[2024-01-24 14:37:45,828] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:37:45,830] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:37:45,830] [INFO] DQC Reference Directory: /var/lib/cwl/stg0110cad4-cec1-4dc1-953f-bab356250144/dqc_reference
[2024-01-24 14:37:49,292] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:37:49,293] [INFO] Task started: Prodigal
[2024-01-24 14:37:49,293] [INFO] Running command: gunzip -c /var/lib/cwl/stg3d35db76-b8a3-4e6a-9a85-c47a0abee288/GCF_004332295.1_ASM433229v1_genomic.fna.gz | prodigal -d GCF_004332295.1_ASM433229v1_genomic.fna/cds.fna -a GCF_004332295.1_ASM433229v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:37:54,534] [INFO] Task succeeded: Prodigal
[2024-01-24 14:37:54,535] [INFO] Task started: HMMsearch
[2024-01-24 14:37:54,535] [INFO] Running command: hmmsearch --tblout GCF_004332295.1_ASM433229v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0110cad4-cec1-4dc1-953f-bab356250144/dqc_reference/reference_markers.hmm GCF_004332295.1_ASM433229v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:37:54,850] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:37:54,852] [INFO] Found 6/6 markers.
[2024-01-24 14:37:54,878] [INFO] Query marker FASTA was written to GCF_004332295.1_ASM433229v1_genomic.fna/markers.fasta
[2024-01-24 14:37:54,879] [INFO] Task started: Blastn
[2024-01-24 14:37:54,880] [INFO] Running command: blastn -query GCF_004332295.1_ASM433229v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0110cad4-cec1-4dc1-953f-bab356250144/dqc_reference/reference_markers.fasta -out GCF_004332295.1_ASM433229v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:37:59,552] [INFO] Task succeeded: Blastn
[2024-01-24 14:37:59,555] [INFO] Selected 16 target genomes.
[2024-01-24 14:37:59,556] [INFO] Target genome list was writen to GCF_004332295.1_ASM433229v1_genomic.fna/target_genomes.txt
[2024-01-24 14:37:59,703] [INFO] Task started: fastANI
[2024-01-24 14:37:59,704] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d35db76-b8a3-4e6a-9a85-c47a0abee288/GCF_004332295.1_ASM433229v1_genomic.fna.gz --refList GCF_004332295.1_ASM433229v1_genomic.fna/target_genomes.txt --output GCF_004332295.1_ASM433229v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:38:06,924] [INFO] Task succeeded: fastANI
[2024-01-24 14:38:06,925] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0110cad4-cec1-4dc1-953f-bab356250144/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:38:06,925] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0110cad4-cec1-4dc1-953f-bab356250144/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:38:06,931] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:38:06,932] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:38:06,932] [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
Alloscardovia theropitheci	strain=GLDI4/2	GCA_004332295.1	2496842	2496842	type	True	100.0	642	642	95	conclusive
Alloscardovia omnicolens	strain=DSM 21503	GCA_000420505.1	419015	419015	type	True	79.3776	139	642	95	below_threshold
Alloscardovia macacae	strain=DSM 24762	GCA_002259705.1	1160091	1160091	type	True	78.6862	110	642	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:38:06,936] [INFO] DFAST Taxonomy check result was written to GCF_004332295.1_ASM433229v1_genomic.fna/tc_result.tsv
[2024-01-24 14:38:06,937] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:38:06,937] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:38:06,937] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0110cad4-cec1-4dc1-953f-bab356250144/dqc_reference/checkm_data
[2024-01-24 14:38:06,939] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:38:06,962] [INFO] Task started: CheckM
[2024-01-24 14:38:06,962] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004332295.1_ASM433229v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004332295.1_ASM433229v1_genomic.fna/checkm_input GCF_004332295.1_ASM433229v1_genomic.fna/checkm_result
[2024-01-24 14:38:33,225] [INFO] Task succeeded: CheckM
[2024-01-24 14:38:33,227] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:38:33,244] [INFO] ===== Completeness check finished =====
[2024-01-24 14:38:33,245] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:38:33,245] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004332295.1_ASM433229v1_genomic.fna/markers.fasta)
[2024-01-24 14:38:33,246] [INFO] Task started: Blastn
[2024-01-24 14:38:33,246] [INFO] Running command: blastn -query GCF_004332295.1_ASM433229v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0110cad4-cec1-4dc1-953f-bab356250144/dqc_reference/reference_markers_gtdb.fasta -out GCF_004332295.1_ASM433229v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:38:34,012] [INFO] Task succeeded: Blastn
[2024-01-24 14:38:34,015] [INFO] Selected 21 target genomes.
[2024-01-24 14:38:34,015] [INFO] Target genome list was writen to GCF_004332295.1_ASM433229v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:38:34,038] [INFO] Task started: fastANI
[2024-01-24 14:38:34,038] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d35db76-b8a3-4e6a-9a85-c47a0abee288/GCF_004332295.1_ASM433229v1_genomic.fna.gz --refList GCF_004332295.1_ASM433229v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004332295.1_ASM433229v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:38:40,991] [INFO] Task succeeded: fastANI
[2024-01-24 14:38:41,000] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:38:41,000] [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_004332295.1	s__Alloscardovia theropitheci	100.0	642	642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Alloscardovia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000376885.1	s__Alloscardovia criceti	79.4628	131	642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Alloscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420505.1	s__Alloscardovia omnicolens	79.3776	139	642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Alloscardovia	95.0	98.68	97.50	0.93	0.88	12	-
GCF_002259705.1	s__Alloscardovia macacae	78.6862	110	642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Alloscardovia	95.0	96.29	96.25	0.92	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:38:41,002] [INFO] GTDB search result was written to GCF_004332295.1_ASM433229v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:38:41,003] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:38:41,005] [INFO] DFAST_QC result json was written to GCF_004332295.1_ASM433229v1_genomic.fna/dqc_result.json
[2024-01-24 14:38:41,005] [INFO] DFAST_QC completed!
[2024-01-24 14:38:41,006] [INFO] Total running time: 0h0m55s