[2023-06-18 17:51:29,899] [INFO] DFAST_QC pipeline started.
[2023-06-18 17:51:29,931] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 17:51:29,931] [INFO] DQC Reference Directory: /var/lib/cwl/stgcfadbca4-3cbe-4d1b-8941-4c2242bf03c8/dqc_reference
[2023-06-18 17:51:31,289] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 17:51:31,290] [INFO] Task started: Prodigal
[2023-06-18 17:51:31,290] [INFO] Running command: gunzip -c /var/lib/cwl/stgf167eebd-ecf9-4d89-ba29-4fe318d9ba17/GCA_018607925.1_ASM1860792v1_genomic.fna.gz | prodigal -d GCA_018607925.1_ASM1860792v1_genomic.fna/cds.fna -a GCA_018607925.1_ASM1860792v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 17:51:40,303] [INFO] Task succeeded: Prodigal
[2023-06-18 17:51:40,304] [INFO] Task started: HMMsearch
[2023-06-18 17:51:40,304] [INFO] Running command: hmmsearch --tblout GCA_018607925.1_ASM1860792v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcfadbca4-3cbe-4d1b-8941-4c2242bf03c8/dqc_reference/reference_markers.hmm GCA_018607925.1_ASM1860792v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 17:51:40,585] [INFO] Task succeeded: HMMsearch
[2023-06-18 17:51:40,586] [INFO] Found 6/6 markers.
[2023-06-18 17:51:40,616] [INFO] Query marker FASTA was written to GCA_018607925.1_ASM1860792v1_genomic.fna/markers.fasta
[2023-06-18 17:51:40,617] [INFO] Task started: Blastn
[2023-06-18 17:51:40,617] [INFO] Running command: blastn -query GCA_018607925.1_ASM1860792v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfadbca4-3cbe-4d1b-8941-4c2242bf03c8/dqc_reference/reference_markers.fasta -out GCA_018607925.1_ASM1860792v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:51:41,317] [INFO] Task succeeded: Blastn
[2023-06-18 17:51:41,322] [INFO] Selected 31 target genomes.
[2023-06-18 17:51:41,322] [INFO] Target genome list was writen to GCA_018607925.1_ASM1860792v1_genomic.fna/target_genomes.txt
[2023-06-18 17:51:41,332] [INFO] Task started: fastANI
[2023-06-18 17:51:41,333] [INFO] Running command: fastANI --query /var/lib/cwl/stgf167eebd-ecf9-4d89-ba29-4fe318d9ba17/GCA_018607925.1_ASM1860792v1_genomic.fna.gz --refList GCA_018607925.1_ASM1860792v1_genomic.fna/target_genomes.txt --output GCA_018607925.1_ASM1860792v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 17:51:59,263] [INFO] Task succeeded: fastANI
[2023-06-18 17:51:59,263] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcfadbca4-3cbe-4d1b-8941-4c2242bf03c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 17:51:59,263] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcfadbca4-3cbe-4d1b-8941-4c2242bf03c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 17:51:59,265] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 17:51:59,265] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 17:51:59,265] [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
--------------------------------------------------------------------------------
[2023-06-18 17:51:59,267] [INFO] DFAST Taxonomy check result was written to GCA_018607925.1_ASM1860792v1_genomic.fna/tc_result.tsv
[2023-06-18 17:51:59,267] [INFO] ===== Taxonomy check completed =====
[2023-06-18 17:51:59,267] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 17:51:59,268] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcfadbca4-3cbe-4d1b-8941-4c2242bf03c8/dqc_reference/checkm_data
[2023-06-18 17:51:59,270] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 17:51:59,309] [INFO] Task started: CheckM
[2023-06-18 17:51:59,309] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018607925.1_ASM1860792v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018607925.1_ASM1860792v1_genomic.fna/checkm_input GCA_018607925.1_ASM1860792v1_genomic.fna/checkm_result
[2023-06-18 17:52:31,652] [INFO] Task succeeded: CheckM
[2023-06-18 17:52:31,653] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 17:52:31,690] [INFO] ===== Completeness check finished =====
[2023-06-18 17:52:31,691] [INFO] ===== Start GTDB Search =====
[2023-06-18 17:52:31,691] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018607925.1_ASM1860792v1_genomic.fna/markers.fasta)
[2023-06-18 17:52:31,692] [INFO] Task started: Blastn
[2023-06-18 17:52:31,692] [INFO] Running command: blastn -query GCA_018607925.1_ASM1860792v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfadbca4-3cbe-4d1b-8941-4c2242bf03c8/dqc_reference/reference_markers_gtdb.fasta -out GCA_018607925.1_ASM1860792v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:52:32,757] [INFO] Task succeeded: Blastn
[2023-06-18 17:52:32,765] [INFO] Selected 27 target genomes.
[2023-06-18 17:52:32,765] [INFO] Target genome list was writen to GCA_018607925.1_ASM1860792v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 17:52:32,808] [INFO] Task started: fastANI
[2023-06-18 17:52:32,808] [INFO] Running command: fastANI --query /var/lib/cwl/stgf167eebd-ecf9-4d89-ba29-4fe318d9ba17/GCA_018607925.1_ASM1860792v1_genomic.fna.gz --refList GCA_018607925.1_ASM1860792v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018607925.1_ASM1860792v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 17:52:47,991] [INFO] Task succeeded: fastANI
[2023-06-18 17:52:48,001] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 17:52:48,001] [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_002389385.1	s__UBA4479 sp002389385	99.5021	844	1017	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA4479	95.0	99.63	99.57	0.92	0.85	8	conclusive
GCA_002389175.1	s__UBA4479 sp002389175	78.1514	92	1017	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA4479	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017640505.1	s__UBA4479 sp017640505	76.2434	86	1017	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA4479	95.0	99.97	99.97	1.00	1.00	2	-
GCA_017644185.1	s__UBA4479 sp017644185	75.9518	79	1017	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA4479	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 17:52:48,003] [INFO] GTDB search result was written to GCA_018607925.1_ASM1860792v1_genomic.fna/result_gtdb.tsv
[2023-06-18 17:52:48,004] [INFO] ===== GTDB Search completed =====
[2023-06-18 17:52:48,006] [INFO] DFAST_QC result json was written to GCA_018607925.1_ASM1860792v1_genomic.fna/dqc_result.json
[2023-06-18 17:52:48,007] [INFO] DFAST_QC completed!
[2023-06-18 17:52:48,007] [INFO] Total running time: 0h1m18s