[2023-06-28 17:00:54,712] [INFO] DFAST_QC pipeline started.
[2023-06-28 17:00:54,716] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 17:00:54,717] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d2220cc-0558-4818-b0ea-f1fa2173adbe/dqc_reference
[2023-06-28 17:00:56,172] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 17:00:56,173] [INFO] Task started: Prodigal
[2023-06-28 17:00:56,173] [INFO] Running command: gunzip -c /var/lib/cwl/stg0aa98d19-4faa-4356-88e4-55c57ae5c6f2/GCA_020440925.1_ASM2044092v1_genomic.fna.gz | prodigal -d GCA_020440925.1_ASM2044092v1_genomic.fna/cds.fna -a GCA_020440925.1_ASM2044092v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 17:01:03,788] [INFO] Task succeeded: Prodigal
[2023-06-28 17:01:03,789] [INFO] Task started: HMMsearch
[2023-06-28 17:01:03,789] [INFO] Running command: hmmsearch --tblout GCA_020440925.1_ASM2044092v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d2220cc-0558-4818-b0ea-f1fa2173adbe/dqc_reference/reference_markers.hmm GCA_020440925.1_ASM2044092v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 17:01:04,080] [INFO] Task succeeded: HMMsearch
[2023-06-28 17:01:04,082] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0aa98d19-4faa-4356-88e4-55c57ae5c6f2/GCA_020440925.1_ASM2044092v1_genomic.fna.gz]
[2023-06-28 17:01:04,125] [INFO] Query marker FASTA was written to GCA_020440925.1_ASM2044092v1_genomic.fna/markers.fasta
[2023-06-28 17:01:04,126] [INFO] Task started: Blastn
[2023-06-28 17:01:04,126] [INFO] Running command: blastn -query GCA_020440925.1_ASM2044092v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d2220cc-0558-4818-b0ea-f1fa2173adbe/dqc_reference/reference_markers.fasta -out GCA_020440925.1_ASM2044092v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:01:04,766] [INFO] Task succeeded: Blastn
[2023-06-28 17:01:04,774] [INFO] Selected 17 target genomes.
[2023-06-28 17:01:04,775] [INFO] Target genome list was writen to GCA_020440925.1_ASM2044092v1_genomic.fna/target_genomes.txt
[2023-06-28 17:01:04,777] [INFO] Task started: fastANI
[2023-06-28 17:01:04,777] [INFO] Running command: fastANI --query /var/lib/cwl/stg0aa98d19-4faa-4356-88e4-55c57ae5c6f2/GCA_020440925.1_ASM2044092v1_genomic.fna.gz --refList GCA_020440925.1_ASM2044092v1_genomic.fna/target_genomes.txt --output GCA_020440925.1_ASM2044092v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 17:01:17,225] [INFO] Task succeeded: fastANI
[2023-06-28 17:01:17,225] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d2220cc-0558-4818-b0ea-f1fa2173adbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 17:01:17,225] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d2220cc-0558-4818-b0ea-f1fa2173adbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 17:01:17,227] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 17:01:17,227] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 17:01:17,227] [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 17:01:17,229] [INFO] DFAST Taxonomy check result was written to GCA_020440925.1_ASM2044092v1_genomic.fna/tc_result.tsv
[2023-06-28 17:01:17,230] [INFO] ===== Taxonomy check completed =====
[2023-06-28 17:01:17,230] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 17:01:17,230] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d2220cc-0558-4818-b0ea-f1fa2173adbe/dqc_reference/checkm_data
[2023-06-28 17:01:17,233] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 17:01:17,272] [INFO] Task started: CheckM
[2023-06-28 17:01:17,273] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020440925.1_ASM2044092v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020440925.1_ASM2044092v1_genomic.fna/checkm_input GCA_020440925.1_ASM2044092v1_genomic.fna/checkm_result
[2023-06-28 17:01:46,086] [INFO] Task succeeded: CheckM
[2023-06-28 17:01:46,088] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 38.89%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 17:01:46,115] [INFO] ===== Completeness check finished =====
[2023-06-28 17:01:46,116] [INFO] ===== Start GTDB Search =====
[2023-06-28 17:01:46,116] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020440925.1_ASM2044092v1_genomic.fna/markers.fasta)
[2023-06-28 17:01:46,116] [INFO] Task started: Blastn
[2023-06-28 17:01:46,117] [INFO] Running command: blastn -query GCA_020440925.1_ASM2044092v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d2220cc-0558-4818-b0ea-f1fa2173adbe/dqc_reference/reference_markers_gtdb.fasta -out GCA_020440925.1_ASM2044092v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:01:47,059] [INFO] Task succeeded: Blastn
[2023-06-28 17:01:47,063] [INFO] Selected 19 target genomes.
[2023-06-28 17:01:47,064] [INFO] Target genome list was writen to GCA_020440925.1_ASM2044092v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 17:01:47,072] [INFO] Task started: fastANI
[2023-06-28 17:01:47,072] [INFO] Running command: fastANI --query /var/lib/cwl/stg0aa98d19-4faa-4356-88e4-55c57ae5c6f2/GCA_020440925.1_ASM2044092v1_genomic.fna.gz --refList GCA_020440925.1_ASM2044092v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020440925.1_ASM2044092v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 17:02:00,996] [INFO] Task succeeded: fastANI
[2023-06-28 17:02:01,004] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 17:02:01,004] [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_002730875.1	s__UBA3465 sp002730875	77.8593	246	840	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptonemataceae;g__UBA3465	95.0	99.98	99.97	0.99	0.98	7	-
GCA_002729885.1	s__UBA3465 sp002729885	77.5836	232	840	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptonemataceae;g__UBA3465	95.0	99.96	99.92	0.99	0.98	4	-
GCA_002717505.1	s__UBA3465 sp002717505	76.953	189	840	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptonemataceae;g__UBA3465	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 17:02:01,007] [INFO] GTDB search result was written to GCA_020440925.1_ASM2044092v1_genomic.fna/result_gtdb.tsv
[2023-06-28 17:02:01,007] [INFO] ===== GTDB Search completed =====
[2023-06-28 17:02:01,010] [INFO] DFAST_QC result json was written to GCA_020440925.1_ASM2044092v1_genomic.fna/dqc_result.json
[2023-06-28 17:02:01,010] [INFO] DFAST_QC completed!
[2023-06-28 17:02:01,010] [INFO] Total running time: 0h1m6s