[2024-01-24 13:28:25,416] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:25,418] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:25,419] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd2872c0-f771-46b7-a83e-dadb8ed924ae/dqc_reference
[2024-01-24 13:28:26,750] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:26,751] [INFO] Task started: Prodigal
[2024-01-24 13:28:26,752] [INFO] Running command: gunzip -c /var/lib/cwl/stg25d9c29f-f1bc-4812-ae22-3905a53e9c33/GCF_009695935.1_ASM969593v1_genomic.fna.gz | prodigal -d GCF_009695935.1_ASM969593v1_genomic.fna/cds.fna -a GCF_009695935.1_ASM969593v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:34,241] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:34,242] [INFO] Task started: HMMsearch
[2024-01-24 13:28:34,242] [INFO] Running command: hmmsearch --tblout GCF_009695935.1_ASM969593v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd2872c0-f771-46b7-a83e-dadb8ed924ae/dqc_reference/reference_markers.hmm GCF_009695935.1_ASM969593v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:34,500] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:34,502] [INFO] Found 6/6 markers.
[2024-01-24 13:28:34,531] [INFO] Query marker FASTA was written to GCF_009695935.1_ASM969593v1_genomic.fna/markers.fasta
[2024-01-24 13:28:34,531] [INFO] Task started: Blastn
[2024-01-24 13:28:34,531] [INFO] Running command: blastn -query GCF_009695935.1_ASM969593v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd2872c0-f771-46b7-a83e-dadb8ed924ae/dqc_reference/reference_markers.fasta -out GCF_009695935.1_ASM969593v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:35,204] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:35,208] [INFO] Selected 20 target genomes.
[2024-01-24 13:28:35,208] [INFO] Target genome list was writen to GCF_009695935.1_ASM969593v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:35,220] [INFO] Task started: fastANI
[2024-01-24 13:28:35,220] [INFO] Running command: fastANI --query /var/lib/cwl/stg25d9c29f-f1bc-4812-ae22-3905a53e9c33/GCF_009695935.1_ASM969593v1_genomic.fna.gz --refList GCF_009695935.1_ASM969593v1_genomic.fna/target_genomes.txt --output GCF_009695935.1_ASM969593v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:48,732] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:48,732] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd2872c0-f771-46b7-a83e-dadb8ed924ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:48,733] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd2872c0-f771-46b7-a83e-dadb8ed924ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:48,740] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:48,740] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:48,740] [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 porci	strain=RF-GAM-744-WT-7	GCA_009695935.1	2652278	2652278	type	True	100.0	779	779	95	conclusive
Mobiluncus mulieris	strain=NCTC11658	GCA_900453215.1	2052	2052	type	True	77.6356	108	779	95	below_threshold
Mobiluncus mulieris	strain=ATCC 35243	GCA_000160615.1	2052	2052	type	True	77.5577	109	779	95	below_threshold
Mobiluncus holmesii	strain=NCTC11657	GCA_900453235.1	144178	144178	suspected-type	True	77.4236	114	779	95	below_threshold
Mobiluncus curtisii subsp. curtisii	strain=ATCC 35241	GCA_000146285.1	144177	2051	suspected-type	True	77.3771	108	779	95	below_threshold
Mobiluncus curtisii	strain=FDAARGOS_1127	GCA_016725225.1	2051	2051	suspected-type	True	77.3336	112	779	95	below_threshold
Mobiluncus holmesii	strain=ATCC 35242	GCA_000185445.1	144178	144178	suspected-type	True	77.2711	106	779	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:48,743] [INFO] DFAST Taxonomy check result was written to GCF_009695935.1_ASM969593v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:48,743] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:48,743] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:48,744] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd2872c0-f771-46b7-a83e-dadb8ed924ae/dqc_reference/checkm_data
[2024-01-24 13:28:48,744] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:48,774] [INFO] Task started: CheckM
[2024-01-24 13:28:48,775] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009695935.1_ASM969593v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009695935.1_ASM969593v1_genomic.fna/checkm_input GCF_009695935.1_ASM969593v1_genomic.fna/checkm_result
[2024-01-24 13:29:15,519] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:15,521] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:15,541] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:15,541] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:15,542] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009695935.1_ASM969593v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:15,542] [INFO] Task started: Blastn
[2024-01-24 13:29:15,542] [INFO] Running command: blastn -query GCF_009695935.1_ASM969593v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd2872c0-f771-46b7-a83e-dadb8ed924ae/dqc_reference/reference_markers_gtdb.fasta -out GCF_009695935.1_ASM969593v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:16,372] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:16,375] [INFO] Selected 21 target genomes.
[2024-01-24 13:29:16,376] [INFO] Target genome list was writen to GCF_009695935.1_ASM969593v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:16,414] [INFO] Task started: fastANI
[2024-01-24 13:29:16,414] [INFO] Running command: fastANI --query /var/lib/cwl/stg25d9c29f-f1bc-4812-ae22-3905a53e9c33/GCF_009695935.1_ASM969593v1_genomic.fna.gz --refList GCF_009695935.1_ASM969593v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009695935.1_ASM969593v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:25,410] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:25,417] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:25,417] [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_009695935.1	s__Mobiluncus porci	100.0	779	779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Mobiluncus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000160615.1	s__Mobiluncus mulieris	77.5286	110	779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Mobiluncus	95.0	98.64	97.66	0.92	0.86	20	-
GCF_000146285.1	s__Mobiluncus curtisii	77.3648	107	779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Mobiluncus	95.0	98.67	96.00	0.95	0.91	18	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:25,419] [INFO] GTDB search result was written to GCF_009695935.1_ASM969593v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:25,420] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:25,425] [INFO] DFAST_QC result json was written to GCF_009695935.1_ASM969593v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:25,426] [INFO] DFAST_QC completed!
[2024-01-24 13:29:25,426] [INFO] Total running time: 0h1m0s