[2023-06-28 17:21:23,276] [INFO] DFAST_QC pipeline started.
[2023-06-28 17:21:23,278] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 17:21:23,278] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf2dca3b-63e8-4650-b5d2-91a7af2e19e8/dqc_reference
[2023-06-28 17:21:24,607] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 17:21:24,608] [INFO] Task started: Prodigal
[2023-06-28 17:21:24,608] [INFO] Running command: gunzip -c /var/lib/cwl/stga52eac24-79e1-42c3-9ce4-d204d2630a22/GCA_020328025.1_ASM2032802v1_genomic.fna.gz | prodigal -d GCA_020328025.1_ASM2032802v1_genomic.fna/cds.fna -a GCA_020328025.1_ASM2032802v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 17:21:27,003] [INFO] Task succeeded: Prodigal
[2023-06-28 17:21:27,003] [INFO] Task started: HMMsearch
[2023-06-28 17:21:27,003] [INFO] Running command: hmmsearch --tblout GCA_020328025.1_ASM2032802v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf2dca3b-63e8-4650-b5d2-91a7af2e19e8/dqc_reference/reference_markers.hmm GCA_020328025.1_ASM2032802v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 17:21:27,242] [INFO] Task succeeded: HMMsearch
[2023-06-28 17:21:27,244] [INFO] Found 6/6 markers.
[2023-06-28 17:21:27,259] [INFO] Query marker FASTA was written to GCA_020328025.1_ASM2032802v1_genomic.fna/markers.fasta
[2023-06-28 17:21:27,259] [INFO] Task started: Blastn
[2023-06-28 17:21:27,260] [INFO] Running command: blastn -query GCA_020328025.1_ASM2032802v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf2dca3b-63e8-4650-b5d2-91a7af2e19e8/dqc_reference/reference_markers.fasta -out GCA_020328025.1_ASM2032802v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:21:28,557] [INFO] Task succeeded: Blastn
[2023-06-28 17:21:28,561] [INFO] Selected 15 target genomes.
[2023-06-28 17:21:28,562] [INFO] Target genome list was writen to GCA_020328025.1_ASM2032802v1_genomic.fna/target_genomes.txt
[2023-06-28 17:21:28,567] [INFO] Task started: fastANI
[2023-06-28 17:21:28,568] [INFO] Running command: fastANI --query /var/lib/cwl/stga52eac24-79e1-42c3-9ce4-d204d2630a22/GCA_020328025.1_ASM2032802v1_genomic.fna.gz --refList GCA_020328025.1_ASM2032802v1_genomic.fna/target_genomes.txt --output GCA_020328025.1_ASM2032802v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 17:21:34,112] [INFO] Task succeeded: fastANI
[2023-06-28 17:21:34,112] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf2dca3b-63e8-4650-b5d2-91a7af2e19e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 17:21:34,112] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf2dca3b-63e8-4650-b5d2-91a7af2e19e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 17:21:34,116] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 17:21:34,116] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 17:21:34,117] [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
Endomicrobium proavitum	strain=Rsa215	GCA_001027545.1	1408281	1408281	type	True	76.9207	58	363	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 17:21:34,119] [INFO] DFAST Taxonomy check result was written to GCA_020328025.1_ASM2032802v1_genomic.fna/tc_result.tsv
[2023-06-28 17:21:34,120] [INFO] ===== Taxonomy check completed =====
[2023-06-28 17:21:34,120] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 17:21:34,121] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf2dca3b-63e8-4650-b5d2-91a7af2e19e8/dqc_reference/checkm_data
[2023-06-28 17:21:34,123] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 17:21:34,151] [INFO] Task started: CheckM
[2023-06-28 17:21:34,151] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020328025.1_ASM2032802v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020328025.1_ASM2032802v1_genomic.fna/checkm_input GCA_020328025.1_ASM2032802v1_genomic.fna/checkm_result
[2023-06-28 17:21:49,814] [INFO] Task succeeded: CheckM
[2023-06-28 17:21:49,815] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 17:21:49,837] [INFO] ===== Completeness check finished =====
[2023-06-28 17:21:49,837] [INFO] ===== Start GTDB Search =====
[2023-06-28 17:21:49,838] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020328025.1_ASM2032802v1_genomic.fna/markers.fasta)
[2023-06-28 17:21:49,838] [INFO] Task started: Blastn
[2023-06-28 17:21:49,838] [INFO] Running command: blastn -query GCA_020328025.1_ASM2032802v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf2dca3b-63e8-4650-b5d2-91a7af2e19e8/dqc_reference/reference_markers_gtdb.fasta -out GCA_020328025.1_ASM2032802v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:21:50,711] [INFO] Task succeeded: Blastn
[2023-06-28 17:21:50,716] [INFO] Selected 20 target genomes.
[2023-06-28 17:21:50,717] [INFO] Target genome list was writen to GCA_020328025.1_ASM2032802v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 17:21:50,731] [INFO] Task started: fastANI
[2023-06-28 17:21:50,731] [INFO] Running command: fastANI --query /var/lib/cwl/stga52eac24-79e1-42c3-9ce4-d204d2630a22/GCA_020328025.1_ASM2032802v1_genomic.fna.gz --refList GCA_020328025.1_ASM2032802v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020328025.1_ASM2032802v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 17:21:57,747] [INFO] Task succeeded: fastANI
[2023-06-28 17:21:57,753] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 17:21:57,753] [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_002355835.1	s__Endomicrobium_A trichonymphae	77.1538	127	363	d__Bacteria;p__Elusimicrobiota;c__Endomicrobia;o__Endomicrobiales;f__Endomicrobiaceae;g__Endomicrobium_A	95.0	99.00	99.00	0.98	0.98	2	-
GCF_001027545.1	s__Endomicrobium proavitum	76.9207	58	363	d__Bacteria;p__Elusimicrobiota;c__Endomicrobia;o__Endomicrobiales;f__Endomicrobiaceae;g__Endomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009781315.1	s__Endomicrobium sp009781315	76.2885	50	363	d__Bacteria;p__Elusimicrobiota;c__Endomicrobia;o__Endomicrobiales;f__Endomicrobiaceae;g__Endomicrobium	95.0	99.96	99.96	1.00	1.00	2	-
GCA_009778965.1	s__Endomicrobium sp009778965	76.127	53	363	d__Bacteria;p__Elusimicrobiota;c__Endomicrobia;o__Endomicrobiales;f__Endomicrobiaceae;g__Endomicrobium	95.0	99.87	99.87	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-06-28 17:21:57,755] [INFO] GTDB search result was written to GCA_020328025.1_ASM2032802v1_genomic.fna/result_gtdb.tsv
[2023-06-28 17:21:57,756] [INFO] ===== GTDB Search completed =====
[2023-06-28 17:21:57,761] [INFO] DFAST_QC result json was written to GCA_020328025.1_ASM2032802v1_genomic.fna/dqc_result.json
[2023-06-28 17:21:57,762] [INFO] DFAST_QC completed!
[2023-06-28 17:21:57,762] [INFO] Total running time: 0h0m34s