[2024-01-24 12:52:26,803] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:52:26,806] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:52:26,806] [INFO] DQC Reference Directory: /var/lib/cwl/stgae5d06fc-4c01-4b5f-be47-46cbb53abfb1/dqc_reference
[2024-01-24 12:52:28,084] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:52:28,085] [INFO] Task started: Prodigal
[2024-01-24 12:52:28,085] [INFO] Running command: gunzip -c /var/lib/cwl/stg5cbe0b74-60a5-4b0c-898c-11f6895d2842/GCF_902806995.1_15-2067_O50_genomic.fna.gz | prodigal -d GCF_902806995.1_15-2067_O50_genomic.fna/cds.fna -a GCF_902806995.1_15-2067_O50_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:52:30,740] [INFO] Task succeeded: Prodigal
[2024-01-24 12:52:30,741] [INFO] Task started: HMMsearch
[2024-01-24 12:52:30,741] [INFO] Running command: hmmsearch --tblout GCF_902806995.1_15-2067_O50_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgae5d06fc-4c01-4b5f-be47-46cbb53abfb1/dqc_reference/reference_markers.hmm GCF_902806995.1_15-2067_O50_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:52:30,991] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:52:30,993] [INFO] Found 6/6 markers.
[2024-01-24 12:52:31,008] [INFO] Query marker FASTA was written to GCF_902806995.1_15-2067_O50_genomic.fna/markers.fasta
[2024-01-24 12:52:31,008] [INFO] Task started: Blastn
[2024-01-24 12:52:31,009] [INFO] Running command: blastn -query GCF_902806995.1_15-2067_O50_genomic.fna/markers.fasta -db /var/lib/cwl/stgae5d06fc-4c01-4b5f-be47-46cbb53abfb1/dqc_reference/reference_markers.fasta -out GCF_902806995.1_15-2067_O50_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:52:31,633] [INFO] Task succeeded: Blastn
[2024-01-24 12:52:31,639] [INFO] Selected 14 target genomes.
[2024-01-24 12:52:31,639] [INFO] Target genome list was writen to GCF_902806995.1_15-2067_O50_genomic.fna/target_genomes.txt
[2024-01-24 12:52:31,720] [INFO] Task started: fastANI
[2024-01-24 12:52:31,720] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cbe0b74-60a5-4b0c-898c-11f6895d2842/GCF_902806995.1_15-2067_O50_genomic.fna.gz --refList GCF_902806995.1_15-2067_O50_genomic.fna/target_genomes.txt --output GCF_902806995.1_15-2067_O50_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:52:36,249] [INFO] Task succeeded: fastANI
[2024-01-24 12:52:36,250] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgae5d06fc-4c01-4b5f-be47-46cbb53abfb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:52:36,250] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgae5d06fc-4c01-4b5f-be47-46cbb53abfb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:52:36,255] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:52:36,255] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:52:36,255] [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
Chlamydiifrater volucris		GCA_902806995.1	2681470	2681470	type	True	100.0	400	401	95	conclusive
Chlamydiifrater phoenicopteri		GCA_902807005.1	2681469	2681469	type	True	79.6865	223	401	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:52:36,257] [INFO] DFAST Taxonomy check result was written to GCF_902806995.1_15-2067_O50_genomic.fna/tc_result.tsv
[2024-01-24 12:52:36,257] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:52:36,257] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:52:36,257] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgae5d06fc-4c01-4b5f-be47-46cbb53abfb1/dqc_reference/checkm_data
[2024-01-24 12:52:36,258] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:52:36,288] [INFO] Task started: CheckM
[2024-01-24 12:52:36,288] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902806995.1_15-2067_O50_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902806995.1_15-2067_O50_genomic.fna/checkm_input GCF_902806995.1_15-2067_O50_genomic.fna/checkm_result
[2024-01-24 12:52:52,508] [INFO] Task succeeded: CheckM
[2024-01-24 12:52:52,509] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:52:52,526] [INFO] ===== Completeness check finished =====
[2024-01-24 12:52:52,526] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:52:52,527] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902806995.1_15-2067_O50_genomic.fna/markers.fasta)
[2024-01-24 12:52:52,527] [INFO] Task started: Blastn
[2024-01-24 12:52:52,527] [INFO] Running command: blastn -query GCF_902806995.1_15-2067_O50_genomic.fna/markers.fasta -db /var/lib/cwl/stgae5d06fc-4c01-4b5f-be47-46cbb53abfb1/dqc_reference/reference_markers_gtdb.fasta -out GCF_902806995.1_15-2067_O50_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:52:53,243] [INFO] Task succeeded: Blastn
[2024-01-24 12:52:53,247] [INFO] Selected 14 target genomes.
[2024-01-24 12:52:53,247] [INFO] Target genome list was writen to GCF_902806995.1_15-2067_O50_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:52:53,276] [INFO] Task started: fastANI
[2024-01-24 12:52:53,276] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cbe0b74-60a5-4b0c-898c-11f6895d2842/GCF_902806995.1_15-2067_O50_genomic.fna.gz --refList GCF_902806995.1_15-2067_O50_genomic.fna/target_genomes_gtdb.txt --output GCF_902806995.1_15-2067_O50_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:52:57,369] [INFO] Task succeeded: fastANI
[2024-01-24 12:52:57,375] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:52:57,375] [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_902806995.1	s__Chlamydiifrater volucris	100.0	400	401	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydiifrater	95.0	99.60	99.60	1.00	1.00	2	conclusive
GCF_902807005.1	s__Chlamydiifrater phoenicopteri	79.6982	222	401	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydiifrater	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:52:57,377] [INFO] GTDB search result was written to GCF_902806995.1_15-2067_O50_genomic.fna/result_gtdb.tsv
[2024-01-24 12:52:57,378] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:52:57,381] [INFO] DFAST_QC result json was written to GCF_902806995.1_15-2067_O50_genomic.fna/dqc_result.json
[2024-01-24 12:52:57,381] [INFO] DFAST_QC completed!
[2024-01-24 12:52:57,381] [INFO] Total running time: 0h0m31s