[2023-06-19 07:29:35,388] [INFO] DFAST_QC pipeline started.
[2023-06-19 07:29:35,390] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 07:29:35,391] [INFO] DQC Reference Directory: /var/lib/cwl/stg060e4d1e-ad88-41b7-8583-61f63cc7d911/dqc_reference
[2023-06-19 07:29:39,055] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 07:29:39,056] [INFO] Task started: Prodigal
[2023-06-19 07:29:39,057] [INFO] Running command: gunzip -c /var/lib/cwl/stgb9458980-697c-4a24-afaa-96096aedd25f/GCA_018670055.1_ASM1867005v1_genomic.fna.gz | prodigal -d GCA_018670055.1_ASM1867005v1_genomic.fna/cds.fna -a GCA_018670055.1_ASM1867005v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 07:29:42,520] [INFO] Task succeeded: Prodigal
[2023-06-19 07:29:42,520] [INFO] Task started: HMMsearch
[2023-06-19 07:29:42,521] [INFO] Running command: hmmsearch --tblout GCA_018670055.1_ASM1867005v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg060e4d1e-ad88-41b7-8583-61f63cc7d911/dqc_reference/reference_markers.hmm GCA_018670055.1_ASM1867005v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 07:29:42,726] [INFO] Task succeeded: HMMsearch
[2023-06-19 07:29:42,728] [INFO] Found 6/6 markers.
[2023-06-19 07:29:42,754] [INFO] Query marker FASTA was written to GCA_018670055.1_ASM1867005v1_genomic.fna/markers.fasta
[2023-06-19 07:29:42,754] [INFO] Task started: Blastn
[2023-06-19 07:29:42,755] [INFO] Running command: blastn -query GCA_018670055.1_ASM1867005v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg060e4d1e-ad88-41b7-8583-61f63cc7d911/dqc_reference/reference_markers.fasta -out GCA_018670055.1_ASM1867005v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 07:29:43,881] [INFO] Task succeeded: Blastn
[2023-06-19 07:29:43,885] [INFO] Selected 25 target genomes.
[2023-06-19 07:29:43,886] [INFO] Target genome list was writen to GCA_018670055.1_ASM1867005v1_genomic.fna/target_genomes.txt
[2023-06-19 07:29:43,906] [INFO] Task started: fastANI
[2023-06-19 07:29:43,907] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9458980-697c-4a24-afaa-96096aedd25f/GCA_018670055.1_ASM1867005v1_genomic.fna.gz --refList GCA_018670055.1_ASM1867005v1_genomic.fna/target_genomes.txt --output GCA_018670055.1_ASM1867005v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 07:29:55,526] [INFO] Task succeeded: fastANI
[2023-06-19 07:29:55,527] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg060e4d1e-ad88-41b7-8583-61f63cc7d911/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 07:29:55,528] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg060e4d1e-ad88-41b7-8583-61f63cc7d911/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 07:29:55,530] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 07:29:55,531] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 07:29:55,531] [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
--------------------------------------------------------------------------------
[2023-06-19 07:29:55,533] [INFO] DFAST Taxonomy check result was written to GCA_018670055.1_ASM1867005v1_genomic.fna/tc_result.tsv
[2023-06-19 07:29:55,534] [INFO] ===== Taxonomy check completed =====
[2023-06-19 07:29:55,534] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 07:29:55,535] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg060e4d1e-ad88-41b7-8583-61f63cc7d911/dqc_reference/checkm_data
[2023-06-19 07:29:55,539] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 07:29:55,566] [INFO] Task started: CheckM
[2023-06-19 07:29:55,567] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018670055.1_ASM1867005v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018670055.1_ASM1867005v1_genomic.fna/checkm_input GCA_018670055.1_ASM1867005v1_genomic.fna/checkm_result
[2023-06-19 07:30:13,725] [INFO] Task succeeded: CheckM
[2023-06-19 07:30:13,727] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 07:30:13,756] [INFO] ===== Completeness check finished =====
[2023-06-19 07:30:13,757] [INFO] ===== Start GTDB Search =====
[2023-06-19 07:30:13,757] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018670055.1_ASM1867005v1_genomic.fna/markers.fasta)
[2023-06-19 07:30:13,758] [INFO] Task started: Blastn
[2023-06-19 07:30:13,758] [INFO] Running command: blastn -query GCA_018670055.1_ASM1867005v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg060e4d1e-ad88-41b7-8583-61f63cc7d911/dqc_reference/reference_markers_gtdb.fasta -out GCA_018670055.1_ASM1867005v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 07:30:14,575] [INFO] Task succeeded: Blastn
[2023-06-19 07:30:14,580] [INFO] Selected 20 target genomes.
[2023-06-19 07:30:14,581] [INFO] Target genome list was writen to GCA_018670055.1_ASM1867005v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 07:30:14,583] [INFO] Task started: fastANI
[2023-06-19 07:30:14,583] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9458980-697c-4a24-afaa-96096aedd25f/GCA_018670055.1_ASM1867005v1_genomic.fna.gz --refList GCA_018670055.1_ASM1867005v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018670055.1_ASM1867005v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 07:30:21,119] [INFO] Task succeeded: fastANI
[2023-06-19 07:30:21,125] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 07:30:21,126] [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_018674095.1	s__GCA-2722105 sp018674095	99.3053	406	450	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-2722105	95.0	99.41	99.30	0.88	0.82	13	conclusive
GCA_018692355.1	s__GCA-2722105 sp018692355	79.0963	155	450	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-2722105	95.0	99.23	99.02	0.79	0.73	14	-
GCA_015658495.1	s__GCA-2722105 sp015658495	78.184	134	450	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-2722105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018649625.1	s__GCA-2722105 sp018649625	77.8445	144	450	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-2722105	95.0	99.96	99.90	0.93	0.85	15	-
GCA_002722105.1	s__GCA-2722105 sp002722105	76.3714	71	450	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-2722105	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 07:30:21,128] [INFO] GTDB search result was written to GCA_018670055.1_ASM1867005v1_genomic.fna/result_gtdb.tsv
[2023-06-19 07:30:21,128] [INFO] ===== GTDB Search completed =====
[2023-06-19 07:30:21,131] [INFO] DFAST_QC result json was written to GCA_018670055.1_ASM1867005v1_genomic.fna/dqc_result.json
[2023-06-19 07:30:21,131] [INFO] DFAST_QC completed!
[2023-06-19 07:30:21,131] [INFO] Total running time: 0h0m46s