[2024-01-25 18:13:05,533] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:13:05,535] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:13:05,535] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a43eebd-96b9-4b99-a9a5-2fd28906b42d/dqc_reference
[2024-01-25 18:13:06,708] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:13:06,709] [INFO] Task started: Prodigal
[2024-01-25 18:13:06,709] [INFO] Running command: gunzip -c /var/lib/cwl/stg4240efb7-e79a-4bbf-b705-1211dcf7301e/GCF_001402935.1_ASM140293v1_genomic.fna.gz | prodigal -d GCF_001402935.1_ASM140293v1_genomic.fna/cds.fna -a GCF_001402935.1_ASM140293v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:13:11,602] [INFO] Task succeeded: Prodigal
[2024-01-25 18:13:11,602] [INFO] Task started: HMMsearch
[2024-01-25 18:13:11,602] [INFO] Running command: hmmsearch --tblout GCF_001402935.1_ASM140293v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a43eebd-96b9-4b99-a9a5-2fd28906b42d/dqc_reference/reference_markers.hmm GCF_001402935.1_ASM140293v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:13:11,770] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:13:11,771] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg4240efb7-e79a-4bbf-b705-1211dcf7301e/GCF_001402935.1_ASM140293v1_genomic.fna.gz]
[2024-01-25 18:13:11,788] [INFO] Query marker FASTA was written to GCF_001402935.1_ASM140293v1_genomic.fna/markers.fasta
[2024-01-25 18:13:11,789] [INFO] Task started: Blastn
[2024-01-25 18:13:11,789] [INFO] Running command: blastn -query GCF_001402935.1_ASM140293v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a43eebd-96b9-4b99-a9a5-2fd28906b42d/dqc_reference/reference_markers.fasta -out GCF_001402935.1_ASM140293v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:12,231] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:12,233] [INFO] Selected 5 target genomes.
[2024-01-25 18:13:12,234] [INFO] Target genome list was writen to GCF_001402935.1_ASM140293v1_genomic.fna/target_genomes.txt
[2024-01-25 18:13:12,244] [INFO] Task started: fastANI
[2024-01-25 18:13:12,244] [INFO] Running command: fastANI --query /var/lib/cwl/stg4240efb7-e79a-4bbf-b705-1211dcf7301e/GCF_001402935.1_ASM140293v1_genomic.fna.gz --refList GCF_001402935.1_ASM140293v1_genomic.fna/target_genomes.txt --output GCF_001402935.1_ASM140293v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:13:13,943] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:13,944] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a43eebd-96b9-4b99-a9a5-2fd28906b42d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:13:13,944] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a43eebd-96b9-4b99-a9a5-2fd28906b42d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:13:13,949] [INFO] Found 5 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 18:13:13,950] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 18:13:13,950] [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
Acidiplasma cupricumulans	strain=BH2	GCA_001402935.1	312540	312540	suspected-type	True	99.9999	427	433	95	inconclusive
Acidiplasma cupricumulans	strain=JCM 13668	GCA_001316225.1	312540	312540	suspected-type	True	99.6487	422	433	95	inconclusive
Acidiplasma aeolicum	strain=VT	GCA_001402945.1	507754	507754	suspected-type	True	99.072	378	433	95	inconclusive
Acidiplasma aeolicum	strain=V	GCA_001399695.1	507754	507754	suspected-type	True	98.8146	330	433	95	inconclusive
Ferroplasma acidiphilum	strain=Y	GCA_002078355.1	74969	74969	type	True	76.6717	52	433	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:13:13,951] [INFO] DFAST Taxonomy check result was written to GCF_001402935.1_ASM140293v1_genomic.fna/tc_result.tsv
[2024-01-25 18:13:13,951] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:13:13,952] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:13:13,952] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a43eebd-96b9-4b99-a9a5-2fd28906b42d/dqc_reference/checkm_data
[2024-01-25 18:13:13,953] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:13:13,974] [INFO] Task started: CheckM
[2024-01-25 18:13:13,974] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001402935.1_ASM140293v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001402935.1_ASM140293v1_genomic.fna/checkm_input GCF_001402935.1_ASM140293v1_genomic.fna/checkm_result
[2024-01-25 18:13:33,414] [INFO] Task succeeded: CheckM
[2024-01-25 18:13:33,418] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:13:33,434] [INFO] ===== Completeness check finished =====
[2024-01-25 18:13:33,435] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:13:33,435] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001402935.1_ASM140293v1_genomic.fna/markers.fasta)
[2024-01-25 18:13:33,435] [INFO] Task started: Blastn
[2024-01-25 18:13:33,435] [INFO] Running command: blastn -query GCF_001402935.1_ASM140293v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a43eebd-96b9-4b99-a9a5-2fd28906b42d/dqc_reference/reference_markers_gtdb.fasta -out GCF_001402935.1_ASM140293v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:33,932] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:33,935] [INFO] Selected 5 target genomes.
[2024-01-25 18:13:33,935] [INFO] Target genome list was writen to GCF_001402935.1_ASM140293v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:13:33,942] [INFO] Task started: fastANI
[2024-01-25 18:13:33,942] [INFO] Running command: fastANI --query /var/lib/cwl/stg4240efb7-e79a-4bbf-b705-1211dcf7301e/GCF_001402935.1_ASM140293v1_genomic.fna.gz --refList GCF_001402935.1_ASM140293v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001402935.1_ASM140293v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:13:35,554] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:35,557] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:13:35,557] [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_001402945.1	s__Acidiplasma aeolicum	99.072	378	433	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Thermoplasmatales;f__Thermoplasmataceae;g__Acidiplasma	95.0	99.19	98.94	0.92	0.87	5	conclusive
GCF_002078355.1	s__Ferroplasma acidiphilum	76.6546	52	433	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Thermoplasmatales;f__Thermoplasmataceae;g__Ferroplasma	96.9486	97.96	97.96	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:13:35,559] [INFO] GTDB search result was written to GCF_001402935.1_ASM140293v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:13:35,559] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:13:35,563] [INFO] DFAST_QC result json was written to GCF_001402935.1_ASM140293v1_genomic.fna/dqc_result.json
[2024-01-25 18:13:35,563] [INFO] DFAST_QC completed!
[2024-01-25 18:13:35,563] [INFO] Total running time: 0h0m30s