[2024-01-25 18:25:35,604] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:25:35,606] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:25:35,606] [INFO] DQC Reference Directory: /var/lib/cwl/stg33aaef3b-4d80-457d-8bbf-be688fa8fc72/dqc_reference
[2024-01-25 18:25:36,712] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:25:36,713] [INFO] Task started: Prodigal
[2024-01-25 18:25:36,713] [INFO] Running command: gunzip -c /var/lib/cwl/stgf79ba0e6-280b-4000-b4dd-61da459143c5/GCF_003585965.1_ASM358596v1_genomic.fna.gz | prodigal -d GCF_003585965.1_ASM358596v1_genomic.fna/cds.fna -a GCF_003585965.1_ASM358596v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:25:39,277] [INFO] Task succeeded: Prodigal
[2024-01-25 18:25:39,277] [INFO] Task started: HMMsearch
[2024-01-25 18:25:39,277] [INFO] Running command: hmmsearch --tblout GCF_003585965.1_ASM358596v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33aaef3b-4d80-457d-8bbf-be688fa8fc72/dqc_reference/reference_markers.hmm GCF_003585965.1_ASM358596v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:25:39,497] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:25:39,498] [INFO] Found 6/6 markers.
[2024-01-25 18:25:39,517] [INFO] Query marker FASTA was written to GCF_003585965.1_ASM358596v1_genomic.fna/markers.fasta
[2024-01-25 18:25:39,518] [INFO] Task started: Blastn
[2024-01-25 18:25:39,518] [INFO] Running command: blastn -query GCF_003585965.1_ASM358596v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33aaef3b-4d80-457d-8bbf-be688fa8fc72/dqc_reference/reference_markers.fasta -out GCF_003585965.1_ASM358596v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:25:40,100] [INFO] Task succeeded: Blastn
[2024-01-25 18:25:40,103] [INFO] Selected 19 target genomes.
[2024-01-25 18:25:40,103] [INFO] Target genome list was writen to GCF_003585965.1_ASM358596v1_genomic.fna/target_genomes.txt
[2024-01-25 18:25:40,114] [INFO] Task started: fastANI
[2024-01-25 18:25:40,114] [INFO] Running command: fastANI --query /var/lib/cwl/stgf79ba0e6-280b-4000-b4dd-61da459143c5/GCF_003585965.1_ASM358596v1_genomic.fna.gz --refList GCF_003585965.1_ASM358596v1_genomic.fna/target_genomes.txt --output GCF_003585965.1_ASM358596v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:25:48,855] [INFO] Task succeeded: fastANI
[2024-01-25 18:25:48,856] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33aaef3b-4d80-457d-8bbf-be688fa8fc72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:25:48,856] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33aaef3b-4d80-457d-8bbf-be688fa8fc72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:25:48,860] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:25:48,860] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:25:48,860] [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
Psittacicella gerlachiana	strain=EEAB3T1	GCA_003585965.1	2028574	2028574	type	True	100.0	579	586	95	conclusive
Psittacicella melopsittaci	strain=B96_4	GCA_003585925.1	2028576	2028576	type	True	79.4174	267	586	95	below_threshold
Psittacicella hinzii	strain=111	GCA_003585935.1	2028575	2028575	type	True	78.9091	128	586	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:25:48,862] [INFO] DFAST Taxonomy check result was written to GCF_003585965.1_ASM358596v1_genomic.fna/tc_result.tsv
[2024-01-25 18:25:48,863] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:25:48,863] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:25:48,863] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33aaef3b-4d80-457d-8bbf-be688fa8fc72/dqc_reference/checkm_data
[2024-01-25 18:25:48,864] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:25:48,889] [INFO] Task started: CheckM
[2024-01-25 18:25:48,889] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003585965.1_ASM358596v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003585965.1_ASM358596v1_genomic.fna/checkm_input GCF_003585965.1_ASM358596v1_genomic.fna/checkm_result
[2024-01-25 18:26:03,080] [INFO] Task succeeded: CheckM
[2024-01-25 18:26:03,081] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:26:03,095] [INFO] ===== Completeness check finished =====
[2024-01-25 18:26:03,095] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:26:03,096] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003585965.1_ASM358596v1_genomic.fna/markers.fasta)
[2024-01-25 18:26:03,096] [INFO] Task started: Blastn
[2024-01-25 18:26:03,096] [INFO] Running command: blastn -query GCF_003585965.1_ASM358596v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33aaef3b-4d80-457d-8bbf-be688fa8fc72/dqc_reference/reference_markers_gtdb.fasta -out GCF_003585965.1_ASM358596v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:26:04,040] [INFO] Task succeeded: Blastn
[2024-01-25 18:26:04,042] [INFO] Selected 15 target genomes.
[2024-01-25 18:26:04,042] [INFO] Target genome list was writen to GCF_003585965.1_ASM358596v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:26:04,057] [INFO] Task started: fastANI
[2024-01-25 18:26:04,057] [INFO] Running command: fastANI --query /var/lib/cwl/stgf79ba0e6-280b-4000-b4dd-61da459143c5/GCF_003585965.1_ASM358596v1_genomic.fna.gz --refList GCF_003585965.1_ASM358596v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003585965.1_ASM358596v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:26:10,101] [INFO] Task succeeded: fastANI
[2024-01-25 18:26:10,105] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:26:10,105] [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_003585965.1	s__Psittacicella gerlachiana	100.0	579	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psittacicellaceae;g__Psittacicella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003585925.1	s__Psittacicella melopsittaci	79.4173	267	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psittacicellaceae;g__Psittacicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003585885.1	s__Psittacicella sp003585885	79.382	203	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psittacicellaceae;g__Psittacicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003585935.1	s__Psittacicella hinzii	78.94	127	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psittacicellaceae;g__Psittacicella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:26:10,107] [INFO] GTDB search result was written to GCF_003585965.1_ASM358596v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:26:10,108] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:26:10,111] [INFO] DFAST_QC result json was written to GCF_003585965.1_ASM358596v1_genomic.fna/dqc_result.json
[2024-01-25 18:26:10,111] [INFO] DFAST_QC completed!
[2024-01-25 18:26:10,111] [INFO] Total running time: 0h0m35s