[2023-06-29 13:15:08,366] [INFO] DFAST_QC pipeline started.
[2023-06-29 13:15:08,368] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 13:15:08,369] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c3bf332-fdf1-4aa2-85a4-dff299099e14/dqc_reference
[2023-06-29 13:15:09,565] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 13:15:09,566] [INFO] Task started: Prodigal
[2023-06-29 13:15:09,566] [INFO] Running command: gunzip -c /var/lib/cwl/stg0fbaf96e-f610-4203-b80f-b18eb7009e65/GCA_024638285.1_ASM2463828v1_genomic.fna.gz | prodigal -d GCA_024638285.1_ASM2463828v1_genomic.fna/cds.fna -a GCA_024638285.1_ASM2463828v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 13:15:17,187] [INFO] Task succeeded: Prodigal
[2023-06-29 13:15:17,187] [INFO] Task started: HMMsearch
[2023-06-29 13:15:17,188] [INFO] Running command: hmmsearch --tblout GCA_024638285.1_ASM2463828v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c3bf332-fdf1-4aa2-85a4-dff299099e14/dqc_reference/reference_markers.hmm GCA_024638285.1_ASM2463828v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 13:15:17,411] [INFO] Task succeeded: HMMsearch
[2023-06-29 13:15:17,412] [INFO] Found 6/6 markers.
[2023-06-29 13:15:17,433] [INFO] Query marker FASTA was written to GCA_024638285.1_ASM2463828v1_genomic.fna/markers.fasta
[2023-06-29 13:15:17,433] [INFO] Task started: Blastn
[2023-06-29 13:15:17,433] [INFO] Running command: blastn -query GCA_024638285.1_ASM2463828v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c3bf332-fdf1-4aa2-85a4-dff299099e14/dqc_reference/reference_markers.fasta -out GCA_024638285.1_ASM2463828v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:15:18,033] [INFO] Task succeeded: Blastn
[2023-06-29 13:15:18,037] [INFO] Selected 26 target genomes.
[2023-06-29 13:15:18,037] [INFO] Target genome list was writen to GCA_024638285.1_ASM2463828v1_genomic.fna/target_genomes.txt
[2023-06-29 13:15:18,042] [INFO] Task started: fastANI
[2023-06-29 13:15:18,042] [INFO] Running command: fastANI --query /var/lib/cwl/stg0fbaf96e-f610-4203-b80f-b18eb7009e65/GCA_024638285.1_ASM2463828v1_genomic.fna.gz --refList GCA_024638285.1_ASM2463828v1_genomic.fna/target_genomes.txt --output GCA_024638285.1_ASM2463828v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 13:15:32,086] [INFO] Task succeeded: fastANI
[2023-06-29 13:15:32,087] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c3bf332-fdf1-4aa2-85a4-dff299099e14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 13:15:32,088] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c3bf332-fdf1-4aa2-85a4-dff299099e14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 13:15:32,090] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 13:15:32,090] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 13:15:32,090] [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
--------------------------------------------------------------------------------
[2023-06-29 13:15:32,092] [INFO] DFAST Taxonomy check result was written to GCA_024638285.1_ASM2463828v1_genomic.fna/tc_result.tsv
[2023-06-29 13:15:32,093] [INFO] ===== Taxonomy check completed =====
[2023-06-29 13:15:32,093] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 13:15:32,094] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c3bf332-fdf1-4aa2-85a4-dff299099e14/dqc_reference/checkm_data
[2023-06-29 13:15:32,098] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 13:15:32,121] [INFO] Task started: CheckM
[2023-06-29 13:15:32,121] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024638285.1_ASM2463828v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024638285.1_ASM2463828v1_genomic.fna/checkm_input GCA_024638285.1_ASM2463828v1_genomic.fna/checkm_result
[2023-06-29 13:16:00,291] [INFO] Task succeeded: CheckM
[2023-06-29 13:16:00,292] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 96.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 13:16:00,315] [INFO] ===== Completeness check finished =====
[2023-06-29 13:16:00,316] [INFO] ===== Start GTDB Search =====
[2023-06-29 13:16:00,316] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024638285.1_ASM2463828v1_genomic.fna/markers.fasta)
[2023-06-29 13:16:00,317] [INFO] Task started: Blastn
[2023-06-29 13:16:00,317] [INFO] Running command: blastn -query GCA_024638285.1_ASM2463828v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c3bf332-fdf1-4aa2-85a4-dff299099e14/dqc_reference/reference_markers_gtdb.fasta -out GCA_024638285.1_ASM2463828v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:16:01,102] [INFO] Task succeeded: Blastn
[2023-06-29 13:16:01,107] [INFO] Selected 15 target genomes.
[2023-06-29 13:16:01,108] [INFO] Target genome list was writen to GCA_024638285.1_ASM2463828v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 13:16:01,118] [INFO] Task started: fastANI
[2023-06-29 13:16:01,118] [INFO] Running command: fastANI --query /var/lib/cwl/stg0fbaf96e-f610-4203-b80f-b18eb7009e65/GCA_024638285.1_ASM2463828v1_genomic.fna.gz --refList GCA_024638285.1_ASM2463828v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024638285.1_ASM2463828v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 13:16:06,761] [INFO] Task succeeded: fastANI
[2023-06-29 13:16:06,779] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 13:16:06,779] [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_018402665.1	s__UBA10364 sp018402665	85.9076	468	527	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	96.42	96.42	0.92	0.92	2	-
GCA_905478295.1	s__UBA10364 sp002387615	84.5776	448	527	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	99.55	99.11	0.94	0.89	10	-
GCA_002685435.1	s__UBA10364 sp002685435	83.719	341	527	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003045825.1	s__UBA10364 sp003045825	82.3288	382	527	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	98.67	96.47	0.88	0.80	20	-
GCA_002430755.1	s__UBA10364 sp002430755	78.3794	78	527	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002378005.1	s__UBA10364 sp002378005	77.9658	142	527	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	99.86	99.85	0.95	0.94	3	-
GCA_012269745.1	s__UBA10364 sp012269745	77.9123	115	527	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525035.1	s__UBA10364 sp011525035	77.9046	123	527	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003545085.1	s__UBA10364 sp003545085	77.5328	70	527	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623275.1	s__UBA10364 sp018623275	77.395	80	527	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003455605.1	s__UBA10364 sp003455605	76.9651	72	527	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 13:16:06,781] [INFO] GTDB search result was written to GCA_024638285.1_ASM2463828v1_genomic.fna/result_gtdb.tsv
[2023-06-29 13:16:06,782] [INFO] ===== GTDB Search completed =====
[2023-06-29 13:16:06,795] [INFO] DFAST_QC result json was written to GCA_024638285.1_ASM2463828v1_genomic.fna/dqc_result.json
[2023-06-29 13:16:06,795] [INFO] DFAST_QC completed!
[2023-06-29 13:16:06,795] [INFO] Total running time: 0h0m58s