[2023-06-17 08:40:12,173] [INFO] DFAST_QC pipeline started.
[2023-06-17 08:40:12,181] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 08:40:12,181] [INFO] DQC Reference Directory: /var/lib/cwl/stg9e585cb3-fde4-4aee-b62f-ac47c798c2f9/dqc_reference
[2023-06-17 08:40:15,179] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 08:40:15,180] [INFO] Task started: Prodigal
[2023-06-17 08:40:15,180] [INFO] Running command: gunzip -c /var/lib/cwl/stgf834611c-7ae8-40bf-87c3-544a1826c971/GCA_028817545.1_ASM2881754v1_genomic.fna.gz | prodigal -d GCA_028817545.1_ASM2881754v1_genomic.fna/cds.fna -a GCA_028817545.1_ASM2881754v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 08:40:22,021] [INFO] Task succeeded: Prodigal
[2023-06-17 08:40:22,021] [INFO] Task started: HMMsearch
[2023-06-17 08:40:22,022] [INFO] Running command: hmmsearch --tblout GCA_028817545.1_ASM2881754v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9e585cb3-fde4-4aee-b62f-ac47c798c2f9/dqc_reference/reference_markers.hmm GCA_028817545.1_ASM2881754v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 08:40:22,258] [INFO] Task succeeded: HMMsearch
[2023-06-17 08:40:22,262] [INFO] Found 6/6 markers.
[2023-06-17 08:40:22,299] [INFO] Query marker FASTA was written to GCA_028817545.1_ASM2881754v1_genomic.fna/markers.fasta
[2023-06-17 08:40:22,300] [INFO] Task started: Blastn
[2023-06-17 08:40:22,300] [INFO] Running command: blastn -query GCA_028817545.1_ASM2881754v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e585cb3-fde4-4aee-b62f-ac47c798c2f9/dqc_reference/reference_markers.fasta -out GCA_028817545.1_ASM2881754v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 08:40:23,068] [INFO] Task succeeded: Blastn
[2023-06-17 08:40:23,072] [INFO] Selected 25 target genomes.
[2023-06-17 08:40:23,073] [INFO] Target genome list was writen to GCA_028817545.1_ASM2881754v1_genomic.fna/target_genomes.txt
[2023-06-17 08:40:23,082] [INFO] Task started: fastANI
[2023-06-17 08:40:23,083] [INFO] Running command: fastANI --query /var/lib/cwl/stgf834611c-7ae8-40bf-87c3-544a1826c971/GCA_028817545.1_ASM2881754v1_genomic.fna.gz --refList GCA_028817545.1_ASM2881754v1_genomic.fna/target_genomes.txt --output GCA_028817545.1_ASM2881754v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 08:40:41,507] [INFO] Task succeeded: fastANI
[2023-06-17 08:40:41,508] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9e585cb3-fde4-4aee-b62f-ac47c798c2f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 08:40:41,508] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9e585cb3-fde4-4aee-b62f-ac47c798c2f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 08:40:41,510] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 08:40:41,510] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 08:40:41,510] [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
--------------------------------------------------------------------------------
[2023-06-17 08:40:41,512] [INFO] DFAST Taxonomy check result was written to GCA_028817545.1_ASM2881754v1_genomic.fna/tc_result.tsv
[2023-06-17 08:40:41,513] [INFO] ===== Taxonomy check completed =====
[2023-06-17 08:40:41,513] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 08:40:41,513] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9e585cb3-fde4-4aee-b62f-ac47c798c2f9/dqc_reference/checkm_data
[2023-06-17 08:40:41,516] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 08:40:41,542] [INFO] Task started: CheckM
[2023-06-17 08:40:41,543] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028817545.1_ASM2881754v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028817545.1_ASM2881754v1_genomic.fna/checkm_input GCA_028817545.1_ASM2881754v1_genomic.fna/checkm_result
[2023-06-17 08:41:08,044] [INFO] Task succeeded: CheckM
[2023-06-17 08:41:08,046] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 08:41:08,069] [INFO] ===== Completeness check finished =====
[2023-06-17 08:41:08,069] [INFO] ===== Start GTDB Search =====
[2023-06-17 08:41:08,070] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028817545.1_ASM2881754v1_genomic.fna/markers.fasta)
[2023-06-17 08:41:08,070] [INFO] Task started: Blastn
[2023-06-17 08:41:08,070] [INFO] Running command: blastn -query GCA_028817545.1_ASM2881754v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e585cb3-fde4-4aee-b62f-ac47c798c2f9/dqc_reference/reference_markers_gtdb.fasta -out GCA_028817545.1_ASM2881754v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 08:41:08,831] [INFO] Task succeeded: Blastn
[2023-06-17 08:41:08,836] [INFO] Selected 18 target genomes.
[2023-06-17 08:41:08,837] [INFO] Target genome list was writen to GCA_028817545.1_ASM2881754v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 08:41:08,860] [INFO] Task started: fastANI
[2023-06-17 08:41:08,860] [INFO] Running command: fastANI --query /var/lib/cwl/stgf834611c-7ae8-40bf-87c3-544a1826c971/GCA_028817545.1_ASM2881754v1_genomic.fna.gz --refList GCA_028817545.1_ASM2881754v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028817545.1_ASM2881754v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 08:41:16,967] [INFO] Task succeeded: fastANI
[2023-06-17 08:41:16,979] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 08:41:16,979] [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
GCA_007570995.1	s__Bin75 sp007570995	94.9852	516	665	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__UBA8639;g__Bin75	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012270585.1	s__Bin75 sp012270585	77.6227	202	665	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__UBA8639;g__Bin75	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002238765.1	s__Bin75 sp002238765	77.4323	188	665	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__UBA8639;g__Bin75	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523385.1	s__Bin75 sp011523385	77.3263	174	665	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__UBA8639;g__Bin75	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009840285.1	s__Bin75 sp009840285	77.0607	165	665	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__UBA8639;g__Bin75	95.0	98.00	98.00	0.87	0.86	3	-
GCA_009842645.1	s__Bin75 sp009842645	76.9959	151	665	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__UBA8639;g__Bin75	95.0	99.11	99.02	0.93	0.92	5	-
--------------------------------------------------------------------------------
[2023-06-17 08:41:16,981] [INFO] GTDB search result was written to GCA_028817545.1_ASM2881754v1_genomic.fna/result_gtdb.tsv
[2023-06-17 08:41:16,982] [INFO] ===== GTDB Search completed =====
[2023-06-17 08:41:16,984] [INFO] DFAST_QC result json was written to GCA_028817545.1_ASM2881754v1_genomic.fna/dqc_result.json
[2023-06-17 08:41:16,985] [INFO] DFAST_QC completed!
[2023-06-17 08:41:16,985] [INFO] Total running time: 0h1m5s