[2023-06-29 23:32:18,793] [INFO] DFAST_QC pipeline started.
[2023-06-29 23:32:18,796] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 23:32:18,796] [INFO] DQC Reference Directory: /var/lib/cwl/stg63bb3531-01fa-4af9-ad73-c9f4bd88118a/dqc_reference
[2023-06-29 23:32:20,217] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 23:32:20,218] [INFO] Task started: Prodigal
[2023-06-29 23:32:20,219] [INFO] Running command: gunzip -c /var/lib/cwl/stg7514538d-a89e-47df-b0e1-a1e54f3ffa39/GCA_016206265.1_ASM1620626v1_genomic.fna.gz | prodigal -d GCA_016206265.1_ASM1620626v1_genomic.fna/cds.fna -a GCA_016206265.1_ASM1620626v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 23:32:23,649] [INFO] Task succeeded: Prodigal
[2023-06-29 23:32:23,649] [INFO] Task started: HMMsearch
[2023-06-29 23:32:23,649] [INFO] Running command: hmmsearch --tblout GCA_016206265.1_ASM1620626v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63bb3531-01fa-4af9-ad73-c9f4bd88118a/dqc_reference/reference_markers.hmm GCA_016206265.1_ASM1620626v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 23:32:23,818] [INFO] Task succeeded: HMMsearch
[2023-06-29 23:32:23,819] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7514538d-a89e-47df-b0e1-a1e54f3ffa39/GCA_016206265.1_ASM1620626v1_genomic.fna.gz]
[2023-06-29 23:32:23,858] [INFO] Query marker FASTA was written to GCA_016206265.1_ASM1620626v1_genomic.fna/markers.fasta
[2023-06-29 23:32:23,859] [INFO] Task started: Blastn
[2023-06-29 23:32:23,859] [INFO] Running command: blastn -query GCA_016206265.1_ASM1620626v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63bb3531-01fa-4af9-ad73-c9f4bd88118a/dqc_reference/reference_markers.fasta -out GCA_016206265.1_ASM1620626v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:32:24,524] [INFO] Task succeeded: Blastn
[2023-06-29 23:32:24,528] [INFO] Selected 25 target genomes.
[2023-06-29 23:32:24,529] [INFO] Target genome list was writen to GCA_016206265.1_ASM1620626v1_genomic.fna/target_genomes.txt
[2023-06-29 23:32:24,530] [INFO] Task started: fastANI
[2023-06-29 23:32:24,530] [INFO] Running command: fastANI --query /var/lib/cwl/stg7514538d-a89e-47df-b0e1-a1e54f3ffa39/GCA_016206265.1_ASM1620626v1_genomic.fna.gz --refList GCA_016206265.1_ASM1620626v1_genomic.fna/target_genomes.txt --output GCA_016206265.1_ASM1620626v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 23:32:43,777] [INFO] Task succeeded: fastANI
[2023-06-29 23:32:43,778] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63bb3531-01fa-4af9-ad73-c9f4bd88118a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 23:32:43,778] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63bb3531-01fa-4af9-ad73-c9f4bd88118a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 23:32:43,782] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 23:32:43,782] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 23:32:43,783] [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
Nocardiopsis potens	strain=DSM 45234	GCA_000341105.1	1246458	1246458	type	True	74.8365	54	328	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 23:32:43,785] [INFO] DFAST Taxonomy check result was written to GCA_016206265.1_ASM1620626v1_genomic.fna/tc_result.tsv
[2023-06-29 23:32:43,785] [INFO] ===== Taxonomy check completed =====
[2023-06-29 23:32:43,786] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 23:32:43,786] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63bb3531-01fa-4af9-ad73-c9f4bd88118a/dqc_reference/checkm_data
[2023-06-29 23:32:43,787] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 23:32:43,808] [INFO] Task started: CheckM
[2023-06-29 23:32:43,808] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016206265.1_ASM1620626v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016206265.1_ASM1620626v1_genomic.fna/checkm_input GCA_016206265.1_ASM1620626v1_genomic.fna/checkm_result
[2023-06-29 23:33:01,294] [INFO] Task succeeded: CheckM
[2023-06-29 23:33:01,296] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.25%
Contamintation: 8.33%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-29 23:33:01,318] [INFO] ===== Completeness check finished =====
[2023-06-29 23:33:01,319] [INFO] ===== Start GTDB Search =====
[2023-06-29 23:33:01,319] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016206265.1_ASM1620626v1_genomic.fna/markers.fasta)
[2023-06-29 23:33:01,319] [INFO] Task started: Blastn
[2023-06-29 23:33:01,320] [INFO] Running command: blastn -query GCA_016206265.1_ASM1620626v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63bb3531-01fa-4af9-ad73-c9f4bd88118a/dqc_reference/reference_markers_gtdb.fasta -out GCA_016206265.1_ASM1620626v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:33:02,326] [INFO] Task succeeded: Blastn
[2023-06-29 23:33:02,330] [INFO] Selected 11 target genomes.
[2023-06-29 23:33:02,330] [INFO] Target genome list was writen to GCA_016206265.1_ASM1620626v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 23:33:02,341] [INFO] Task started: fastANI
[2023-06-29 23:33:02,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg7514538d-a89e-47df-b0e1-a1e54f3ffa39/GCA_016206265.1_ASM1620626v1_genomic.fna.gz --refList GCA_016206265.1_ASM1620626v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016206265.1_ASM1620626v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 23:33:08,967] [INFO] Task succeeded: fastANI
[2023-06-29 23:33:08,978] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 23:33:08,979] [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_016184445.1	s__2-12-FULL-69-37 sp016184445	96.4307	235	328	d__Bacteria;p__UBA8248;c__UBA8248;o__UBA8248;f__UBA8248;g__2-12-FULL-69-37	95.0	97.02	97.02	0.69	0.69	2	conclusive
GCA_001790955.1	s__2-12-FULL-69-37 sp001790955	89.3646	281	328	d__Bacteria;p__UBA8248;c__UBA8248;o__UBA8248;f__UBA8248;g__2-12-FULL-69-37	95.0	99.54	99.54	0.87	0.87	2	-
GCA_016192135.1	s__2-12-FULL-69-37 sp016192135	84.6772	288	328	d__Bacteria;p__UBA8248;c__UBA8248;o__UBA8248;f__UBA8248;g__2-12-FULL-69-37	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009839615.1	s__Bin107 sp009839615	77.0034	57	328	d__Bacteria;p__UBA8248;c__UBA8248;o__UBA8248;f__UBA8248;g__Bin107	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523725.1	s__Bin107 sp011523725	76.8229	56	328	d__Bacteria;p__UBA8248;c__UBA8248;o__UBA8248;f__UBA8248;g__Bin107	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 23:33:08,981] [INFO] GTDB search result was written to GCA_016206265.1_ASM1620626v1_genomic.fna/result_gtdb.tsv
[2023-06-29 23:33:08,981] [INFO] ===== GTDB Search completed =====
[2023-06-29 23:33:08,984] [INFO] DFAST_QC result json was written to GCA_016206265.1_ASM1620626v1_genomic.fna/dqc_result.json
[2023-06-29 23:33:08,984] [INFO] DFAST_QC completed!
[2023-06-29 23:33:08,984] [INFO] Total running time: 0h0m50s