[2023-06-12 23:05:50,752] [INFO] DFAST_QC pipeline started.
[2023-06-12 23:05:50,766] [INFO] DFAST_QC version: 0.5.7
[2023-06-12 23:05:50,766] [INFO] DQC Reference Directory: /var/lib/cwl/stg1692bd8e-ee2e-48d1-843a-8d71a9d2297d/dqc_reference
[2023-06-12 23:05:52,148] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-12 23:05:52,149] [INFO] Task started: Prodigal
[2023-06-12 23:05:52,149] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c96d4bb-d289-4d9f-b64c-8115b912776f/GCA_022708705.1_ASM2270870v1_genomic.fna.gz | prodigal -d GCA_022708705.1_ASM2270870v1_genomic.fna/cds.fna -a GCA_022708705.1_ASM2270870v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-12 23:06:01,442] [INFO] Task succeeded: Prodigal
[2023-06-12 23:06:01,442] [INFO] Task started: HMMsearch
[2023-06-12 23:06:01,442] [INFO] Running command: hmmsearch --tblout GCA_022708705.1_ASM2270870v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1692bd8e-ee2e-48d1-843a-8d71a9d2297d/dqc_reference/reference_markers.hmm GCA_022708705.1_ASM2270870v1_genomic.fna/protein.faa > /dev/null
[2023-06-12 23:06:01,697] [INFO] Task succeeded: HMMsearch
[2023-06-12 23:06:01,699] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg0c96d4bb-d289-4d9f-b64c-8115b912776f/GCA_022708705.1_ASM2270870v1_genomic.fna.gz]
[2023-06-12 23:06:01,721] [INFO] Query marker FASTA was written to GCA_022708705.1_ASM2270870v1_genomic.fna/markers.fasta
[2023-06-12 23:06:01,722] [INFO] Task started: Blastn
[2023-06-12 23:06:01,722] [INFO] Running command: blastn -query GCA_022708705.1_ASM2270870v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1692bd8e-ee2e-48d1-843a-8d71a9d2297d/dqc_reference/reference_markers.fasta -out GCA_022708705.1_ASM2270870v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 23:06:02,284] [INFO] Task succeeded: Blastn
[2023-06-12 23:06:02,288] [INFO] Selected 10 target genomes.
[2023-06-12 23:06:02,289] [INFO] Target genome list was writen to GCA_022708705.1_ASM2270870v1_genomic.fna/target_genomes.txt
[2023-06-12 23:06:02,292] [INFO] Task started: fastANI
[2023-06-12 23:06:02,292] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c96d4bb-d289-4d9f-b64c-8115b912776f/GCA_022708705.1_ASM2270870v1_genomic.fna.gz --refList GCA_022708705.1_ASM2270870v1_genomic.fna/target_genomes.txt --output GCA_022708705.1_ASM2270870v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-12 23:06:08,407] [INFO] Task succeeded: fastANI
[2023-06-12 23:06:08,407] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1692bd8e-ee2e-48d1-843a-8d71a9d2297d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-12 23:06:08,408] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1692bd8e-ee2e-48d1-843a-8d71a9d2297d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-12 23:06:08,409] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-12 23:06:08,410] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-12 23:06:08,410] [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
--------------------------------------------------------------------------------
[2023-06-12 23:06:08,412] [INFO] DFAST Taxonomy check result was written to GCA_022708705.1_ASM2270870v1_genomic.fna/tc_result.tsv
[2023-06-12 23:06:08,413] [INFO] ===== Taxonomy check completed =====
[2023-06-12 23:06:08,413] [INFO] ===== Start completeness check using CheckM =====
[2023-06-12 23:06:08,413] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1692bd8e-ee2e-48d1-843a-8d71a9d2297d/dqc_reference/checkm_data
[2023-06-12 23:06:08,416] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-12 23:06:08,444] [INFO] Task started: CheckM
[2023-06-12 23:06:08,444] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022708705.1_ASM2270870v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022708705.1_ASM2270870v1_genomic.fna/checkm_input GCA_022708705.1_ASM2270870v1_genomic.fna/checkm_result
[2023-06-12 23:06:41,252] [INFO] Task succeeded: CheckM
[2023-06-12 23:06:41,253] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 39.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-12 23:06:41,275] [INFO] ===== Completeness check finished =====
[2023-06-12 23:06:41,276] [INFO] ===== Start GTDB Search =====
[2023-06-12 23:06:41,276] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022708705.1_ASM2270870v1_genomic.fna/markers.fasta)
[2023-06-12 23:06:41,277] [INFO] Task started: Blastn
[2023-06-12 23:06:41,277] [INFO] Running command: blastn -query GCA_022708705.1_ASM2270870v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1692bd8e-ee2e-48d1-843a-8d71a9d2297d/dqc_reference/reference_markers_gtdb.fasta -out GCA_022708705.1_ASM2270870v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 23:06:41,944] [INFO] Task succeeded: Blastn
[2023-06-12 23:06:41,949] [INFO] Selected 6 target genomes.
[2023-06-12 23:06:41,949] [INFO] Target genome list was writen to GCA_022708705.1_ASM2270870v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-12 23:06:41,954] [INFO] Task started: fastANI
[2023-06-12 23:06:41,954] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c96d4bb-d289-4d9f-b64c-8115b912776f/GCA_022708705.1_ASM2270870v1_genomic.fna.gz --refList GCA_022708705.1_ASM2270870v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022708705.1_ASM2270870v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-12 23:06:45,527] [INFO] Task succeeded: fastANI
[2023-06-12 23:06:45,538] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-12 23:06:45,538] [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_016699635.1	s__OLB10 sp016699635	98.8026	628	710	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767-A;f__OLB10;g__OLB10	95.0	99.73	99.71	0.98	0.98	4	conclusive
GCA_002455375.1	s__OLB10 sp002455375	88.523	534	710	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767-A;f__OLB10;g__OLB10	95.0	99.14	99.00	0.89	0.83	5	-
GCA_019136655.1	s__OLB10 sp019136655	76.8828	155	710	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767-A;f__OLB10;g__OLB10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001567275.1	s__OLB10 sp001567275	76.8064	154	710	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767-A;f__OLB10;g__OLB10	95.0	98.86	98.55	0.94	0.93	4	-
GCA_018268195.1	s__OLB10 sp018268195	76.7059	131	710	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767-A;f__OLB10;g__OLB10	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-12 23:06:45,540] [INFO] GTDB search result was written to GCA_022708705.1_ASM2270870v1_genomic.fna/result_gtdb.tsv
[2023-06-12 23:06:45,541] [INFO] ===== GTDB Search completed =====
[2023-06-12 23:06:45,543] [INFO] DFAST_QC result json was written to GCA_022708705.1_ASM2270870v1_genomic.fna/dqc_result.json
[2023-06-12 23:06:45,543] [INFO] DFAST_QC completed!
[2023-06-12 23:06:45,543] [INFO] Total running time: 0h0m55s