[2024-01-24 12:23:03,941] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:03,945] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:03,945] [INFO] DQC Reference Directory: /var/lib/cwl/stge31e0353-068c-4bd5-82c9-a24f47262ed8/dqc_reference
[2024-01-24 12:23:05,266] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:05,267] [INFO] Task started: Prodigal
[2024-01-24 12:23:05,268] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb0f2e5e-6ab1-4257-a8a6-82184a45a90f/GCF_015594845.1_ASM1559484v1_genomic.fna.gz | prodigal -d GCF_015594845.1_ASM1559484v1_genomic.fna/cds.fna -a GCF_015594845.1_ASM1559484v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:11,497] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:11,498] [INFO] Task started: HMMsearch
[2024-01-24 12:23:11,498] [INFO] Running command: hmmsearch --tblout GCF_015594845.1_ASM1559484v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge31e0353-068c-4bd5-82c9-a24f47262ed8/dqc_reference/reference_markers.hmm GCF_015594845.1_ASM1559484v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:11,728] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:11,730] [INFO] Found 6/6 markers.
[2024-01-24 12:23:11,759] [INFO] Query marker FASTA was written to GCF_015594845.1_ASM1559484v1_genomic.fna/markers.fasta
[2024-01-24 12:23:11,760] [INFO] Task started: Blastn
[2024-01-24 12:23:11,760] [INFO] Running command: blastn -query GCF_015594845.1_ASM1559484v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge31e0353-068c-4bd5-82c9-a24f47262ed8/dqc_reference/reference_markers.fasta -out GCF_015594845.1_ASM1559484v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:12,339] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:12,343] [INFO] Selected 17 target genomes.
[2024-01-24 12:23:12,343] [INFO] Target genome list was writen to GCF_015594845.1_ASM1559484v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:12,350] [INFO] Task started: fastANI
[2024-01-24 12:23:12,350] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb0f2e5e-6ab1-4257-a8a6-82184a45a90f/GCF_015594845.1_ASM1559484v1_genomic.fna.gz --refList GCF_015594845.1_ASM1559484v1_genomic.fna/target_genomes.txt --output GCF_015594845.1_ASM1559484v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:20,276] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:20,277] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge31e0353-068c-4bd5-82c9-a24f47262ed8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:20,278] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge31e0353-068c-4bd5-82c9-a24f47262ed8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:20,287] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:20,287] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:20,288] [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
Alkalibacter mobilis	strain=M17 DMB	GCA_015594845.1	2787712	2787712	type	True	100.0	797	802	95	conclusive
Alkalibacter rhizosphaerae	strain=ES005	GCA_017352215.1	2815577	2815577	type	True	78.205	91	802	95	below_threshold
Alkalibacter saccharofermentans	strain=DSM 14828	GCA_900128885.1	235931	235931	type	True	77.9314	93	802	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:20,289] [INFO] DFAST Taxonomy check result was written to GCF_015594845.1_ASM1559484v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:20,290] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:20,290] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:20,290] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge31e0353-068c-4bd5-82c9-a24f47262ed8/dqc_reference/checkm_data
[2024-01-24 12:23:20,292] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:20,321] [INFO] Task started: CheckM
[2024-01-24 12:23:20,321] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015594845.1_ASM1559484v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015594845.1_ASM1559484v1_genomic.fna/checkm_input GCF_015594845.1_ASM1559484v1_genomic.fna/checkm_result
[2024-01-24 12:23:45,115] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:45,117] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:45,143] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:45,143] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:45,144] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015594845.1_ASM1559484v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:45,144] [INFO] Task started: Blastn
[2024-01-24 12:23:45,144] [INFO] Running command: blastn -query GCF_015594845.1_ASM1559484v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge31e0353-068c-4bd5-82c9-a24f47262ed8/dqc_reference/reference_markers_gtdb.fasta -out GCF_015594845.1_ASM1559484v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:45,898] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:45,901] [INFO] Selected 22 target genomes.
[2024-01-24 12:23:45,901] [INFO] Target genome list was writen to GCF_015594845.1_ASM1559484v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:45,918] [INFO] Task started: fastANI
[2024-01-24 12:23:45,918] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb0f2e5e-6ab1-4257-a8a6-82184a45a90f/GCF_015594845.1_ASM1559484v1_genomic.fna.gz --refList GCF_015594845.1_ASM1559484v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015594845.1_ASM1559484v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:55,721] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:55,727] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:55,728] [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_015594845.1	s__Alkalibacter sp015594845	100.0	797	802	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Eubacteriales;f__Alkalibacteraceae;g__Alkalibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017352215.1	s__Alkalibacter sp017352215	78.205	91	802	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Eubacteriales;f__Alkalibacteraceae;g__Alkalibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128885.1	s__Alkalibacter saccharofermentans	77.9314	93	802	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Eubacteriales;f__Alkalibacteraceae;g__Alkalibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003446375.1	s__Alkalibacter sp003446375	77.9285	106	802	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Eubacteriales;f__Alkalibacteraceae;g__Alkalibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:55,729] [INFO] GTDB search result was written to GCF_015594845.1_ASM1559484v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:55,730] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:55,733] [INFO] DFAST_QC result json was written to GCF_015594845.1_ASM1559484v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:55,733] [INFO] DFAST_QC completed!
[2024-01-24 12:23:55,733] [INFO] Total running time: 0h0m52s