[2023-06-18 12:48:40,705] [INFO] DFAST_QC pipeline started.
[2023-06-18 12:48:40,708] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 12:48:40,708] [INFO] DQC Reference Directory: /var/lib/cwl/stg73ca4a8d-95de-46aa-8065-1a78af882d1f/dqc_reference
[2023-06-18 12:48:44,286] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 12:48:44,287] [INFO] Task started: Prodigal
[2023-06-18 12:48:44,288] [INFO] Running command: gunzip -c /var/lib/cwl/stg79e065c0-e573-4d18-9463-0252f3dc1ca7/GCA_018059435.1_ASM1805943v1_genomic.fna.gz | prodigal -d GCA_018059435.1_ASM1805943v1_genomic.fna/cds.fna -a GCA_018059435.1_ASM1805943v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 12:48:46,253] [INFO] Task succeeded: Prodigal
[2023-06-18 12:48:46,254] [INFO] Task started: HMMsearch
[2023-06-18 12:48:46,254] [INFO] Running command: hmmsearch --tblout GCA_018059435.1_ASM1805943v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg73ca4a8d-95de-46aa-8065-1a78af882d1f/dqc_reference/reference_markers.hmm GCA_018059435.1_ASM1805943v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 12:48:46,498] [INFO] Task succeeded: HMMsearch
[2023-06-18 12:48:46,500] [INFO] Found 6/6 markers.
[2023-06-18 12:48:46,527] [INFO] Query marker FASTA was written to GCA_018059435.1_ASM1805943v1_genomic.fna/markers.fasta
[2023-06-18 12:48:46,528] [INFO] Task started: Blastn
[2023-06-18 12:48:46,528] [INFO] Running command: blastn -query GCA_018059435.1_ASM1805943v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg73ca4a8d-95de-46aa-8065-1a78af882d1f/dqc_reference/reference_markers.fasta -out GCA_018059435.1_ASM1805943v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 12:48:49,759] [INFO] Task succeeded: Blastn
[2023-06-18 12:48:49,769] [INFO] Selected 15 target genomes.
[2023-06-18 12:48:49,769] [INFO] Target genome list was writen to GCA_018059435.1_ASM1805943v1_genomic.fna/target_genomes.txt
[2023-06-18 12:48:49,778] [INFO] Task started: fastANI
[2023-06-18 12:48:49,778] [INFO] Running command: fastANI --query /var/lib/cwl/stg79e065c0-e573-4d18-9463-0252f3dc1ca7/GCA_018059435.1_ASM1805943v1_genomic.fna.gz --refList GCA_018059435.1_ASM1805943v1_genomic.fna/target_genomes.txt --output GCA_018059435.1_ASM1805943v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 12:48:59,495] [INFO] Task succeeded: fastANI
[2023-06-18 12:48:59,495] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg73ca4a8d-95de-46aa-8065-1a78af882d1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 12:48:59,495] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg73ca4a8d-95de-46aa-8065-1a78af882d1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 12:48:59,501] [INFO] Found 3 fastANI hits (2 hits with ANI > threshold)
[2023-06-18 12:48:59,501] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-06-18 12:48:59,501] [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
Acetoanaerobium noterae	strain=ATCC 35199	GCA_900168025.1	745369	745369	type	True	98.4052	314	341	95	inconclusive
Acetoanaerobium sticklandii	strain=DSM 519	GCA_000196455.1	1511	1511	type	True	97.0635	310	341	95	inconclusive
Acetoanaerobium pronyense	strain=DSM 27512	GCA_017874355.1	1482736	1482736	type	True	76.8169	74	341	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 12:48:59,507] [INFO] DFAST Taxonomy check result was written to GCA_018059435.1_ASM1805943v1_genomic.fna/tc_result.tsv
[2023-06-18 12:48:59,508] [INFO] ===== Taxonomy check completed =====
[2023-06-18 12:48:59,508] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 12:48:59,509] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg73ca4a8d-95de-46aa-8065-1a78af882d1f/dqc_reference/checkm_data
[2023-06-18 12:48:59,510] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 12:48:59,529] [INFO] Task started: CheckM
[2023-06-18 12:48:59,530] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018059435.1_ASM1805943v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018059435.1_ASM1805943v1_genomic.fna/checkm_input GCA_018059435.1_ASM1805943v1_genomic.fna/checkm_result
[2023-06-18 12:49:14,021] [INFO] Task succeeded: CheckM
[2023-06-18 12:49:14,022] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 12:49:14,058] [INFO] ===== Completeness check finished =====
[2023-06-18 12:49:14,058] [INFO] ===== Start GTDB Search =====
[2023-06-18 12:49:14,059] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018059435.1_ASM1805943v1_genomic.fna/markers.fasta)
[2023-06-18 12:49:14,059] [INFO] Task started: Blastn
[2023-06-18 12:49:14,059] [INFO] Running command: blastn -query GCA_018059435.1_ASM1805943v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg73ca4a8d-95de-46aa-8065-1a78af882d1f/dqc_reference/reference_markers_gtdb.fasta -out GCA_018059435.1_ASM1805943v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 12:49:14,883] [INFO] Task succeeded: Blastn
[2023-06-18 12:49:14,888] [INFO] Selected 14 target genomes.
[2023-06-18 12:49:14,889] [INFO] Target genome list was writen to GCA_018059435.1_ASM1805943v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 12:49:14,935] [INFO] Task started: fastANI
[2023-06-18 12:49:14,935] [INFO] Running command: fastANI --query /var/lib/cwl/stg79e065c0-e573-4d18-9463-0252f3dc1ca7/GCA_018059435.1_ASM1805943v1_genomic.fna.gz --refList GCA_018059435.1_ASM1805943v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018059435.1_ASM1805943v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 12:49:22,223] [INFO] Task succeeded: fastANI
[2023-06-18 12:49:22,228] [INFO] Found 3 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-18 12:49:22,228] [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_900168025.1	s__Acetoanaerobium noterae	98.4052	314	341	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Filifactoraceae;g__Acetoanaerobium	96.3037	98.02	97.03	0.90	0.82	5	inconclusive
GCF_000196455.1	s__Acetoanaerobium sticklandii	97.0635	310	341	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Filifactoraceae;g__Acetoanaerobium	96.3037	N/A	N/A	N/A	N/A	1	inconclusive
GCF_017874355.1	s__Acetoanaerobium pronyense	76.8169	74	341	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Filifactoraceae;g__Acetoanaerobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 12:49:22,233] [INFO] GTDB search result was written to GCA_018059435.1_ASM1805943v1_genomic.fna/result_gtdb.tsv
[2023-06-18 12:49:22,234] [INFO] ===== GTDB Search completed =====
[2023-06-18 12:49:22,241] [INFO] DFAST_QC result json was written to GCA_018059435.1_ASM1805943v1_genomic.fna/dqc_result.json
[2023-06-18 12:49:22,241] [INFO] DFAST_QC completed!
[2023-06-18 12:49:22,241] [INFO] Total running time: 0h0m42s