[2024-01-24 13:57:42,180] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:42,182] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:42,182] [INFO] DQC Reference Directory: /var/lib/cwl/stg305265bc-127f-4a64-9200-6be46ad0d288/dqc_reference
[2024-01-24 13:57:43,588] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:43,589] [INFO] Task started: Prodigal
[2024-01-24 13:57:43,589] [INFO] Running command: gunzip -c /var/lib/cwl/stgf471d7ed-35c4-4d5f-ba14-4bdedba00932/GCF_002878295.2_ASM287829v2_genomic.fna.gz | prodigal -d GCF_002878295.2_ASM287829v2_genomic.fna/cds.fna -a GCF_002878295.2_ASM287829v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:48,942] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:48,942] [INFO] Task started: HMMsearch
[2024-01-24 13:57:48,942] [INFO] Running command: hmmsearch --tblout GCF_002878295.2_ASM287829v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg305265bc-127f-4a64-9200-6be46ad0d288/dqc_reference/reference_markers.hmm GCF_002878295.2_ASM287829v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:49,200] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:49,202] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf471d7ed-35c4-4d5f-ba14-4bdedba00932/GCF_002878295.2_ASM287829v2_genomic.fna.gz]
[2024-01-24 13:57:49,227] [INFO] Query marker FASTA was written to GCF_002878295.2_ASM287829v2_genomic.fna/markers.fasta
[2024-01-24 13:57:49,227] [INFO] Task started: Blastn
[2024-01-24 13:57:49,227] [INFO] Running command: blastn -query GCF_002878295.2_ASM287829v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg305265bc-127f-4a64-9200-6be46ad0d288/dqc_reference/reference_markers.fasta -out GCF_002878295.2_ASM287829v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:49,822] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:49,826] [INFO] Selected 13 target genomes.
[2024-01-24 13:57:49,826] [INFO] Target genome list was writen to GCF_002878295.2_ASM287829v2_genomic.fna/target_genomes.txt
[2024-01-24 13:57:49,836] [INFO] Task started: fastANI
[2024-01-24 13:57:49,836] [INFO] Running command: fastANI --query /var/lib/cwl/stgf471d7ed-35c4-4d5f-ba14-4bdedba00932/GCF_002878295.2_ASM287829v2_genomic.fna.gz --refList GCF_002878295.2_ASM287829v2_genomic.fna/target_genomes.txt --output GCF_002878295.2_ASM287829v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:57,111] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:57,112] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg305265bc-127f-4a64-9200-6be46ad0d288/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:57,112] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg305265bc-127f-4a64-9200-6be46ad0d288/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:57,119] [INFO] Found 4 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:57:57,119] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:57,120] [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
Candidatus Dehalogenimonas etheniformans	strain=GP	GCA_002878295.2	1536648	1536648	type	True	100.0	666	666	95	conclusive
Candidatus Dehalogenimonas etheniformans	strain=GP	GCA_014672715.2	1536648	1536648	type	True	99.9866	663	666	95	conclusive
Dehalogenimonas formicexedens	strain=NSZ-14	GCA_001953175.1	1839801	1839801	type	True	81.3497	379	666	95	below_threshold
Dehalogenimonas alkenigignens	strain=IP3-3	GCA_001466665.1	1217799	1217799	type	True	77.9332	137	666	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:57,121] [INFO] DFAST Taxonomy check result was written to GCF_002878295.2_ASM287829v2_genomic.fna/tc_result.tsv
[2024-01-24 13:57:57,122] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:57,122] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:57,122] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg305265bc-127f-4a64-9200-6be46ad0d288/dqc_reference/checkm_data
[2024-01-24 13:57:57,123] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:57,149] [INFO] Task started: CheckM
[2024-01-24 13:57:57,149] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002878295.2_ASM287829v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002878295.2_ASM287829v2_genomic.fna/checkm_input GCF_002878295.2_ASM287829v2_genomic.fna/checkm_result
[2024-01-24 13:58:19,999] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:20,001] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:20,023] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:20,023] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:20,023] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002878295.2_ASM287829v2_genomic.fna/markers.fasta)
[2024-01-24 13:58:20,024] [INFO] Task started: Blastn
[2024-01-24 13:58:20,024] [INFO] Running command: blastn -query GCF_002878295.2_ASM287829v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg305265bc-127f-4a64-9200-6be46ad0d288/dqc_reference/reference_markers_gtdb.fasta -out GCF_002878295.2_ASM287829v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:20,825] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:20,829] [INFO] Selected 16 target genomes.
[2024-01-24 13:58:20,830] [INFO] Target genome list was writen to GCF_002878295.2_ASM287829v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:20,846] [INFO] Task started: fastANI
[2024-01-24 13:58:20,846] [INFO] Running command: fastANI --query /var/lib/cwl/stgf471d7ed-35c4-4d5f-ba14-4bdedba00932/GCF_002878295.2_ASM287829v2_genomic.fna.gz --refList GCF_002878295.2_ASM287829v2_genomic.fna/target_genomes_gtdb.txt --output GCF_002878295.2_ASM287829v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:26,800] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:26,809] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:26,809] [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_014672715.2	s__Dehalogenimonas sp002878295	99.9866	663	666	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Dehalococcoidales;f__Dehalococcoidaceae;g__Dehalogenimonas	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_001953175.1	s__Dehalogenimonas formicexedens	81.3394	380	666	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Dehalococcoidales;f__Dehalococcoidaceae;g__Dehalogenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001005265.1	s__Dehalogenimonas sp001005265	78.4486	64	666	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Dehalococcoidales;f__Dehalococcoidaceae;g__Dehalogenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001466665.1	s__Dehalogenimonas alkenigignens	77.9332	137	666	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Dehalococcoidales;f__Dehalococcoidaceae;g__Dehalogenimonas	95.0	99.11	99.11	0.94	0.94	2	-
GCF_000143165.1	s__Dehalogenimonas lykanthroporepellens	77.4796	63	666	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Dehalococcoidales;f__Dehalococcoidaceae;g__Dehalogenimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:26,811] [INFO] GTDB search result was written to GCF_002878295.2_ASM287829v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:26,811] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:26,815] [INFO] DFAST_QC result json was written to GCF_002878295.2_ASM287829v2_genomic.fna/dqc_result.json
[2024-01-24 13:58:26,815] [INFO] DFAST_QC completed!
[2024-01-24 13:58:26,815] [INFO] Total running time: 0h0m45s