[2024-01-24 12:40:08,057] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:08,059] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:08,059] [INFO] DQC Reference Directory: /var/lib/cwl/stge09c8540-5fbc-4b9a-9747-074a00fabcde/dqc_reference
[2024-01-24 12:40:09,351] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:09,352] [INFO] Task started: Prodigal
[2024-01-24 12:40:09,352] [INFO] Running command: gunzip -c /var/lib/cwl/stg93f73b7b-1c80-4d4c-86c3-b0ebd4ff8702/GCF_000146285.1_ASM14628v1_genomic.fna.gz | prodigal -d GCF_000146285.1_ASM14628v1_genomic.fna/cds.fna -a GCF_000146285.1_ASM14628v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:15,979] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:15,980] [INFO] Task started: HMMsearch
[2024-01-24 12:40:15,980] [INFO] Running command: hmmsearch --tblout GCF_000146285.1_ASM14628v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge09c8540-5fbc-4b9a-9747-074a00fabcde/dqc_reference/reference_markers.hmm GCF_000146285.1_ASM14628v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:16,205] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:16,206] [INFO] Found 6/6 markers.
[2024-01-24 12:40:16,244] [INFO] Query marker FASTA was written to GCF_000146285.1_ASM14628v1_genomic.fna/markers.fasta
[2024-01-24 12:40:16,245] [INFO] Task started: Blastn
[2024-01-24 12:40:16,245] [INFO] Running command: blastn -query GCF_000146285.1_ASM14628v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge09c8540-5fbc-4b9a-9747-074a00fabcde/dqc_reference/reference_markers.fasta -out GCF_000146285.1_ASM14628v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:16,867] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:16,870] [INFO] Selected 10 target genomes.
[2024-01-24 12:40:16,870] [INFO] Target genome list was writen to GCF_000146285.1_ASM14628v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:16,874] [INFO] Task started: fastANI
[2024-01-24 12:40:16,874] [INFO] Running command: fastANI --query /var/lib/cwl/stg93f73b7b-1c80-4d4c-86c3-b0ebd4ff8702/GCF_000146285.1_ASM14628v1_genomic.fna.gz --refList GCF_000146285.1_ASM14628v1_genomic.fna/target_genomes.txt --output GCF_000146285.1_ASM14628v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:23,025] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:23,026] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge09c8540-5fbc-4b9a-9747-074a00fabcde/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:23,026] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge09c8540-5fbc-4b9a-9747-074a00fabcde/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:23,037] [INFO] Found 5 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 12:40:23,038] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:40:23,038] [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
Mobiluncus curtisii subsp. curtisii	strain=ATCC 35241	GCA_000146285.1	144177	2051	suspected-type	True	99.9998	713	713	95	inconclusive
Mobiluncus curtisii	strain=FDAARGOS_1127	GCA_016725225.1	2051	2051	suspected-type	True	99.9647	709	713	95	inconclusive
Mobiluncus curtisii subsp. curtisii	strain=NCTC11656	GCA_900453315.1	144177	2051	suspected-type	True	99.9629	709	713	95	inconclusive
Mobiluncus holmesii	strain=NCTC11657	GCA_900453235.1	144178	144178	suspected-type	True	98.1631	664	713	95	inconclusive
Mobiluncus holmesii	strain=ATCC 35242	GCA_000185445.1	144178	144178	suspected-type	True	98.1364	670	713	95	inconclusive
--------------------------------------------------------------------------------
[2024-01-24 12:40:23,040] [INFO] DFAST Taxonomy check result was written to GCF_000146285.1_ASM14628v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:23,041] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:23,041] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:23,041] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge09c8540-5fbc-4b9a-9747-074a00fabcde/dqc_reference/checkm_data
[2024-01-24 12:40:23,043] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:23,076] [INFO] Task started: CheckM
[2024-01-24 12:40:23,076] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000146285.1_ASM14628v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000146285.1_ASM14628v1_genomic.fna/checkm_input GCF_000146285.1_ASM14628v1_genomic.fna/checkm_result
[2024-01-24 12:40:47,882] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:47,883] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:47,903] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:47,903] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:47,904] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000146285.1_ASM14628v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:47,904] [INFO] Task started: Blastn
[2024-01-24 12:40:47,904] [INFO] Running command: blastn -query GCF_000146285.1_ASM14628v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge09c8540-5fbc-4b9a-9747-074a00fabcde/dqc_reference/reference_markers_gtdb.fasta -out GCF_000146285.1_ASM14628v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:48,710] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:48,714] [INFO] Selected 25 target genomes.
[2024-01-24 12:40:48,714] [INFO] Target genome list was writen to GCF_000146285.1_ASM14628v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:48,732] [INFO] Task started: fastANI
[2024-01-24 12:40:48,733] [INFO] Running command: fastANI --query /var/lib/cwl/stg93f73b7b-1c80-4d4c-86c3-b0ebd4ff8702/GCF_000146285.1_ASM14628v1_genomic.fna.gz --refList GCF_000146285.1_ASM14628v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000146285.1_ASM14628v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:00,189] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:00,197] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:00,197] [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_000146285.1	s__Mobiluncus curtisii	99.9998	713	713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Mobiluncus	95.0	98.67	96.00	0.95	0.91	18	conclusive
GCF_000160615.1	s__Mobiluncus mulieris	83.2026	115	713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Mobiluncus	95.0	98.64	97.66	0.92	0.86	20	-
GCF_009695935.1	s__Mobiluncus porci	77.4201	114	713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Mobiluncus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:00,200] [INFO] GTDB search result was written to GCF_000146285.1_ASM14628v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:00,201] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:00,204] [INFO] DFAST_QC result json was written to GCF_000146285.1_ASM14628v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:00,204] [INFO] DFAST_QC completed!
[2024-01-24 12:41:00,204] [INFO] Total running time: 0h0m52s