[2024-01-24 11:19:54,811] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:19:54,814] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:19:54,814] [INFO] DQC Reference Directory: /var/lib/cwl/stgcda92e7c-5e35-40be-a259-46b2d31db1ac/dqc_reference
[2024-01-24 11:19:56,237] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:19:56,238] [INFO] Task started: Prodigal
[2024-01-24 11:19:56,238] [INFO] Running command: gunzip -c /var/lib/cwl/stg12a9e7db-978a-4870-8c1f-acc82a5a2ba3/GCF_017352215.1_ASM1735221v1_genomic.fna.gz | prodigal -d GCF_017352215.1_ASM1735221v1_genomic.fna/cds.fna -a GCF_017352215.1_ASM1735221v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:04,332] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:04,332] [INFO] Task started: HMMsearch
[2024-01-24 11:20:04,332] [INFO] Running command: hmmsearch --tblout GCF_017352215.1_ASM1735221v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcda92e7c-5e35-40be-a259-46b2d31db1ac/dqc_reference/reference_markers.hmm GCF_017352215.1_ASM1735221v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:04,573] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:04,574] [INFO] Found 6/6 markers.
[2024-01-24 11:20:04,600] [INFO] Query marker FASTA was written to GCF_017352215.1_ASM1735221v1_genomic.fna/markers.fasta
[2024-01-24 11:20:04,600] [INFO] Task started: Blastn
[2024-01-24 11:20:04,600] [INFO] Running command: blastn -query GCF_017352215.1_ASM1735221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcda92e7c-5e35-40be-a259-46b2d31db1ac/dqc_reference/reference_markers.fasta -out GCF_017352215.1_ASM1735221v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:05,199] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:05,202] [INFO] Selected 22 target genomes.
[2024-01-24 11:20:05,203] [INFO] Target genome list was writen to GCF_017352215.1_ASM1735221v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:05,213] [INFO] Task started: fastANI
[2024-01-24 11:20:05,213] [INFO] Running command: fastANI --query /var/lib/cwl/stg12a9e7db-978a-4870-8c1f-acc82a5a2ba3/GCF_017352215.1_ASM1735221v1_genomic.fna.gz --refList GCF_017352215.1_ASM1735221v1_genomic.fna/target_genomes.txt --output GCF_017352215.1_ASM1735221v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:17,999] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:18,000] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcda92e7c-5e35-40be-a259-46b2d31db1ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:18,001] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcda92e7c-5e35-40be-a259-46b2d31db1ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:18,012] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:20:18,013] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:18,013] [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 rhizosphaerae	strain=ES005	GCA_017352215.1	2815577	2815577	type	True	100.0	816	816	95	conclusive
Alkalibacter mobilis	strain=M17 DMB	GCA_015594845.1	2787712	2787712	type	True	78.4886	91	816	95	below_threshold
Alkalibacter saccharofermentans	strain=DSM 14828	GCA_900128885.1	235931	235931	type	True	77.5382	57	816	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:18,018] [INFO] DFAST Taxonomy check result was written to GCF_017352215.1_ASM1735221v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:18,021] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:18,021] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:18,022] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcda92e7c-5e35-40be-a259-46b2d31db1ac/dqc_reference/checkm_data
[2024-01-24 11:20:18,023] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:18,056] [INFO] Task started: CheckM
[2024-01-24 11:20:18,057] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017352215.1_ASM1735221v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017352215.1_ASM1735221v1_genomic.fna/checkm_input GCF_017352215.1_ASM1735221v1_genomic.fna/checkm_result
[2024-01-24 11:20:47,544] [INFO] Task succeeded: CheckM
[2024-01-24 11:20:47,546] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:20:47,567] [INFO] ===== Completeness check finished =====
[2024-01-24 11:20:47,567] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:20:47,568] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017352215.1_ASM1735221v1_genomic.fna/markers.fasta)
[2024-01-24 11:20:47,568] [INFO] Task started: Blastn
[2024-01-24 11:20:47,568] [INFO] Running command: blastn -query GCF_017352215.1_ASM1735221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcda92e7c-5e35-40be-a259-46b2d31db1ac/dqc_reference/reference_markers_gtdb.fasta -out GCF_017352215.1_ASM1735221v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:48,465] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:48,470] [INFO] Selected 24 target genomes.
[2024-01-24 11:20:48,470] [INFO] Target genome list was writen to GCF_017352215.1_ASM1735221v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:20:48,494] [INFO] Task started: fastANI
[2024-01-24 11:20:48,494] [INFO] Running command: fastANI --query /var/lib/cwl/stg12a9e7db-978a-4870-8c1f-acc82a5a2ba3/GCF_017352215.1_ASM1735221v1_genomic.fna.gz --refList GCF_017352215.1_ASM1735221v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017352215.1_ASM1735221v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:00,701] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:00,710] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:00,711] [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_017352215.1	s__Alkalibacter sp017352215	100.0	816	816	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_015594845.1	s__Alkalibacter sp015594845	78.4477	92	816	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	77.5382	57	816	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	76.9964	56	816	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 11:21:00,713] [INFO] GTDB search result was written to GCF_017352215.1_ASM1735221v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:00,714] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:00,717] [INFO] DFAST_QC result json was written to GCF_017352215.1_ASM1735221v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:00,718] [INFO] DFAST_QC completed!
[2024-01-24 11:21:00,718] [INFO] Total running time: 0h1m6s