[2024-01-24 13:56:56,484] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:56:56,486] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:56:56,486] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd36da80-9de4-4a03-b237-6a7a91837abf/dqc_reference
[2024-01-24 13:56:57,722] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:56:57,723] [INFO] Task started: Prodigal
[2024-01-24 13:56:57,723] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb153bf1-7184-49e0-a88e-327021800c01/GCF_002078355.1_ASM207835v1_genomic.fna.gz | prodigal -d GCF_002078355.1_ASM207835v1_genomic.fna/cds.fna -a GCF_002078355.1_ASM207835v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:01,711] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:01,712] [INFO] Task started: HMMsearch
[2024-01-24 13:57:01,712] [INFO] Running command: hmmsearch --tblout GCF_002078355.1_ASM207835v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd36da80-9de4-4a03-b237-6a7a91837abf/dqc_reference/reference_markers.hmm GCF_002078355.1_ASM207835v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:01,939] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:01,941] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgdb153bf1-7184-49e0-a88e-327021800c01/GCF_002078355.1_ASM207835v1_genomic.fna.gz]
[2024-01-24 13:57:01,964] [INFO] Query marker FASTA was written to GCF_002078355.1_ASM207835v1_genomic.fna/markers.fasta
[2024-01-24 13:57:01,964] [INFO] Task started: Blastn
[2024-01-24 13:57:01,964] [INFO] Running command: blastn -query GCF_002078355.1_ASM207835v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd36da80-9de4-4a03-b237-6a7a91837abf/dqc_reference/reference_markers.fasta -out GCF_002078355.1_ASM207835v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:02,453] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:02,457] [INFO] Selected 5 target genomes.
[2024-01-24 13:57:02,458] [INFO] Target genome list was writen to GCF_002078355.1_ASM207835v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:02,461] [INFO] Task started: fastANI
[2024-01-24 13:57:02,462] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb153bf1-7184-49e0-a88e-327021800c01/GCF_002078355.1_ASM207835v1_genomic.fna.gz --refList GCF_002078355.1_ASM207835v1_genomic.fna/target_genomes.txt --output GCF_002078355.1_ASM207835v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:04,414] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:04,414] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd36da80-9de4-4a03-b237-6a7a91837abf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:04,415] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd36da80-9de4-4a03-b237-6a7a91837abf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:04,427] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:57:04,427] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:57:04,428] [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
Ferroplasma acidiphilum	strain=Y	GCA_002078355.1	74969	74969	type	True	100.0	608	608	95	inconclusive
Ferroplasma acidarmanus	strain=Fer1	GCA_000152265.2	97393	97393	type	True	96.8773	544	608	95	inconclusive
Acidiplasma aeolicum	strain=V	GCA_001399695.1	507754	507754	suspected-type	True	76.4885	57	608	95	below_threshold
Acidiplasma aeolicum	strain=VT	GCA_001402945.1	507754	507754	suspected-type	True	76.478	64	608	95	below_threshold
Acidiplasma cupricumulans	strain=BH2	GCA_001402935.1	312540	312540	suspected-type	True	76.458	56	608	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:04,429] [INFO] DFAST Taxonomy check result was written to GCF_002078355.1_ASM207835v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:04,431] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:04,431] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:04,432] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd36da80-9de4-4a03-b237-6a7a91837abf/dqc_reference/checkm_data
[2024-01-24 13:57:04,434] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:04,461] [INFO] Task started: CheckM
[2024-01-24 13:57:04,461] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002078355.1_ASM207835v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002078355.1_ASM207835v1_genomic.fna/checkm_input GCF_002078355.1_ASM207835v1_genomic.fna/checkm_result
[2024-01-24 13:57:24,164] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:24,165] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:24,183] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:24,183] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:24,184] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002078355.1_ASM207835v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:24,184] [INFO] Task started: Blastn
[2024-01-24 13:57:24,185] [INFO] Running command: blastn -query GCF_002078355.1_ASM207835v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd36da80-9de4-4a03-b237-6a7a91837abf/dqc_reference/reference_markers_gtdb.fasta -out GCF_002078355.1_ASM207835v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:24,623] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:24,628] [INFO] Selected 6 target genomes.
[2024-01-24 13:57:24,628] [INFO] Target genome list was writen to GCF_002078355.1_ASM207835v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:24,636] [INFO] Task started: fastANI
[2024-01-24 13:57:24,636] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb153bf1-7184-49e0-a88e-327021800c01/GCF_002078355.1_ASM207835v1_genomic.fna.gz --refList GCF_002078355.1_ASM207835v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002078355.1_ASM207835v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:27,239] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:27,248] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:27,248] [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_002078355.1	s__Ferroplasma acidiphilum	100.0	608	608	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Thermoplasmatales;f__Thermoplasmataceae;g__Ferroplasma	96.9486	97.96	97.96	0.93	0.93	2	conclusive
GCF_000152265.2	s__Ferroplasma acidarmanus	96.8615	545	608	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Thermoplasmatales;f__Thermoplasmataceae;g__Ferroplasma	96.9486	N/A	N/A	N/A	N/A	1	-
GCA_002505185.1	s__Ferroplasma sp002505185	79.4728	217	608	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Thermoplasmatales;f__Thermoplasmataceae;g__Ferroplasma	95.0	99.08	99.02	0.82	0.82	3	-
GCF_001402945.1	s__Acidiplasma aeolicum	76.478	64	608	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Thermoplasmatales;f__Thermoplasmataceae;g__Acidiplasma	95.0	99.19	98.94	0.92	0.87	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:27,250] [INFO] GTDB search result was written to GCF_002078355.1_ASM207835v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:27,251] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:27,254] [INFO] DFAST_QC result json was written to GCF_002078355.1_ASM207835v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:27,255] [INFO] DFAST_QC completed!
[2024-01-24 13:57:27,255] [INFO] Total running time: 0h0m31s