[2024-01-24 14:22:33,256] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:33,258] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:33,258] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb9755e3-f472-444d-8620-1b325ba55063/dqc_reference
[2024-01-24 14:22:34,517] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:34,518] [INFO] Task started: Prodigal
[2024-01-24 14:22:34,519] [INFO] Running command: gunzip -c /var/lib/cwl/stg6d815660-644d-4d6e-b540-20db5d891d79/GCF_001545115.1_Protochlamydia_greubae_genomic.fna.gz | prodigal -d GCF_001545115.1_Protochlamydia_greubae_genomic.fna/cds.fna -a GCF_001545115.1_Protochlamydia_greubae_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:42,110] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:42,110] [INFO] Task started: HMMsearch
[2024-01-24 14:22:42,111] [INFO] Running command: hmmsearch --tblout GCF_001545115.1_Protochlamydia_greubae_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb9755e3-f472-444d-8620-1b325ba55063/dqc_reference/reference_markers.hmm GCF_001545115.1_Protochlamydia_greubae_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:42,416] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:42,417] [INFO] Found 6/6 markers.
[2024-01-24 14:22:42,451] [INFO] Query marker FASTA was written to GCF_001545115.1_Protochlamydia_greubae_genomic.fna/markers.fasta
[2024-01-24 14:22:42,451] [INFO] Task started: Blastn
[2024-01-24 14:22:42,452] [INFO] Running command: blastn -query GCF_001545115.1_Protochlamydia_greubae_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb9755e3-f472-444d-8620-1b325ba55063/dqc_reference/reference_markers.fasta -out GCF_001545115.1_Protochlamydia_greubae_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:43,085] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:43,092] [INFO] Selected 10 target genomes.
[2024-01-24 14:22:43,093] [INFO] Target genome list was writen to GCF_001545115.1_Protochlamydia_greubae_genomic.fna/target_genomes.txt
[2024-01-24 14:22:43,099] [INFO] Task started: fastANI
[2024-01-24 14:22:43,099] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d815660-644d-4d6e-b540-20db5d891d79/GCF_001545115.1_Protochlamydia_greubae_genomic.fna.gz --refList GCF_001545115.1_Protochlamydia_greubae_genomic.fna/target_genomes.txt --output GCF_001545115.1_Protochlamydia_greubae_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:48,544] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:48,545] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb9755e3-f472-444d-8620-1b325ba55063/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:48,545] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb9755e3-f472-444d-8620-1b325ba55063/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:48,548] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:22:48,548] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:22:48,548] [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
Candidatus Protochlamydia naegleriophila	strain=KNic	GCA_001499655.1	389348	389348	type	True	77.7494	132	1124	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:48,550] [INFO] DFAST Taxonomy check result was written to GCF_001545115.1_Protochlamydia_greubae_genomic.fna/tc_result.tsv
[2024-01-24 14:22:48,550] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:48,551] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:48,551] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb9755e3-f472-444d-8620-1b325ba55063/dqc_reference/checkm_data
[2024-01-24 14:22:48,552] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:48,627] [INFO] Task started: CheckM
[2024-01-24 14:22:48,627] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001545115.1_Protochlamydia_greubae_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001545115.1_Protochlamydia_greubae_genomic.fna/checkm_input GCF_001545115.1_Protochlamydia_greubae_genomic.fna/checkm_result
[2024-01-24 14:23:18,428] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:18,429] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:18,451] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:18,451] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:18,452] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001545115.1_Protochlamydia_greubae_genomic.fna/markers.fasta)
[2024-01-24 14:23:18,452] [INFO] Task started: Blastn
[2024-01-24 14:23:18,452] [INFO] Running command: blastn -query GCF_001545115.1_Protochlamydia_greubae_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb9755e3-f472-444d-8620-1b325ba55063/dqc_reference/reference_markers_gtdb.fasta -out GCF_001545115.1_Protochlamydia_greubae_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:19,491] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:19,495] [INFO] Selected 18 target genomes.
[2024-01-24 14:23:19,495] [INFO] Target genome list was writen to GCF_001545115.1_Protochlamydia_greubae_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:19,533] [INFO] Task started: fastANI
[2024-01-24 14:23:19,534] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d815660-644d-4d6e-b540-20db5d891d79/GCF_001545115.1_Protochlamydia_greubae_genomic.fna.gz --refList GCF_001545115.1_Protochlamydia_greubae_genomic.fna/target_genomes_gtdb.txt --output GCF_001545115.1_Protochlamydia_greubae_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:28,017] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:28,023] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:28,023] [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
GCF_001545115.1	s__Protochlamydia sp001545115	100.0	1120	1124	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Parachlamydiaceae;g__Protochlamydia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001499655.1	s__Protochlamydia naegleriophila	77.7294	132	1124	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Parachlamydiaceae;g__Protochlamydia	95.0	99.09	99.09	0.96	0.96	2	-
GCF_000011565.2	s__Protochlamydia amoebophila	77.6421	66	1124	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Parachlamydiaceae;g__Protochlamydia	95.0	96.71	95.90	0.92	0.88	5	-
GCA_013695355.1	s__Protochlamydia sp013695355	76.4146	60	1124	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Parachlamydiaceae;g__Protochlamydia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:28,026] [INFO] GTDB search result was written to GCF_001545115.1_Protochlamydia_greubae_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:28,027] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:28,029] [INFO] DFAST_QC result json was written to GCF_001545115.1_Protochlamydia_greubae_genomic.fna/dqc_result.json
[2024-01-24 14:23:28,029] [INFO] DFAST_QC completed!
[2024-01-24 14:23:28,029] [INFO] Total running time: 0h0m55s