[2023-06-13 04:47:26,480] [INFO] DFAST_QC pipeline started.
[2023-06-13 04:47:26,482] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 04:47:26,482] [INFO] DQC Reference Directory: /var/lib/cwl/stgee053b04-68cb-41c1-92ba-00d63b1ff530/dqc_reference
[2023-06-13 04:47:28,818] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 04:47:28,874] [INFO] Task started: Prodigal
[2023-06-13 04:47:28,875] [INFO] Running command: gunzip -c /var/lib/cwl/stgc511b3ae-5299-4bb4-be55-ca2e3a93fda6/GCA_022014015.1_ASM2201401v1_genomic.fna.gz | prodigal -d GCA_022014015.1_ASM2201401v1_genomic.fna/cds.fna -a GCA_022014015.1_ASM2201401v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 04:47:37,650] [INFO] Task succeeded: Prodigal
[2023-06-13 04:47:37,651] [INFO] Task started: HMMsearch
[2023-06-13 04:47:37,651] [INFO] Running command: hmmsearch --tblout GCA_022014015.1_ASM2201401v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee053b04-68cb-41c1-92ba-00d63b1ff530/dqc_reference/reference_markers.hmm GCA_022014015.1_ASM2201401v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 04:47:38,039] [INFO] Task succeeded: HMMsearch
[2023-06-13 04:47:38,041] [INFO] Found 6/6 markers.
[2023-06-13 04:47:38,092] [INFO] Query marker FASTA was written to GCA_022014015.1_ASM2201401v1_genomic.fna/markers.fasta
[2023-06-13 04:47:38,093] [INFO] Task started: Blastn
[2023-06-13 04:47:38,093] [INFO] Running command: blastn -query GCA_022014015.1_ASM2201401v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee053b04-68cb-41c1-92ba-00d63b1ff530/dqc_reference/reference_markers.fasta -out GCA_022014015.1_ASM2201401v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 04:47:39,863] [INFO] Task succeeded: Blastn
[2023-06-13 04:47:39,867] [INFO] Selected 24 target genomes.
[2023-06-13 04:47:39,868] [INFO] Target genome list was writen to GCA_022014015.1_ASM2201401v1_genomic.fna/target_genomes.txt
[2023-06-13 04:47:39,889] [INFO] Task started: fastANI
[2023-06-13 04:47:39,890] [INFO] Running command: fastANI --query /var/lib/cwl/stgc511b3ae-5299-4bb4-be55-ca2e3a93fda6/GCA_022014015.1_ASM2201401v1_genomic.fna.gz --refList GCA_022014015.1_ASM2201401v1_genomic.fna/target_genomes.txt --output GCA_022014015.1_ASM2201401v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 04:48:03,749] [INFO] Task succeeded: fastANI
[2023-06-13 04:48:03,750] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee053b04-68cb-41c1-92ba-00d63b1ff530/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 04:48:03,750] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee053b04-68cb-41c1-92ba-00d63b1ff530/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 04:48:03,757] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 04:48:03,757] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 04:48:03,757] [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
--------------------------------------------------------------------------------
[2023-06-13 04:48:03,760] [INFO] DFAST Taxonomy check result was written to GCA_022014015.1_ASM2201401v1_genomic.fna/tc_result.tsv
[2023-06-13 04:48:03,760] [INFO] ===== Taxonomy check completed =====
[2023-06-13 04:48:03,761] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 04:48:03,761] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee053b04-68cb-41c1-92ba-00d63b1ff530/dqc_reference/checkm_data
[2023-06-13 04:48:03,764] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 04:48:03,806] [INFO] Task started: CheckM
[2023-06-13 04:48:03,806] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022014015.1_ASM2201401v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022014015.1_ASM2201401v1_genomic.fna/checkm_input GCA_022014015.1_ASM2201401v1_genomic.fna/checkm_result
[2023-06-13 04:48:35,278] [INFO] Task succeeded: CheckM
[2023-06-13 04:48:35,280] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 04:48:35,308] [INFO] ===== Completeness check finished =====
[2023-06-13 04:48:35,308] [INFO] ===== Start GTDB Search =====
[2023-06-13 04:48:35,309] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022014015.1_ASM2201401v1_genomic.fna/markers.fasta)
[2023-06-13 04:48:35,309] [INFO] Task started: Blastn
[2023-06-13 04:48:35,309] [INFO] Running command: blastn -query GCA_022014015.1_ASM2201401v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee053b04-68cb-41c1-92ba-00d63b1ff530/dqc_reference/reference_markers_gtdb.fasta -out GCA_022014015.1_ASM2201401v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 04:48:36,254] [INFO] Task succeeded: Blastn
[2023-06-13 04:48:36,259] [INFO] Selected 24 target genomes.
[2023-06-13 04:48:36,260] [INFO] Target genome list was writen to GCA_022014015.1_ASM2201401v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 04:48:36,353] [INFO] Task started: fastANI
[2023-06-13 04:48:36,354] [INFO] Running command: fastANI --query /var/lib/cwl/stgc511b3ae-5299-4bb4-be55-ca2e3a93fda6/GCA_022014015.1_ASM2201401v1_genomic.fna.gz --refList GCA_022014015.1_ASM2201401v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022014015.1_ASM2201401v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 04:48:51,718] [INFO] Task succeeded: fastANI
[2023-06-13 04:48:51,725] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 04:48:51,725] [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_018896525.1	s__JAHIPE01 sp018896525	99.8896	865	984	d__Bacteria;p__Actinobacteriota;c__Geothermincolia;o__Fen-727;f__Anoxymicrobiaceae;g__JAHIPE01	95.0	99.92	99.86	0.95	0.93	6	conclusive
GCA_018894655.1	s__JAHIPE01 sp018894655	85.3625	394	984	d__Bacteria;p__Actinobacteriota;c__Geothermincolia;o__Fen-727;f__Anoxymicrobiaceae;g__JAHIPE01	95.0	99.01	98.98	0.81	0.81	3	-
--------------------------------------------------------------------------------
[2023-06-13 04:48:51,728] [INFO] GTDB search result was written to GCA_022014015.1_ASM2201401v1_genomic.fna/result_gtdb.tsv
[2023-06-13 04:48:51,729] [INFO] ===== GTDB Search completed =====
[2023-06-13 04:48:51,732] [INFO] DFAST_QC result json was written to GCA_022014015.1_ASM2201401v1_genomic.fna/dqc_result.json
[2023-06-13 04:48:51,733] [INFO] DFAST_QC completed!
[2023-06-13 04:48:51,733] [INFO] Total running time: 0h1m25s