[2023-06-27 05:20:34,319] [INFO] DFAST_QC pipeline started.
[2023-06-27 05:20:34,322] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 05:20:34,322] [INFO] DQC Reference Directory: /var/lib/cwl/stg35e4e623-51fd-4c61-affb-4796fe089667/dqc_reference
[2023-06-27 05:20:35,568] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 05:20:35,568] [INFO] Task started: Prodigal
[2023-06-27 05:20:35,569] [INFO] Running command: gunzip -c /var/lib/cwl/stg89fa4299-caa9-469b-87e4-5e1e061e1810/GCA_002717855.1_ASM271785v1_genomic.fna.gz | prodigal -d GCA_002717855.1_ASM271785v1_genomic.fna/cds.fna -a GCA_002717855.1_ASM271785v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 05:20:37,383] [INFO] Task succeeded: Prodigal
[2023-06-27 05:20:37,384] [INFO] Task started: HMMsearch
[2023-06-27 05:20:37,384] [INFO] Running command: hmmsearch --tblout GCA_002717855.1_ASM271785v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35e4e623-51fd-4c61-affb-4796fe089667/dqc_reference/reference_markers.hmm GCA_002717855.1_ASM271785v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 05:20:37,567] [INFO] Task succeeded: HMMsearch
[2023-06-27 05:20:37,568] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg89fa4299-caa9-469b-87e4-5e1e061e1810/GCA_002717855.1_ASM271785v1_genomic.fna.gz]
[2023-06-27 05:20:37,584] [INFO] Query marker FASTA was written to GCA_002717855.1_ASM271785v1_genomic.fna/markers.fasta
[2023-06-27 05:20:37,585] [INFO] Task started: Blastn
[2023-06-27 05:20:37,585] [INFO] Running command: blastn -query GCA_002717855.1_ASM271785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35e4e623-51fd-4c61-affb-4796fe089667/dqc_reference/reference_markers.fasta -out GCA_002717855.1_ASM271785v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:20:38,069] [INFO] Task succeeded: Blastn
[2023-06-27 05:20:38,077] [INFO] Selected 10 target genomes.
[2023-06-27 05:20:38,077] [INFO] Target genome list was writen to GCA_002717855.1_ASM271785v1_genomic.fna/target_genomes.txt
[2023-06-27 05:20:38,080] [INFO] Task started: fastANI
[2023-06-27 05:20:38,080] [INFO] Running command: fastANI --query /var/lib/cwl/stg89fa4299-caa9-469b-87e4-5e1e061e1810/GCA_002717855.1_ASM271785v1_genomic.fna.gz --refList GCA_002717855.1_ASM271785v1_genomic.fna/target_genomes.txt --output GCA_002717855.1_ASM271785v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 05:20:42,948] [INFO] Task succeeded: fastANI
[2023-06-27 05:20:42,949] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35e4e623-51fd-4c61-affb-4796fe089667/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 05:20:42,949] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35e4e623-51fd-4c61-affb-4796fe089667/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 05:20:42,963] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 05:20:42,963] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 05:20:42,963] [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
--------------------------------------------------------------------------------
[2023-06-27 05:20:42,966] [INFO] DFAST Taxonomy check result was written to GCA_002717855.1_ASM271785v1_genomic.fna/tc_result.tsv
[2023-06-27 05:20:42,967] [INFO] ===== Taxonomy check completed =====
[2023-06-27 05:20:42,967] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 05:20:42,967] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35e4e623-51fd-4c61-affb-4796fe089667/dqc_reference/checkm_data
[2023-06-27 05:20:42,971] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 05:20:42,984] [INFO] Task started: CheckM
[2023-06-27 05:20:42,984] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002717855.1_ASM271785v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002717855.1_ASM271785v1_genomic.fna/checkm_input GCA_002717855.1_ASM271785v1_genomic.fna/checkm_result
[2023-06-27 05:20:56,343] [INFO] Task succeeded: CheckM
[2023-06-27 05:20:56,344] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 05:20:56,364] [INFO] ===== Completeness check finished =====
[2023-06-27 05:20:56,364] [INFO] ===== Start GTDB Search =====
[2023-06-27 05:20:56,365] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002717855.1_ASM271785v1_genomic.fna/markers.fasta)
[2023-06-27 05:20:56,365] [INFO] Task started: Blastn
[2023-06-27 05:20:56,365] [INFO] Running command: blastn -query GCA_002717855.1_ASM271785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35e4e623-51fd-4c61-affb-4796fe089667/dqc_reference/reference_markers_gtdb.fasta -out GCA_002717855.1_ASM271785v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:20:56,822] [INFO] Task succeeded: Blastn
[2023-06-27 05:20:56,827] [INFO] Selected 11 target genomes.
[2023-06-27 05:20:56,827] [INFO] Target genome list was writen to GCA_002717855.1_ASM271785v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 05:20:56,887] [INFO] Task started: fastANI
[2023-06-27 05:20:56,888] [INFO] Running command: fastANI --query /var/lib/cwl/stg89fa4299-caa9-469b-87e4-5e1e061e1810/GCA_002717855.1_ASM271785v1_genomic.fna.gz --refList GCA_002717855.1_ASM271785v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002717855.1_ASM271785v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 05:20:59,093] [INFO] Task succeeded: fastANI
[2023-06-27 05:20:59,099] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 05:20:59,100] [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_002717855.1	s__SP4073 sp002717855	100.0	192	193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__SP4073	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902524895.1	s__SP4073 sp902524895	84.6105	147	193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__SP4073	95.0	96.76	96.76	0.88	0.88	2	-
GCA_902523675.1	s__SP4073 sp902523675	84.3428	111	193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__SP4073	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 05:20:59,103] [INFO] GTDB search result was written to GCA_002717855.1_ASM271785v1_genomic.fna/result_gtdb.tsv
[2023-06-27 05:20:59,104] [INFO] ===== GTDB Search completed =====
[2023-06-27 05:20:59,116] [INFO] DFAST_QC result json was written to GCA_002717855.1_ASM271785v1_genomic.fna/dqc_result.json
[2023-06-27 05:20:59,117] [INFO] DFAST_QC completed!
[2023-06-27 05:20:59,117] [INFO] Total running time: 0h0m25s