[2024-01-24 13:40:43,879] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:43,881] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:43,882] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c04d347-13ed-48d7-93ae-830f7aa8c439/dqc_reference
[2024-01-24 13:40:45,212] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:45,213] [INFO] Task started: Prodigal
[2024-01-24 13:40:45,213] [INFO] Running command: gunzip -c /var/lib/cwl/stga5501216-061a-4b26-bd8d-8dce2a0d7fdb/GCF_024583985.1_ASM2458398v1_genomic.fna.gz | prodigal -d GCF_024583985.1_ASM2458398v1_genomic.fna/cds.fna -a GCF_024583985.1_ASM2458398v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:49,336] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:49,337] [INFO] Task started: HMMsearch
[2024-01-24 13:40:49,337] [INFO] Running command: hmmsearch --tblout GCF_024583985.1_ASM2458398v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c04d347-13ed-48d7-93ae-830f7aa8c439/dqc_reference/reference_markers.hmm GCF_024583985.1_ASM2458398v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:49,592] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:49,593] [INFO] Found 6/6 markers.
[2024-01-24 13:40:49,619] [INFO] Query marker FASTA was written to GCF_024583985.1_ASM2458398v1_genomic.fna/markers.fasta
[2024-01-24 13:40:49,620] [INFO] Task started: Blastn
[2024-01-24 13:40:49,620] [INFO] Running command: blastn -query GCF_024583985.1_ASM2458398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c04d347-13ed-48d7-93ae-830f7aa8c439/dqc_reference/reference_markers.fasta -out GCF_024583985.1_ASM2458398v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:50,321] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:50,325] [INFO] Selected 8 target genomes.
[2024-01-24 13:40:50,325] [INFO] Target genome list was writen to GCF_024583985.1_ASM2458398v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:50,332] [INFO] Task started: fastANI
[2024-01-24 13:40:50,332] [INFO] Running command: fastANI --query /var/lib/cwl/stga5501216-061a-4b26-bd8d-8dce2a0d7fdb/GCF_024583985.1_ASM2458398v1_genomic.fna.gz --refList GCF_024583985.1_ASM2458398v1_genomic.fna/target_genomes.txt --output GCF_024583985.1_ASM2458398v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:55,420] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:55,420] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c04d347-13ed-48d7-93ae-830f7aa8c439/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:55,421] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c04d347-13ed-48d7-93ae-830f7aa8c439/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:55,429] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:40:55,430] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:55,430] [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 vitoriensis	strain=LMG 30050	GCA_024583985.1	2011099	2011099	type	True	100.0	782	787	95	conclusive
Aliarcobacter vitoriensis	strain=CECT 9230	GCA_003316695.1	2011099	2011099	type	True	99.9932	776	787	95	conclusive
Aliarcobacter lanthieri	strain=LMG 28516	GCA_013201625.1	1355374	1355374	type	True	87.9201	620	787	95	below_threshold
Aliarcobacter lanthieri	strain=AF1440	GCA_000585115.1	1355374	1355374	type	True	87.9116	613	787	95	below_threshold
Aliarcobacter lanthieri	strain=LMG 28516	GCA_024584095.1	1355374	1355374	type	True	87.9047	605	787	95	below_threshold
Aliarcobacter faecis	strain=CCUG 66484	GCA_013201705.1	1564138	1564138	type	True	83.0101	506	787	95	below_threshold
Aliarcobacter faecis	strain=LMG 28519	GCA_024584135.1	1564138	1564138	type	True	82.9822	515	787	95	below_threshold
Aliarcobacter faecis	strain=AF1078	GCA_000585155.1	1564138	1564138	type	True	82.98	518	787	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:55,463] [INFO] DFAST Taxonomy check result was written to GCF_024583985.1_ASM2458398v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:55,464] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:55,464] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:55,464] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c04d347-13ed-48d7-93ae-830f7aa8c439/dqc_reference/checkm_data
[2024-01-24 13:40:55,466] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:55,495] [INFO] Task started: CheckM
[2024-01-24 13:40:55,495] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024583985.1_ASM2458398v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024583985.1_ASM2458398v1_genomic.fna/checkm_input GCF_024583985.1_ASM2458398v1_genomic.fna/checkm_result
[2024-01-24 13:41:15,909] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:15,911] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:15,932] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:15,933] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:15,933] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024583985.1_ASM2458398v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:15,933] [INFO] Task started: Blastn
[2024-01-24 13:41:15,934] [INFO] Running command: blastn -query GCF_024583985.1_ASM2458398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c04d347-13ed-48d7-93ae-830f7aa8c439/dqc_reference/reference_markers_gtdb.fasta -out GCF_024583985.1_ASM2458398v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:16,967] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:16,971] [INFO] Selected 14 target genomes.
[2024-01-24 13:41:16,971] [INFO] Target genome list was writen to GCF_024583985.1_ASM2458398v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:16,980] [INFO] Task started: fastANI
[2024-01-24 13:41:16,980] [INFO] Running command: fastANI --query /var/lib/cwl/stga5501216-061a-4b26-bd8d-8dce2a0d7fdb/GCF_024583985.1_ASM2458398v1_genomic.fna.gz --refList GCF_024583985.1_ASM2458398v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024583985.1_ASM2458398v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:25,219] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:25,232] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:25,232] [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
GCA_003316695.1	s__Aliarcobacter sp003316695	99.9932	776	787	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.67	97.67	0.88	0.88	2	conclusive
GCF_013201625.1	s__Aliarcobacter lanthieri	87.9312	619	787	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.15	95.77	0.93	0.89	6	-
GCF_013201705.1	s__Aliarcobacter faecis	83.0297	504	787	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.88	99.77	0.97	0.95	3	-
GCF_900187115.1	s__Aliarcobacter butzleri	82.8606	519	787	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	82.7658	506	787	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003660105.1	s__Aliarcobacter cryaerophilus	82.6633	479	787	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	82.5524	489	787	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.54	96.41	0.86	0.82	23	-
GCF_016106035.1	s__Aliarcobacter sp016106035	82.1917	455	787	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	81.9779	441	787	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.32	95.07	0.91	0.85	16	-
GCF_013372265.1	s__Aliarcobacter cibarius	81.569	451	787	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.17	98.67	0.91	0.84	6	-
GCF_004299785.2	s__Aliarcobacter porcinus	81.527	426	787	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.76	98.06	0.91	0.88	6	-
GCF_003544915.1	s__Aliarcobacter ellisii	80.7963	456	787	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.73	97.46	0.92	0.84	3	-
GCF_003346775.1	s__Malaciobacter mytili	78.8137	348	787	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	99.45	98.91	0.96	0.92	3	-
GCF_003667345.1	s__Poseidonibacter antarcticus	78.6491	306	787	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:25,234] [INFO] GTDB search result was written to GCF_024583985.1_ASM2458398v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:25,234] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:25,238] [INFO] DFAST_QC result json was written to GCF_024583985.1_ASM2458398v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:25,238] [INFO] DFAST_QC completed!
[2024-01-24 13:41:25,238] [INFO] Total running time: 0h0m41s