[2023-06-29 20:10:38,190] [INFO] DFAST_QC pipeline started.
[2023-06-29 20:10:38,192] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 20:10:38,193] [INFO] DQC Reference Directory: /var/lib/cwl/stgc591f62f-5416-4c22-8c6b-50068206ac75/dqc_reference
[2023-06-29 20:10:40,558] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 20:10:40,559] [INFO] Task started: Prodigal
[2023-06-29 20:10:40,560] [INFO] Running command: gunzip -c /var/lib/cwl/stgf92a4c4e-c8df-430e-b655-4d53de278212/GCA_016706435.1_ASM1670643v1_genomic.fna.gz | prodigal -d GCA_016706435.1_ASM1670643v1_genomic.fna/cds.fna -a GCA_016706435.1_ASM1670643v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 20:11:16,031] [INFO] Task succeeded: Prodigal
[2023-06-29 20:11:16,032] [INFO] Task started: HMMsearch
[2023-06-29 20:11:16,032] [INFO] Running command: hmmsearch --tblout GCA_016706435.1_ASM1670643v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc591f62f-5416-4c22-8c6b-50068206ac75/dqc_reference/reference_markers.hmm GCA_016706435.1_ASM1670643v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 20:11:16,321] [INFO] Task succeeded: HMMsearch
[2023-06-29 20:11:16,323] [INFO] Found 6/6 markers.
[2023-06-29 20:11:16,371] [INFO] Query marker FASTA was written to GCA_016706435.1_ASM1670643v1_genomic.fna/markers.fasta
[2023-06-29 20:11:16,371] [INFO] Task started: Blastn
[2023-06-29 20:11:16,371] [INFO] Running command: blastn -query GCA_016706435.1_ASM1670643v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc591f62f-5416-4c22-8c6b-50068206ac75/dqc_reference/reference_markers.fasta -out GCA_016706435.1_ASM1670643v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:11:16,952] [INFO] Task succeeded: Blastn
[2023-06-29 20:11:16,956] [INFO] Selected 27 target genomes.
[2023-06-29 20:11:16,957] [INFO] Target genome list was writen to GCA_016706435.1_ASM1670643v1_genomic.fna/target_genomes.txt
[2023-06-29 20:11:16,958] [INFO] Task started: fastANI
[2023-06-29 20:11:16,958] [INFO] Running command: fastANI --query /var/lib/cwl/stgf92a4c4e-c8df-430e-b655-4d53de278212/GCA_016706435.1_ASM1670643v1_genomic.fna.gz --refList GCA_016706435.1_ASM1670643v1_genomic.fna/target_genomes.txt --output GCA_016706435.1_ASM1670643v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 20:11:33,016] [INFO] Task succeeded: fastANI
[2023-06-29 20:11:33,017] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc591f62f-5416-4c22-8c6b-50068206ac75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 20:11:33,017] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc591f62f-5416-4c22-8c6b-50068206ac75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 20:11:33,019] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 20:11:33,019] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 20:11:33,019] [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
--------------------------------------------------------------------------------
[2023-06-29 20:11:33,022] [INFO] DFAST Taxonomy check result was written to GCA_016706435.1_ASM1670643v1_genomic.fna/tc_result.tsv
[2023-06-29 20:11:33,023] [INFO] ===== Taxonomy check completed =====
[2023-06-29 20:11:33,023] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 20:11:33,023] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc591f62f-5416-4c22-8c6b-50068206ac75/dqc_reference/checkm_data
[2023-06-29 20:11:33,027] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 20:11:33,071] [INFO] Task started: CheckM
[2023-06-29 20:11:33,072] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016706435.1_ASM1670643v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016706435.1_ASM1670643v1_genomic.fna/checkm_input GCA_016706435.1_ASM1670643v1_genomic.fna/checkm_result
[2023-06-29 20:13:11,572] [INFO] Task succeeded: CheckM
[2023-06-29 20:13:11,573] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 20:13:11,594] [INFO] ===== Completeness check finished =====
[2023-06-29 20:13:11,594] [INFO] ===== Start GTDB Search =====
[2023-06-29 20:13:11,595] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016706435.1_ASM1670643v1_genomic.fna/markers.fasta)
[2023-06-29 20:13:11,595] [INFO] Task started: Blastn
[2023-06-29 20:13:11,595] [INFO] Running command: blastn -query GCA_016706435.1_ASM1670643v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc591f62f-5416-4c22-8c6b-50068206ac75/dqc_reference/reference_markers_gtdb.fasta -out GCA_016706435.1_ASM1670643v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:13:12,367] [INFO] Task succeeded: Blastn
[2023-06-29 20:13:12,372] [INFO] Selected 17 target genomes.
[2023-06-29 20:13:12,373] [INFO] Target genome list was writen to GCA_016706435.1_ASM1670643v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 20:13:12,383] [INFO] Task started: fastANI
[2023-06-29 20:13:12,384] [INFO] Running command: fastANI --query /var/lib/cwl/stgf92a4c4e-c8df-430e-b655-4d53de278212/GCA_016706435.1_ASM1670643v1_genomic.fna.gz --refList GCA_016706435.1_ASM1670643v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016706435.1_ASM1670643v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 20:13:23,961] [INFO] Task succeeded: fastANI
[2023-06-29 20:13:23,987] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 20:13:23,988] [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_016703005.1	s__PHOS-HE28 sp016703005	98.5791	1250	1435	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	98.27	97.81	0.89	0.87	4	conclusive
GCA_902825795.1	s__PHOS-HE28 sp902825795	90.3881	1018	1435	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016702645.1	s__PHOS-HE28 sp016702645	80.733	377	1435	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016699575.1	s__PHOS-HE28 sp016699575	79.4768	675	1435	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016710965.1	s__PHOS-HE28 sp016710965	79.3037	330	1435	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016715995.1	s__PHOS-HE28 sp016715995	78.911	310	1435	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716605.1	s__PHOS-HE28 sp016716605	78.7058	315	1435	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016705955.1	s__PHOS-HE28 sp016705955	78.5894	312	1435	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016788205.1	s__PHOS-HE28 sp016788205	78.5253	311	1435	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016715895.1	s__PHOS-HE28 sp016715895	78.4667	361	1435	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018267055.1	s__PHOS-HE28 sp018267055	78.3546	341	1435	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013360395.1	s__PHOS-HE28 sp013360395	78.2654	304	1435	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	99.56	99.56	0.97	0.97	2	-
GCA_016788485.1	s__PHOS-HE28 sp016788485	78.1889	298	1435	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002342985.1	s__PHOS-HE28 sp002342985	78.1784	275	1435	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014584605.1	s__PHOS-HE28 sp014584605	77.9895	306	1435	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016788405.1	s__PHOS-HE28 sp016788405	77.8802	176	1435	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016788285.1	s__PHOS-HE28 sp016788285	77.801	295	1435	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 20:13:23,990] [INFO] GTDB search result was written to GCA_016706435.1_ASM1670643v1_genomic.fna/result_gtdb.tsv
[2023-06-29 20:13:23,990] [INFO] ===== GTDB Search completed =====
[2023-06-29 20:13:23,995] [INFO] DFAST_QC result json was written to GCA_016706435.1_ASM1670643v1_genomic.fna/dqc_result.json
[2023-06-29 20:13:23,996] [INFO] DFAST_QC completed!
[2023-06-29 20:13:23,996] [INFO] Total running time: 0h2m46s