[2024-01-24 14:28:08,566] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:08,570] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:08,570] [INFO] DQC Reference Directory: /var/lib/cwl/stg13c62b7b-f17b-4443-9c44-0f787a922c1e/dqc_reference
[2024-01-24 14:28:10,415] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:10,416] [INFO] Task started: Prodigal
[2024-01-24 14:28:10,417] [INFO] Running command: gunzip -c /var/lib/cwl/stg60c7f7a7-c64d-4ef2-b8e5-fedaab520228/GCF_004115735.1_ASM411573v1_genomic.fna.gz | prodigal -d GCF_004115735.1_ASM411573v1_genomic.fna/cds.fna -a GCF_004115735.1_ASM411573v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:13,758] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:13,759] [INFO] Task started: HMMsearch
[2024-01-24 14:28:13,759] [INFO] Running command: hmmsearch --tblout GCF_004115735.1_ASM411573v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13c62b7b-f17b-4443-9c44-0f787a922c1e/dqc_reference/reference_markers.hmm GCF_004115735.1_ASM411573v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:14,123] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:14,125] [INFO] Found 6/6 markers.
[2024-01-24 14:28:14,154] [INFO] Query marker FASTA was written to GCF_004115735.1_ASM411573v1_genomic.fna/markers.fasta
[2024-01-24 14:28:14,154] [INFO] Task started: Blastn
[2024-01-24 14:28:14,154] [INFO] Running command: blastn -query GCF_004115735.1_ASM411573v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13c62b7b-f17b-4443-9c44-0f787a922c1e/dqc_reference/reference_markers.fasta -out GCF_004115735.1_ASM411573v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:18,377] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:18,381] [INFO] Selected 5 target genomes.
[2024-01-24 14:28:18,381] [INFO] Target genome list was writen to GCF_004115735.1_ASM411573v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:18,389] [INFO] Task started: fastANI
[2024-01-24 14:28:18,390] [INFO] Running command: fastANI --query /var/lib/cwl/stg60c7f7a7-c64d-4ef2-b8e5-fedaab520228/GCF_004115735.1_ASM411573v1_genomic.fna.gz --refList GCF_004115735.1_ASM411573v1_genomic.fna/target_genomes.txt --output GCF_004115735.1_ASM411573v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:21,256] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:21,257] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13c62b7b-f17b-4443-9c44-0f787a922c1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:21,258] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13c62b7b-f17b-4443-9c44-0f787a922c1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:21,265] [INFO] Found 5 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 14:28:21,265] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:21,265] [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 skirrowii	strain=LMG 6621	GCA_004115735.1	28200	28200	type	True	100.0	642	643	95	conclusive
Aliarcobacter skirrowii	strain=CCUG 10374	GCA_003544835.1	28200	28200	type	True	99.998	642	643	95	conclusive
Aliarcobacter skirrowii	strain=LMG 6621	GCA_024584055.1	28200	28200	type	True	99.9956	639	643	95	conclusive
Aliarcobacter skirrowii	strain=CCUG 10374	GCA_008802155.1	28200	28200	type	True	99.9939	635	643	95	conclusive
Aliarcobacter skirrowii	strain=NCTC12713	GCA_900445295.1	28200	28200	type	True	99.9847	641	643	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 14:28:21,267] [INFO] DFAST Taxonomy check result was written to GCF_004115735.1_ASM411573v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:21,268] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:21,268] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:21,268] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13c62b7b-f17b-4443-9c44-0f787a922c1e/dqc_reference/checkm_data
[2024-01-24 14:28:21,269] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:21,293] [INFO] Task started: CheckM
[2024-01-24 14:28:21,293] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004115735.1_ASM411573v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004115735.1_ASM411573v1_genomic.fna/checkm_input GCF_004115735.1_ASM411573v1_genomic.fna/checkm_result
[2024-01-24 14:28:44,097] [INFO] Task succeeded: CheckM
[2024-01-24 14:28:44,099] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:28:44,154] [INFO] ===== Completeness check finished =====
[2024-01-24 14:28:44,154] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:28:44,154] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004115735.1_ASM411573v1_genomic.fna/markers.fasta)
[2024-01-24 14:28:44,155] [INFO] Task started: Blastn
[2024-01-24 14:28:44,155] [INFO] Running command: blastn -query GCF_004115735.1_ASM411573v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13c62b7b-f17b-4443-9c44-0f787a922c1e/dqc_reference/reference_markers_gtdb.fasta -out GCF_004115735.1_ASM411573v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:45,199] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:45,205] [INFO] Selected 8 target genomes.
[2024-01-24 14:28:45,205] [INFO] Target genome list was writen to GCF_004115735.1_ASM411573v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:28:45,215] [INFO] Task started: fastANI
[2024-01-24 14:28:45,216] [INFO] Running command: fastANI --query /var/lib/cwl/stg60c7f7a7-c64d-4ef2-b8e5-fedaab520228/GCF_004115735.1_ASM411573v1_genomic.fna.gz --refList GCF_004115735.1_ASM411573v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004115735.1_ASM411573v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:28:49,938] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:49,946] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:28:49,946] [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_003544835.1	s__Aliarcobacter skirrowii	99.998	642	643	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.32	95.07	0.91	0.85	16	conclusive
GCF_014352935.1	s__Aliarcobacter cryaerophilus_A	86.728	476	643	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	86.0067	207	643	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.83	97.42	0.84	0.83	6	-
GCF_002993025.1	s__Aliarcobacter cryaerophilus_B	85.7811	455	643	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.88	97.88	0.90	0.90	2	-
GCF_003660105.1	s__Aliarcobacter cryaerophilus	84.8767	469	643	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.99	99.99	1.00	0.99	3	-
GCF_004214815.1	s__Aliarcobacter thereius	83.505	453	643	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.14	98.62	0.93	0.89	8	-
GCF_004299785.2	s__Aliarcobacter porcinus	83.4946	475	643	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.76	98.06	0.91	0.88	6	-
GCF_013201705.1	s__Aliarcobacter faecis	82.5818	464	643	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.88	99.77	0.97	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:28:49,948] [INFO] GTDB search result was written to GCF_004115735.1_ASM411573v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:28:49,952] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:28:49,969] [INFO] DFAST_QC result json was written to GCF_004115735.1_ASM411573v1_genomic.fna/dqc_result.json
[2024-01-24 14:28:49,969] [INFO] DFAST_QC completed!
[2024-01-24 14:28:49,969] [INFO] Total running time: 0h0m41s