCA_024584015.1	708186	708186	type	True	100.0	604	606	95	conclusive
Aliarcobacter trophiarum	strain=LMG 25534	GCA_003355515.1	708186	708186	type	True	99.9996	605	606	95	conclusive
Aliarcobacter trophiarum	strain=LMG 25534	GCA_004116585.1	708186	708186	type	True	99.9924	605	606	95	conclusive
Aliarcobacter cryaerophilus	strain=ATCC 43158	GCA_003660105.1	28198	28198	suspected-type	True	86.6709	490	606	95	below_threshold
Aliarcobacter cryaerophilus	strain=LMG 24291	GCA_002992955.1	28198	28198	suspected-type	True	86.603	486	606	95	below_threshold
Aliarcobacter cryaerophilus	strain=LMG 9904	GCA_006165035.1	28198	28198	suspected-type	True	86.5982	510	606	95	below_threshold
Aliarcobacter faecis	strain=AF1078	GCA_000585155.1	1564138	1564138	type	True	83.3121	444	606	95	below_threshold
Aliarcobacter faecis	strain=CCUG 66484	GCA_013201705.1	1564138	1564138	type	True	83.3048	439	606	95	below_threshold
Aliarcobacter thereius	strain=LMG 24486	GCA_001695395.1	544718	544718	type	True	82.1955	411	606	95	below_threshold
Aliarcobacter thereius	strain=LMG 24486	GCA_024584025.1	544718	544718	type	True	82.1729	412	606	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:02:58,512] [INFO] DFAST Taxonomy check result was written to GCF_024584015.1_ASM2458401v1_genomic.fna/tc_result.tsv
[2024-01-24 11:02:58,513] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:02:58,513] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:02:58,513] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd703049f-2198-4040-9fc8-d10a7ed0289a/dqc_reference/checkm_data
[2024-01-24 11:02:58,514] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:02:58,536] [INFO] Task started: CheckM
[2024-01-24 11:02:58,537] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024584015.1_ASM2458401v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024584015.1_ASM2458401v1_genomic.fna/checkm_input GCF_024584015.1_ASM2458401v1_genomic.fna/checkm_result
[2024-01-24 11:03:14,965] [INFO] Task succeeded: CheckM
[2024-01-24 11:03:14,967] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:03:14,987] [INFO] ===== Completeness check finished =====
[2024-01-24 11:03:14,988] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:03:14,988] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024584015.1_ASM2458401v1_genomic.fna/markers.fasta)
[2024-01-24 11:03:14,989] [INFO] Task started: Blastn
[2024-01-24 11:03:14,989] [INFO] Running command: blastn -query GCF_024584015.1_ASM2458401v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd703049f-2198-4040-9fc8-d10a7ed0289a/dqc_reference/reference_markers_gtdb.fasta -out GCF_024584015.1_ASM2458401v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:03:15,803] [INFO] Task succeeded: Blastn
[2024-01-24 11:03:15,807] [INFO] Selected 11 target genomes.
[2024-01-24 11:03:15,807] [INFO] Target genome list was writen to GCF_024584015.1_ASM2458401v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:03:15,842] [INFO] Task started: fastANI
[2024-01-24 11:03:15,843] [INFO] Running command: fastANI --query /var/lib/cwl/stg8adc54d9-6c6d-4131-95eb-cf32119164eb/GCF_024584015.1_ASM2458401v1_genomic.fna.gz --refList GCF_024584015.1_ASM2458401v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024584015.1_ASM2458401v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:03:21,290] [INFO] Task succeeded: fastANI
[2024-01-24 11:03:21,303] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:03:21,303] [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_003355515.1	s__Aliarcobacter trophiarum	99.9996	605	606	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.76	99.53	0.96	0.92	3	conclusive
GCF_003660105.1	s__Aliarcobacter cryaerophilus	86.6908	489	606	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.99	99.99	1.00	0.99	3	-
GCF_014352935.1	s__Aliarcobacter cryaerophilus_A	86.4089	495	606	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.54	96.41	0.86	0.82	23	-
GCF_002993025.1	s__Aliarcobacter cryaerophilus_B	86.3352	491	606	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.88	97.88	0.90	0.90	2	-
GCF_013201705.1	s__Aliarcobacter faecis	83.3017	441	606	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	83.0522	418	606	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003544835.1	s__Aliarcobacter skirrowii	82.9706	424	606	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.32	95.07	0.91	0.85	16	-
GCF_004299785.2	s__Aliarcobacter porcinus	82.3354	408	606	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.76	98.06	0.91	0.88	6	-
GCA_003316695.1	s__Aliarcobacter sp003316695	82.1523	441	606	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.67	97.67	0.88	0.88	2	-
GCF_004214815.1	s__Aliarcobacter thereius	82.0917	422	606	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.14	98.62	0.93	0.89	8	-
GCF_013201625.1	s__Aliarcobacter lanthieri	82.0317	439	606	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.15	95.77	0.93	0.89	6	-
--------------------------------------------------------------------------------
[2024-01-24 11:03:21,305] [INFO] GTDB search result was written to GCF_024584015.1_ASM2458401v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:03:21,306] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:03:21,309] [INFO] DFAST_QC result json was written to GCF_024584015.1_ASM2458401v1_genomic.fna/dqc_result.json
[2024-01-24 11:03:21,309] [INFO] DFAST_QC completed!
[2024-01-24 11:03:21,309] [INFO] Total running time: 0h0m33s