[2023-06-28 22:15:30,956] [INFO] DFAST_QC pipeline started.
[2023-06-28 22:15:30,960] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 22:15:30,960] [INFO] DQC Reference Directory: /var/lib/cwl/stg1dfe96ab-ad4b-4a16-b1dc-c9b5c25de036/dqc_reference
[2023-06-28 22:15:32,188] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 22:15:32,189] [INFO] Task started: Prodigal
[2023-06-28 22:15:32,189] [INFO] Running command: gunzip -c /var/lib/cwl/stgdff6d34d-0d26-404e-ad72-6cd9f5c824cf/GCA_027620975.1_ASM2762097v1_genomic.fna.gz | prodigal -d GCA_027620975.1_ASM2762097v1_genomic.fna/cds.fna -a GCA_027620975.1_ASM2762097v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 22:15:34,774] [INFO] Task succeeded: Prodigal
[2023-06-28 22:15:34,775] [INFO] Task started: HMMsearch
[2023-06-28 22:15:34,775] [INFO] Running command: hmmsearch --tblout GCA_027620975.1_ASM2762097v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1dfe96ab-ad4b-4a16-b1dc-c9b5c25de036/dqc_reference/reference_markers.hmm GCA_027620975.1_ASM2762097v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 22:15:34,978] [INFO] Task succeeded: HMMsearch
[2023-06-28 22:15:34,979] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgdff6d34d-0d26-404e-ad72-6cd9f5c824cf/GCA_027620975.1_ASM2762097v1_genomic.fna.gz]
[2023-06-28 22:15:34,996] [INFO] Query marker FASTA was written to GCA_027620975.1_ASM2762097v1_genomic.fna/markers.fasta
[2023-06-28 22:15:34,996] [INFO] Task started: Blastn
[2023-06-28 22:15:34,996] [INFO] Running command: blastn -query GCA_027620975.1_ASM2762097v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dfe96ab-ad4b-4a16-b1dc-c9b5c25de036/dqc_reference/reference_markers.fasta -out GCA_027620975.1_ASM2762097v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:15:35,545] [INFO] Task succeeded: Blastn
[2023-06-28 22:15:35,549] [INFO] Selected 8 target genomes.
[2023-06-28 22:15:35,550] [INFO] Target genome list was writen to GCA_027620975.1_ASM2762097v1_genomic.fna/target_genomes.txt
[2023-06-28 22:15:35,557] [INFO] Task started: fastANI
[2023-06-28 22:15:35,557] [INFO] Running command: fastANI --query /var/lib/cwl/stgdff6d34d-0d26-404e-ad72-6cd9f5c824cf/GCA_027620975.1_ASM2762097v1_genomic.fna.gz --refList GCA_027620975.1_ASM2762097v1_genomic.fna/target_genomes.txt --output GCA_027620975.1_ASM2762097v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 22:15:40,380] [INFO] Task succeeded: fastANI
[2023-06-28 22:15:40,381] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1dfe96ab-ad4b-4a16-b1dc-c9b5c25de036/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 22:15:40,381] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1dfe96ab-ad4b-4a16-b1dc-c9b5c25de036/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 22:15:40,383] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 22:15:40,384] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 22:15:40,384] [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
--------------------------------------------------------------------------------
[2023-06-28 22:15:40,386] [INFO] DFAST Taxonomy check result was written to GCA_027620975.1_ASM2762097v1_genomic.fna/tc_result.tsv
[2023-06-28 22:15:40,386] [INFO] ===== Taxonomy check completed =====
[2023-06-28 22:15:40,386] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 22:15:40,387] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1dfe96ab-ad4b-4a16-b1dc-c9b5c25de036/dqc_reference/checkm_data
[2023-06-28 22:15:40,389] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 22:15:40,407] [INFO] Task started: CheckM
[2023-06-28 22:15:40,408] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027620975.1_ASM2762097v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027620975.1_ASM2762097v1_genomic.fna/checkm_input GCA_027620975.1_ASM2762097v1_genomic.fna/checkm_result
[2023-06-28 22:15:56,167] [INFO] Task succeeded: CheckM
[2023-06-28 22:15:56,169] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 22:15:56,192] [INFO] ===== Completeness check finished =====
[2023-06-28 22:15:56,192] [INFO] ===== Start GTDB Search =====
[2023-06-28 22:15:56,193] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027620975.1_ASM2762097v1_genomic.fna/markers.fasta)
[2023-06-28 22:15:56,193] [INFO] Task started: Blastn
[2023-06-28 22:15:56,193] [INFO] Running command: blastn -query GCA_027620975.1_ASM2762097v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dfe96ab-ad4b-4a16-b1dc-c9b5c25de036/dqc_reference/reference_markers_gtdb.fasta -out GCA_027620975.1_ASM2762097v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:15:56,923] [INFO] Task succeeded: Blastn
[2023-06-28 22:15:56,928] [INFO] Selected 13 target genomes.
[2023-06-28 22:15:56,928] [INFO] Target genome list was writen to GCA_027620975.1_ASM2762097v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 22:15:56,994] [INFO] Task started: fastANI
[2023-06-28 22:15:56,994] [INFO] Running command: fastANI --query /var/lib/cwl/stgdff6d34d-0d26-404e-ad72-6cd9f5c824cf/GCA_027620975.1_ASM2762097v1_genomic.fna.gz --refList GCA_027620975.1_ASM2762097v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027620975.1_ASM2762097v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 22:16:00,037] [INFO] Task succeeded: fastANI
[2023-06-28 22:16:00,051] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 22:16:00,052] [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_002358345.1	s__D2472 sp002358345	99.1363	355	405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	99.61	97.74	0.92	0.85	27	conclusive
GCA_002469975.1	s__D2472 sp002469975	82.151	260	405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	99.56	99.38	0.87	0.81	4	-
GCA_905181595.1	s__D2472 sp905181595	79.8731	214	405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779505.1	s__D2472 sp016779505	77.5187	78	405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	98.99	98.50	0.76	0.70	3	-
GCA_902511575.1	s__D2472 sp902511575	77.4116	79	405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902515455.1	s__D2472 sp902515455	77.3072	50	405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902595065.1	s__D2472 sp902595065	77.2782	98	405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	98.09	97.88	0.94	0.91	4	-
GCA_000307935.1	s__D2472 sp000307935	77.247	92	405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902608115.1	s__D2472 sp902608115	77.0638	69	405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902593675.1	s__D2472 sp902593675	77.0016	91	405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 22:16:00,054] [INFO] GTDB search result was written to GCA_027620975.1_ASM2762097v1_genomic.fna/result_gtdb.tsv
[2023-06-28 22:16:00,055] [INFO] ===== GTDB Search completed =====
[2023-06-28 22:16:00,058] [INFO] DFAST_QC result json was written to GCA_027620975.1_ASM2762097v1_genomic.fna/dqc_result.json
[2023-06-28 22:16:00,058] [INFO] DFAST_QC completed!
[2023-06-28 22:16:00,058] [INFO] Total running time: 0h0m29s