[2023-06-27 06:26:23,396] [INFO] DFAST_QC pipeline started.
[2023-06-27 06:26:23,398] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 06:26:23,398] [INFO] DQC Reference Directory: /var/lib/cwl/stgb31f16c9-7c15-404d-81d8-ff7dac1c06dd/dqc_reference
[2023-06-27 06:26:24,641] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 06:26:24,642] [INFO] Task started: Prodigal
[2023-06-27 06:26:24,642] [INFO] Running command: gunzip -c /var/lib/cwl/stg4b5e50f3-4d2d-49f7-8e26-bf4f343000e1/GCA_002310235.1_ASM231023v1_genomic.fna.gz | prodigal -d GCA_002310235.1_ASM231023v1_genomic.fna/cds.fna -a GCA_002310235.1_ASM231023v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 06:26:39,654] [INFO] Task succeeded: Prodigal
[2023-06-27 06:26:39,655] [INFO] Task started: HMMsearch
[2023-06-27 06:26:39,655] [INFO] Running command: hmmsearch --tblout GCA_002310235.1_ASM231023v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb31f16c9-7c15-404d-81d8-ff7dac1c06dd/dqc_reference/reference_markers.hmm GCA_002310235.1_ASM231023v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 06:26:39,957] [INFO] Task succeeded: HMMsearch
[2023-06-27 06:26:39,959] [INFO] Found 6/6 markers.
[2023-06-27 06:26:39,999] [INFO] Query marker FASTA was written to GCA_002310235.1_ASM231023v1_genomic.fna/markers.fasta
[2023-06-27 06:26:39,999] [INFO] Task started: Blastn
[2023-06-27 06:26:40,000] [INFO] Running command: blastn -query GCA_002310235.1_ASM231023v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb31f16c9-7c15-404d-81d8-ff7dac1c06dd/dqc_reference/reference_markers.fasta -out GCA_002310235.1_ASM231023v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:26:40,665] [INFO] Task succeeded: Blastn
[2023-06-27 06:26:40,669] [INFO] Selected 24 target genomes.
[2023-06-27 06:26:40,670] [INFO] Target genome list was writen to GCA_002310235.1_ASM231023v1_genomic.fna/target_genomes.txt
[2023-06-27 06:26:40,673] [INFO] Task started: fastANI
[2023-06-27 06:26:40,674] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b5e50f3-4d2d-49f7-8e26-bf4f343000e1/GCA_002310235.1_ASM231023v1_genomic.fna.gz --refList GCA_002310235.1_ASM231023v1_genomic.fna/target_genomes.txt --output GCA_002310235.1_ASM231023v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 06:26:55,679] [INFO] Task succeeded: fastANI
[2023-06-27 06:26:55,680] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb31f16c9-7c15-404d-81d8-ff7dac1c06dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 06:26:55,681] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb31f16c9-7c15-404d-81d8-ff7dac1c06dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 06:26:55,683] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 06:26:55,683] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 06:26:55,683] [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
--------------------------------------------------------------------------------
[2023-06-27 06:26:55,686] [INFO] DFAST Taxonomy check result was written to GCA_002310235.1_ASM231023v1_genomic.fna/tc_result.tsv
[2023-06-27 06:26:55,686] [INFO] ===== Taxonomy check completed =====
[2023-06-27 06:26:55,687] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 06:26:55,687] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb31f16c9-7c15-404d-81d8-ff7dac1c06dd/dqc_reference/checkm_data
[2023-06-27 06:26:55,690] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 06:26:55,722] [INFO] Task started: CheckM
[2023-06-27 06:26:55,723] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002310235.1_ASM231023v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002310235.1_ASM231023v1_genomic.fna/checkm_input GCA_002310235.1_ASM231023v1_genomic.fna/checkm_result
[2023-06-27 06:27:40,092] [INFO] Task succeeded: CheckM
[2023-06-27 06:27:40,093] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.88%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 06:27:40,124] [INFO] ===== Completeness check finished =====
[2023-06-27 06:27:40,125] [INFO] ===== Start GTDB Search =====
[2023-06-27 06:27:40,125] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002310235.1_ASM231023v1_genomic.fna/markers.fasta)
[2023-06-27 06:27:40,126] [INFO] Task started: Blastn
[2023-06-27 06:27:40,126] [INFO] Running command: blastn -query GCA_002310235.1_ASM231023v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb31f16c9-7c15-404d-81d8-ff7dac1c06dd/dqc_reference/reference_markers_gtdb.fasta -out GCA_002310235.1_ASM231023v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:27:40,928] [INFO] Task succeeded: Blastn
[2023-06-27 06:27:40,933] [INFO] Selected 13 target genomes.
[2023-06-27 06:27:40,933] [INFO] Target genome list was writen to GCA_002310235.1_ASM231023v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 06:27:40,995] [INFO] Task started: fastANI
[2023-06-27 06:27:40,996] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b5e50f3-4d2d-49f7-8e26-bf4f343000e1/GCA_002310235.1_ASM231023v1_genomic.fna.gz --refList GCA_002310235.1_ASM231023v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002310235.1_ASM231023v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 06:27:51,936] [INFO] Task succeeded: fastANI
[2023-06-27 06:27:51,952] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 06:27:51,952] [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_002310235.1	s__Bact-19 sp002310235	100.0	904	908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__ML635J-15;g__Bact-19	95.0	97.60	97.60	0.89	0.89	2	conclusive
GCA_017617125.1	s__Bact-19 sp017617125	88.0067	702	908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__ML635J-15;g__Bact-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902800045.1	s__Bact-19 sp902800045	86.9282	698	908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__ML635J-15;g__Bact-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902790405.1	s__Bact-19 sp902790405	86.9048	625	908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__ML635J-15;g__Bact-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017620015.1	s__Bact-19 sp017620015	85.4724	583	908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__ML635J-15;g__Bact-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902776565.1	s__Bact-19 sp902776565	85.1661	584	908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__ML635J-15;g__Bact-19	95.0	96.47	95.98	0.86	0.82	3	-
GCA_902791865.1	s__Bact-19 sp902791865	84.8168	598	908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__ML635J-15;g__Bact-19	95.0	95.98	95.98	0.86	0.86	2	-
GCA_902762455.1	s__Bact-19 sp902762455	84.7982	454	908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__ML635J-15;g__Bact-19	95.0	95.34	95.27	0.87	0.87	3	-
GCA_905233405.1	s__Bact-19 sp905233405	84.3944	413	908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__ML635J-15;g__Bact-19	95.0	95.16	95.16	0.76	0.76	2	-
GCA_905234755.1	s__Bact-19 sp905234755	83.3471	571	908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__ML635J-15;g__Bact-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017651185.1	s__Bact-19 sp017651185	82.8952	571	908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__ML635J-15;g__Bact-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017551515.1	s__Bact-19 sp017551515	82.3574	542	908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__ML635J-15;g__Bact-19	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 06:27:51,954] [INFO] GTDB search result was written to GCA_002310235.1_ASM231023v1_genomic.fna/result_gtdb.tsv
[2023-06-27 06:27:51,955] [INFO] ===== GTDB Search completed =====
[2023-06-27 06:27:51,959] [INFO] DFAST_QC result json was written to GCA_002310235.1_ASM231023v1_genomic.fna/dqc_result.json
[2023-06-27 06:27:51,959] [INFO] DFAST_QC completed!
[2023-06-27 06:27:51,959] [INFO] Total running time: 0h1m29s