[2023-06-28 21:01:54,183] [INFO] DFAST_QC pipeline started.
[2023-06-28 21:01:54,186] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 21:01:54,186] [INFO] DQC Reference Directory: /var/lib/cwl/stg50b2eaea-d183-4ca1-bd3e-c3041455f938/dqc_reference
[2023-06-28 21:01:55,454] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 21:01:55,455] [INFO] Task started: Prodigal
[2023-06-28 21:01:55,456] [INFO] Running command: gunzip -c /var/lib/cwl/stgf576ed7d-0f1f-4c5e-9bd0-32c777bbbb96/GCA_015263715.1_ASM1526371v1_genomic.fna.gz | prodigal -d GCA_015263715.1_ASM1526371v1_genomic.fna/cds.fna -a GCA_015263715.1_ASM1526371v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 21:01:57,994] [INFO] Task succeeded: Prodigal
[2023-06-28 21:01:57,995] [INFO] Task started: HMMsearch
[2023-06-28 21:01:57,995] [INFO] Running command: hmmsearch --tblout GCA_015263715.1_ASM1526371v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50b2eaea-d183-4ca1-bd3e-c3041455f938/dqc_reference/reference_markers.hmm GCA_015263715.1_ASM1526371v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 21:01:58,298] [INFO] Task succeeded: HMMsearch
[2023-06-28 21:01:58,300] [INFO] Found 6/6 markers.
[2023-06-28 21:01:58,322] [INFO] Query marker FASTA was written to GCA_015263715.1_ASM1526371v1_genomic.fna/markers.fasta
[2023-06-28 21:01:58,323] [INFO] Task started: Blastn
[2023-06-28 21:01:58,323] [INFO] Running command: blastn -query GCA_015263715.1_ASM1526371v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50b2eaea-d183-4ca1-bd3e-c3041455f938/dqc_reference/reference_markers.fasta -out GCA_015263715.1_ASM1526371v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:01:58,960] [INFO] Task succeeded: Blastn
[2023-06-28 21:01:58,964] [INFO] Selected 8 target genomes.
[2023-06-28 21:01:58,965] [INFO] Target genome list was writen to GCA_015263715.1_ASM1526371v1_genomic.fna/target_genomes.txt
[2023-06-28 21:01:58,968] [INFO] Task started: fastANI
[2023-06-28 21:01:58,968] [INFO] Running command: fastANI --query /var/lib/cwl/stgf576ed7d-0f1f-4c5e-9bd0-32c777bbbb96/GCA_015263715.1_ASM1526371v1_genomic.fna.gz --refList GCA_015263715.1_ASM1526371v1_genomic.fna/target_genomes.txt --output GCA_015263715.1_ASM1526371v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 21:02:02,298] [INFO] Task succeeded: fastANI
[2023-06-28 21:02:02,298] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50b2eaea-d183-4ca1-bd3e-c3041455f938/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 21:02:02,298] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50b2eaea-d183-4ca1-bd3e-c3041455f938/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 21:02:02,304] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2023-06-28 21:02:02,304] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-28 21:02:02,304] [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
Mogibacterium diversum	strain=CCUG 47132	GCA_002998925.1	114527	114527	type	True	97.3109	334	350	95	conclusive
Mogibacterium pumilum	strain=ATCC 700696	GCA_002243385.1	86332	86332	type	True	84.734	279	350	95	below_threshold
Mogibacterium timidum	strain=ATCC 33093	GCA_000525775.1	35519	35519	type	True	79.5831	153	350	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 21:02:02,306] [INFO] DFAST Taxonomy check result was written to GCA_015263715.1_ASM1526371v1_genomic.fna/tc_result.tsv
[2023-06-28 21:02:02,307] [INFO] ===== Taxonomy check completed =====
[2023-06-28 21:02:02,307] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 21:02:02,307] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50b2eaea-d183-4ca1-bd3e-c3041455f938/dqc_reference/checkm_data
[2023-06-28 21:02:02,308] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 21:02:02,325] [INFO] Task started: CheckM
[2023-06-28 21:02:02,325] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015263715.1_ASM1526371v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015263715.1_ASM1526371v1_genomic.fna/checkm_input GCA_015263715.1_ASM1526371v1_genomic.fna/checkm_result
[2023-06-28 21:02:19,342] [INFO] Task succeeded: CheckM
[2023-06-28 21:02:19,343] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 21:02:19,373] [INFO] ===== Completeness check finished =====
[2023-06-28 21:02:19,373] [INFO] ===== Start GTDB Search =====
[2023-06-28 21:02:19,374] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015263715.1_ASM1526371v1_genomic.fna/markers.fasta)
[2023-06-28 21:02:19,374] [INFO] Task started: Blastn
[2023-06-28 21:02:19,374] [INFO] Running command: blastn -query GCA_015263715.1_ASM1526371v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50b2eaea-d183-4ca1-bd3e-c3041455f938/dqc_reference/reference_markers_gtdb.fasta -out GCA_015263715.1_ASM1526371v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:02:20,259] [INFO] Task succeeded: Blastn
[2023-06-28 21:02:20,267] [INFO] Selected 14 target genomes.
[2023-06-28 21:02:20,268] [INFO] Target genome list was writen to GCA_015263715.1_ASM1526371v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 21:02:20,283] [INFO] Task started: fastANI
[2023-06-28 21:02:20,284] [INFO] Running command: fastANI --query /var/lib/cwl/stgf576ed7d-0f1f-4c5e-9bd0-32c777bbbb96/GCA_015263715.1_ASM1526371v1_genomic.fna.gz --refList GCA_015263715.1_ASM1526371v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015263715.1_ASM1526371v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 21:02:26,441] [INFO] Task succeeded: fastANI
[2023-06-28 21:02:26,446] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 21:02:26,446] [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_002998925.1	s__Mogibacterium diversum	97.3109	334	350	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Mogibacterium	95.0	97.57	97.06	0.95	0.90	11	conclusive
GCF_002243385.1	s__Mogibacterium pumilum	84.734	279	350	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Mogibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000525775.1	s__Mogibacterium timidum	79.5831	153	350	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Mogibacterium	95.0	98.94	98.78	0.92	0.88	4	-
--------------------------------------------------------------------------------
[2023-06-28 21:02:26,448] [INFO] GTDB search result was written to GCA_015263715.1_ASM1526371v1_genomic.fna/result_gtdb.tsv
[2023-06-28 21:02:26,449] [INFO] ===== GTDB Search completed =====
[2023-06-28 21:02:26,457] [INFO] DFAST_QC result json was written to GCA_015263715.1_ASM1526371v1_genomic.fna/dqc_result.json
[2023-06-28 21:02:26,458] [INFO] DFAST_QC completed!
[2023-06-28 21:02:26,458] [INFO] Total running time: 0h0m32s