[2023-06-08 12:26:31,762] [INFO] DFAST_QC pipeline started.
[2023-06-08 12:26:31,764] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 12:26:31,764] [INFO] DQC Reference Directory: /var/lib/cwl/stg908cb6cb-7b16-4a6d-8c77-8bd99bbb752a/dqc_reference
[2023-06-08 12:26:33,432] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 12:26:33,433] [INFO] Task started: Prodigal
[2023-06-08 12:26:33,434] [INFO] Running command: gunzip -c /var/lib/cwl/stg81815e66-d707-447d-a72a-61e1f888ff66/GCA_947485015.1_RH-9nov16-341_genomic.fna.gz | prodigal -d GCA_947485015.1_RH-9nov16-341_genomic.fna/cds.fna -a GCA_947485015.1_RH-9nov16-341_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 12:26:45,953] [INFO] Task succeeded: Prodigal
[2023-06-08 12:26:45,953] [INFO] Task started: HMMsearch
[2023-06-08 12:26:45,953] [INFO] Running command: hmmsearch --tblout GCA_947485015.1_RH-9nov16-341_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg908cb6cb-7b16-4a6d-8c77-8bd99bbb752a/dqc_reference/reference_markers.hmm GCA_947485015.1_RH-9nov16-341_genomic.fna/protein.faa > /dev/null
[2023-06-08 12:26:46,179] [INFO] Task succeeded: HMMsearch
[2023-06-08 12:26:46,180] [INFO] Found 6/6 markers.
[2023-06-08 12:26:46,209] [INFO] Query marker FASTA was written to GCA_947485015.1_RH-9nov16-341_genomic.fna/markers.fasta
[2023-06-08 12:26:46,209] [INFO] Task started: Blastn
[2023-06-08 12:26:46,210] [INFO] Running command: blastn -query GCA_947485015.1_RH-9nov16-341_genomic.fna/markers.fasta -db /var/lib/cwl/stg908cb6cb-7b16-4a6d-8c77-8bd99bbb752a/dqc_reference/reference_markers.fasta -out GCA_947485015.1_RH-9nov16-341_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:26:46,931] [INFO] Task succeeded: Blastn
[2023-06-08 12:26:46,935] [INFO] Selected 10 target genomes.
[2023-06-08 12:26:46,935] [INFO] Target genome list was writen to GCA_947485015.1_RH-9nov16-341_genomic.fna/target_genomes.txt
[2023-06-08 12:26:46,940] [INFO] Task started: fastANI
[2023-06-08 12:26:46,941] [INFO] Running command: fastANI --query /var/lib/cwl/stg81815e66-d707-447d-a72a-61e1f888ff66/GCA_947485015.1_RH-9nov16-341_genomic.fna.gz --refList GCA_947485015.1_RH-9nov16-341_genomic.fna/target_genomes.txt --output GCA_947485015.1_RH-9nov16-341_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 12:26:54,484] [INFO] Task succeeded: fastANI
[2023-06-08 12:26:54,484] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg908cb6cb-7b16-4a6d-8c77-8bd99bbb752a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 12:26:54,485] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg908cb6cb-7b16-4a6d-8c77-8bd99bbb752a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 12:26:54,487] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 12:26:54,487] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 12:26:54,487] [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
--------------------------------------------------------------------------------
[2023-06-08 12:26:54,490] [INFO] DFAST Taxonomy check result was written to GCA_947485015.1_RH-9nov16-341_genomic.fna/tc_result.tsv
[2023-06-08 12:26:54,490] [INFO] ===== Taxonomy check completed =====
[2023-06-08 12:26:54,491] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 12:26:54,491] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg908cb6cb-7b16-4a6d-8c77-8bd99bbb752a/dqc_reference/checkm_data
[2023-06-08 12:26:54,494] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 12:26:54,525] [INFO] Task started: CheckM
[2023-06-08 12:26:54,525] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947485015.1_RH-9nov16-341_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947485015.1_RH-9nov16-341_genomic.fna/checkm_input GCA_947485015.1_RH-9nov16-341_genomic.fna/checkm_result
[2023-06-08 12:27:35,155] [INFO] Task succeeded: CheckM
[2023-06-08 12:27:35,156] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-08 12:27:35,180] [INFO] ===== Completeness check finished =====
[2023-06-08 12:27:35,180] [INFO] ===== Start GTDB Search =====
[2023-06-08 12:27:35,181] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947485015.1_RH-9nov16-341_genomic.fna/markers.fasta)
[2023-06-08 12:27:35,182] [INFO] Task started: Blastn
[2023-06-08 12:27:35,182] [INFO] Running command: blastn -query GCA_947485015.1_RH-9nov16-341_genomic.fna/markers.fasta -db /var/lib/cwl/stg908cb6cb-7b16-4a6d-8c77-8bd99bbb752a/dqc_reference/reference_markers_gtdb.fasta -out GCA_947485015.1_RH-9nov16-341_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:27:36,229] [INFO] Task succeeded: Blastn
[2023-06-08 12:27:36,233] [INFO] Selected 11 target genomes.
[2023-06-08 12:27:36,234] [INFO] Target genome list was writen to GCA_947485015.1_RH-9nov16-341_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 12:27:36,247] [INFO] Task started: fastANI
[2023-06-08 12:27:36,247] [INFO] Running command: fastANI --query /var/lib/cwl/stg81815e66-d707-447d-a72a-61e1f888ff66/GCA_947485015.1_RH-9nov16-341_genomic.fna.gz --refList GCA_947485015.1_RH-9nov16-341_genomic.fna/target_genomes_gtdb.txt --output GCA_947485015.1_RH-9nov16-341_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 12:27:42,481] [INFO] Task succeeded: fastANI
[2023-06-08 12:27:42,488] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 12:27:42,489] [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_903856725.1	s__Lacunisphaera sp903856725	99.41	685	741	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	99.44	98.84	0.92	0.87	10	conclusive
GCA_903906135.1	s__Lacunisphaera sp903906135	88.0794	611	741	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	98.45	98.45	0.84	0.84	2	-
GCA_005787865.1	s__Lacunisphaera sp005787865	87.1394	406	741	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	96.88	96.49	0.76	0.70	4	-
GCA_002304425.1	s__Lacunisphaera sp002304425	86.5501	347	741	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903898675.1	s__Lacunisphaera sp903898675	77.5074	118	741	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	99.99	99.98	0.99	0.98	5	-
GCA_009695095.1	s__Lacunisphaera sp009695095	77.1801	75	741	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 12:27:42,490] [INFO] GTDB search result was written to GCA_947485015.1_RH-9nov16-341_genomic.fna/result_gtdb.tsv
[2023-06-08 12:27:42,491] [INFO] ===== GTDB Search completed =====
[2023-06-08 12:27:42,493] [INFO] DFAST_QC result json was written to GCA_947485015.1_RH-9nov16-341_genomic.fna/dqc_result.json
[2023-06-08 12:27:42,493] [INFO] DFAST_QC completed!
[2023-06-08 12:27:42,493] [INFO] Total running time: 0h1m11s