[2023-06-28 10:16:17,632] [INFO] DFAST_QC pipeline started.
[2023-06-28 10:16:17,634] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 10:16:17,635] [INFO] DQC Reference Directory: /var/lib/cwl/stg37d87e96-830f-4517-a91c-89d59bc2192a/dqc_reference
[2023-06-28 10:16:18,981] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 10:16:18,982] [INFO] Task started: Prodigal
[2023-06-28 10:16:18,982] [INFO] Running command: gunzip -c /var/lib/cwl/stg0f8eb0e0-9cb9-452f-bbc3-0ac331cc29fd/GCA_002708005.1_ASM270800v1_genomic.fna.gz | prodigal -d GCA_002708005.1_ASM270800v1_genomic.fna/cds.fna -a GCA_002708005.1_ASM270800v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 10:16:27,529] [INFO] Task succeeded: Prodigal
[2023-06-28 10:16:27,529] [INFO] Task started: HMMsearch
[2023-06-28 10:16:27,529] [INFO] Running command: hmmsearch --tblout GCA_002708005.1_ASM270800v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37d87e96-830f-4517-a91c-89d59bc2192a/dqc_reference/reference_markers.hmm GCA_002708005.1_ASM270800v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 10:16:27,748] [INFO] Task succeeded: HMMsearch
[2023-06-28 10:16:27,750] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg0f8eb0e0-9cb9-452f-bbc3-0ac331cc29fd/GCA_002708005.1_ASM270800v1_genomic.fna.gz]
[2023-06-28 10:16:27,791] [INFO] Query marker FASTA was written to GCA_002708005.1_ASM270800v1_genomic.fna/markers.fasta
[2023-06-28 10:16:27,791] [INFO] Task started: Blastn
[2023-06-28 10:16:27,792] [INFO] Running command: blastn -query GCA_002708005.1_ASM270800v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37d87e96-830f-4517-a91c-89d59bc2192a/dqc_reference/reference_markers.fasta -out GCA_002708005.1_ASM270800v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:16:28,273] [INFO] Task succeeded: Blastn
[2023-06-28 10:16:28,277] [INFO] Selected 1 target genomes.
[2023-06-28 10:16:28,278] [INFO] Target genome list was writen to GCA_002708005.1_ASM270800v1_genomic.fna/target_genomes.txt
[2023-06-28 10:16:28,279] [INFO] Task started: fastANI
[2023-06-28 10:16:28,279] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f8eb0e0-9cb9-452f-bbc3-0ac331cc29fd/GCA_002708005.1_ASM270800v1_genomic.fna.gz --refList GCA_002708005.1_ASM270800v1_genomic.fna/target_genomes.txt --output GCA_002708005.1_ASM270800v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 10:16:28,702] [INFO] Task succeeded: fastANI
[2023-06-28 10:16:28,703] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37d87e96-830f-4517-a91c-89d59bc2192a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 10:16:28,704] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37d87e96-830f-4517-a91c-89d59bc2192a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 10:16:28,710] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 10:16:28,711] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 10:16:28,711] [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 10:16:28,718] [INFO] DFAST Taxonomy check result was written to GCA_002708005.1_ASM270800v1_genomic.fna/tc_result.tsv
[2023-06-28 10:16:28,720] [INFO] ===== Taxonomy check completed =====
[2023-06-28 10:16:28,721] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 10:16:28,721] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37d87e96-830f-4517-a91c-89d59bc2192a/dqc_reference/checkm_data
[2023-06-28 10:16:28,726] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 10:16:28,756] [INFO] Task started: CheckM
[2023-06-28 10:16:28,756] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002708005.1_ASM270800v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002708005.1_ASM270800v1_genomic.fna/checkm_input GCA_002708005.1_ASM270800v1_genomic.fna/checkm_result
[2023-06-28 10:16:59,255] [INFO] Task succeeded: CheckM
[2023-06-28 10:16:59,257] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 4.17%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-28 10:16:59,283] [INFO] ===== Completeness check finished =====
[2023-06-28 10:16:59,284] [INFO] ===== Start GTDB Search =====
[2023-06-28 10:16:59,284] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002708005.1_ASM270800v1_genomic.fna/markers.fasta)
[2023-06-28 10:16:59,284] [INFO] Task started: Blastn
[2023-06-28 10:16:59,284] [INFO] Running command: blastn -query GCA_002708005.1_ASM270800v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37d87e96-830f-4517-a91c-89d59bc2192a/dqc_reference/reference_markers_gtdb.fasta -out GCA_002708005.1_ASM270800v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:16:59,732] [INFO] Task succeeded: Blastn
[2023-06-28 10:16:59,739] [INFO] Selected 9 target genomes.
[2023-06-28 10:16:59,739] [INFO] Target genome list was writen to GCA_002708005.1_ASM270800v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 10:16:59,742] [INFO] Task started: fastANI
[2023-06-28 10:16:59,742] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f8eb0e0-9cb9-452f-bbc3-0ac331cc29fd/GCA_002708005.1_ASM270800v1_genomic.fna.gz --refList GCA_002708005.1_ASM270800v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002708005.1_ASM270800v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 10:17:03,749] [INFO] Task succeeded: fastANI
[2023-06-28 10:17:03,757] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 10:17:03,757] [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_002708005.1	s__UBA1096 sp002708005	100.0	663	669	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	97.71	97.68	0.70	0.66	3	conclusive
GCA_002684915.1	s__UBA1096 sp002684915	84.6493	483	669	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	98.82	98.82	0.77	0.77	2	-
GCA_004213515.1	s__UBA1096 sp002170545	82.2329	439	669	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	98.87	98.49	0.79	0.67	5	-
--------------------------------------------------------------------------------
[2023-06-28 10:17:03,760] [INFO] GTDB search result was written to GCA_002708005.1_ASM270800v1_genomic.fna/result_gtdb.tsv
[2023-06-28 10:17:03,760] [INFO] ===== GTDB Search completed =====
[2023-06-28 10:17:03,764] [INFO] DFAST_QC result json was written to GCA_002708005.1_ASM270800v1_genomic.fna/dqc_result.json
[2023-06-28 10:17:03,764] [INFO] DFAST_QC completed!
[2023-06-28 10:17:03,764] [INFO] Total running time: 0h0m46s