[2024-01-25 20:08:05,683] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:08:05,685] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:08:05,685] [INFO] DQC Reference Directory: /var/lib/cwl/stge1674f3e-b6c4-428e-aba1-c92a5f7419c2/dqc_reference
[2024-01-25 20:08:06,828] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:08:06,828] [INFO] Task started: Prodigal
[2024-01-25 20:08:06,828] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc3cd237-b60d-42bf-9728-36433699e250/GCF_013372265.1_ASM1337226v1_genomic.fna.gz | prodigal -d GCF_013372265.1_ASM1337226v1_genomic.fna/cds.fna -a GCF_013372265.1_ASM1337226v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:08:10,001] [INFO] Task succeeded: Prodigal
[2024-01-25 20:08:10,001] [INFO] Task started: HMMsearch
[2024-01-25 20:08:10,001] [INFO] Running command: hmmsearch --tblout GCF_013372265.1_ASM1337226v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1674f3e-b6c4-428e-aba1-c92a5f7419c2/dqc_reference/reference_markers.hmm GCF_013372265.1_ASM1337226v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:08:10,195] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:08:10,196] [INFO] Found 6/6 markers.
[2024-01-25 20:08:10,215] [INFO] Query marker FASTA was written to GCF_013372265.1_ASM1337226v1_genomic.fna/markers.fasta
[2024-01-25 20:08:10,216] [INFO] Task started: Blastn
[2024-01-25 20:08:10,216] [INFO] Running command: blastn -query GCF_013372265.1_ASM1337226v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1674f3e-b6c4-428e-aba1-c92a5f7419c2/dqc_reference/reference_markers.fasta -out GCF_013372265.1_ASM1337226v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:08:10,812] [INFO] Task succeeded: Blastn
[2024-01-25 20:08:10,814] [INFO] Selected 10 target genomes.
[2024-01-25 20:08:10,815] [INFO] Target genome list was writen to GCF_013372265.1_ASM1337226v1_genomic.fna/target_genomes.txt
[2024-01-25 20:08:10,824] [INFO] Task started: fastANI
[2024-01-25 20:08:10,824] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc3cd237-b60d-42bf-9728-36433699e250/GCF_013372265.1_ASM1337226v1_genomic.fna.gz --refList GCF_013372265.1_ASM1337226v1_genomic.fna/target_genomes.txt --output GCF_013372265.1_ASM1337226v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:08:16,097] [INFO] Task succeeded: fastANI
[2024-01-25 20:08:16,097] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1674f3e-b6c4-428e-aba1-c92a5f7419c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:08:16,098] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1674f3e-b6c4-428e-aba1-c92a5f7419c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:08:16,104] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 20:08:16,104] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:08:16,104] [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 cibarius	strain=LMG 21996	GCA_013372265.1	255507	255507	type	True	100.0	775	778	95	conclusive
Aliarcobacter cibarius	strain=LMG 21996	GCA_000522465.1	255507	255507	type	True	99.9317	704	778	95	conclusive
Aliarcobacter cibarius	strain=DSM 17680	GCA_005818875.1	255507	255507	type	True	99.0787	641	778	95	conclusive
Aliarcobacter faecis	strain=AF1078	GCA_000585155.1	1564138	1564138	type	True	85.3337	539	778	95	below_threshold
Aliarcobacter faecis	strain=LMG 28519	GCA_024584135.1	1564138	1564138	type	True	85.2958	524	778	95	below_threshold
Aliarcobacter faecis	strain=CCUG 66484	GCA_013201705.1	1564138	1564138	type	True	85.2581	548	778	95	below_threshold
Arcobacter vandammei	strain=R-73987	GCA_016106035.1	2782243	2782243	type	True	84.1792	500	778	95	below_threshold
Arcobacter vandammei	strain=LMG 31429	GCA_024583975.1	2782243	2782243	type	True	84.1587	495	778	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:08:16,106] [INFO] DFAST Taxonomy check result was written to GCF_013372265.1_ASM1337226v1_genomic.fna/tc_result.tsv
[2024-01-25 20:08:16,106] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:08:16,106] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:08:16,106] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1674f3e-b6c4-428e-aba1-c92a5f7419c2/dqc_reference/checkm_data
[2024-01-25 20:08:16,107] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:08:16,133] [INFO] Task started: CheckM
[2024-01-25 20:08:16,133] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013372265.1_ASM1337226v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013372265.1_ASM1337226v1_genomic.fna/checkm_input GCF_013372265.1_ASM1337226v1_genomic.fna/checkm_result
[2024-01-25 20:08:31,839] [INFO] Task succeeded: CheckM
[2024-01-25 20:08:31,840] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:08:31,855] [INFO] ===== Completeness check finished =====
[2024-01-25 20:08:31,855] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:08:31,855] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013372265.1_ASM1337226v1_genomic.fna/markers.fasta)
[2024-01-25 20:08:31,855] [INFO] Task started: Blastn
[2024-01-25 20:08:31,856] [INFO] Running command: blastn -query GCF_013372265.1_ASM1337226v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1674f3e-b6c4-428e-aba1-c92a5f7419c2/dqc_reference/reference_markers_gtdb.fasta -out GCF_013372265.1_ASM1337226v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:08:32,803] [INFO] Task succeeded: Blastn
[2024-01-25 20:08:32,806] [INFO] Selected 12 target genomes.
[2024-01-25 20:08:32,806] [INFO] Target genome list was writen to GCF_013372265.1_ASM1337226v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:08:32,822] [INFO] Task started: fastANI
[2024-01-25 20:08:32,822] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc3cd237-b60d-42bf-9728-36433699e250/GCF_013372265.1_ASM1337226v1_genomic.fna.gz --refList GCF_013372265.1_ASM1337226v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013372265.1_ASM1337226v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:08:39,384] [INFO] Task succeeded: fastANI
[2024-01-25 20:08:39,392] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:08:39,392] [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_013372265.1	s__Aliarcobacter cibarius	100.0	772	778	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.17	98.67	0.91	0.84	6	conclusive
GCF_013201705.1	s__Aliarcobacter faecis	85.238	547	778	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	84.1212	503	778	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014352935.1	s__Aliarcobacter cryaerophilus_A	83.347	462	778	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.54	96.41	0.86	0.82	23	-
GCA_017996075.1	s__Aliarcobacter sp017996075	83.2524	202	778	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.83	97.42	0.84	0.83	6	-
GCF_003660105.1	s__Aliarcobacter cryaerophilus	83.1399	462	778	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.99	99.99	1.00	0.99	3	-
GCF_002993025.1	s__Aliarcobacter cryaerophilus_B	82.7469	441	778	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.88	97.88	0.90	0.90	2	-
GCF_013201625.1	s__Aliarcobacter lanthieri	82.1874	446	778	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.15	95.77	0.93	0.89	6	-
GCF_004299785.2	s__Aliarcobacter porcinus	81.8026	395	778	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	81.7816	438	778	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.67	97.67	0.88	0.88	2	-
GCF_013201725.1	s__Aliarcobacter defluvii	80.7368	471	778	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.85	98.15	0.93	0.88	4	-
GCF_013177675.1	s__Aliarcobacter acticola	80.0543	393	778	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:08:39,393] [INFO] GTDB search result was written to GCF_013372265.1_ASM1337226v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:08:39,394] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:08:39,396] [INFO] DFAST_QC result json was written to GCF_013372265.1_ASM1337226v1_genomic.fna/dqc_result.json
[2024-01-25 20:08:39,396] [INFO] DFAST_QC completed!
[2024-01-25 20:08:39,396] [INFO] Total running time: 0h0m34s