[2024-01-24 13:40:28,571] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:28,574] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:28,575] [INFO] DQC Reference Directory: /var/lib/cwl/stg24b3ee75-ce50-4ebe-8f3b-b88217645d5f/dqc_reference
[2024-01-24 13:40:31,143] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:31,145] [INFO] Task started: Prodigal
[2024-01-24 13:40:31,145] [INFO] Running command: gunzip -c /var/lib/cwl/stg71dfb6e1-fc70-4ae7-bf36-a3a0e31230ed/GCF_003585935.1_ASM358593v1_genomic.fna.gz | prodigal -d GCF_003585935.1_ASM358593v1_genomic.fna/cds.fna -a GCF_003585935.1_ASM358593v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:34,506] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:34,507] [INFO] Task started: HMMsearch
[2024-01-24 13:40:34,507] [INFO] Running command: hmmsearch --tblout GCF_003585935.1_ASM358593v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24b3ee75-ce50-4ebe-8f3b-b88217645d5f/dqc_reference/reference_markers.hmm GCF_003585935.1_ASM358593v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:34,916] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:34,917] [INFO] Found 6/6 markers.
[2024-01-24 13:40:34,946] [INFO] Query marker FASTA was written to GCF_003585935.1_ASM358593v1_genomic.fna/markers.fasta
[2024-01-24 13:40:34,947] [INFO] Task started: Blastn
[2024-01-24 13:40:34,947] [INFO] Running command: blastn -query GCF_003585935.1_ASM358593v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24b3ee75-ce50-4ebe-8f3b-b88217645d5f/dqc_reference/reference_markers.fasta -out GCF_003585935.1_ASM358593v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:36,342] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:36,347] [INFO] Selected 12 target genomes.
[2024-01-24 13:40:36,348] [INFO] Target genome list was writen to GCF_003585935.1_ASM358593v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:36,357] [INFO] Task started: fastANI
[2024-01-24 13:40:36,357] [INFO] Running command: fastANI --query /var/lib/cwl/stg71dfb6e1-fc70-4ae7-bf36-a3a0e31230ed/GCF_003585935.1_ASM358593v1_genomic.fna.gz --refList GCF_003585935.1_ASM358593v1_genomic.fna/target_genomes.txt --output GCF_003585935.1_ASM358593v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:42,054] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:42,055] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24b3ee75-ce50-4ebe-8f3b-b88217645d5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:42,055] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24b3ee75-ce50-4ebe-8f3b-b88217645d5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:42,060] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:40:42,060] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:42,060] [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 hinzii	strain=111	GCA_003585935.1	2028575	2028575	type	True	100.0	715	723	95	conclusive
Psittacicella melopsittaci	strain=B96_4	GCA_003585925.1	2028576	2028576	type	True	79.3146	168	723	95	below_threshold
Psittacicella gerlachiana	strain=EEAB3T1	GCA_003585965.1	2028574	2028574	type	True	78.8988	133	723	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:42,062] [INFO] DFAST Taxonomy check result was written to GCF_003585935.1_ASM358593v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:42,062] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:42,062] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:42,063] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24b3ee75-ce50-4ebe-8f3b-b88217645d5f/dqc_reference/checkm_data
[2024-01-24 13:40:42,064] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:42,099] [INFO] Task started: CheckM
[2024-01-24 13:40:42,099] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003585935.1_ASM358593v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003585935.1_ASM358593v1_genomic.fna/checkm_input GCF_003585935.1_ASM358593v1_genomic.fna/checkm_result
[2024-01-24 13:41:02,134] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:02,136] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:02,159] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:02,160] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:02,160] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003585935.1_ASM358593v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:02,161] [INFO] Task started: Blastn
[2024-01-24 13:41:02,161] [INFO] Running command: blastn -query GCF_003585935.1_ASM358593v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24b3ee75-ce50-4ebe-8f3b-b88217645d5f/dqc_reference/reference_markers_gtdb.fasta -out GCF_003585935.1_ASM358593v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:03,171] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:03,175] [INFO] Selected 14 target genomes.
[2024-01-24 13:41:03,175] [INFO] Target genome list was writen to GCF_003585935.1_ASM358593v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:03,195] [INFO] Task started: fastANI
[2024-01-24 13:41:03,196] [INFO] Running command: fastANI --query /var/lib/cwl/stg71dfb6e1-fc70-4ae7-bf36-a3a0e31230ed/GCF_003585935.1_ASM358593v1_genomic.fna.gz --refList GCF_003585935.1_ASM358593v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003585935.1_ASM358593v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:08,172] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:08,178] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:08,178] [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_003585935.1	s__Psittacicella hinzii	100.0	715	723	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	79.3291	167	723	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	79.1415	156	723	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psittacicellaceae;g__Psittacicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003585965.1	s__Psittacicella gerlachiana	78.9281	132	723	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psittacicellaceae;g__Psittacicella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:08,180] [INFO] GTDB search result was written to GCF_003585935.1_ASM358593v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:08,181] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:08,184] [INFO] DFAST_QC result json was written to GCF_003585935.1_ASM358593v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:08,184] [INFO] DFAST_QC completed!
[2024-01-24 13:41:08,185] [INFO] Total running time: 0h0m40s