[2023-06-13 02:32:30,436] [INFO] DFAST_QC pipeline started.
[2023-06-13 02:32:30,439] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 02:32:30,439] [INFO] DQC Reference Directory: /var/lib/cwl/stg8cd2e009-30a9-4704-b11e-8214cb0f1079/dqc_reference
[2023-06-13 02:32:32,660] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 02:32:32,661] [INFO] Task started: Prodigal
[2023-06-13 02:32:32,661] [INFO] Running command: gunzip -c /var/lib/cwl/stgaff5f534-7017-4731-ade4-2a05d3181ec5/GCA_022425665.1_ASM2242566v1_genomic.fna.gz | prodigal -d GCA_022425665.1_ASM2242566v1_genomic.fna/cds.fna -a GCA_022425665.1_ASM2242566v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 02:32:36,252] [INFO] Task succeeded: Prodigal
[2023-06-13 02:32:36,252] [INFO] Task started: HMMsearch
[2023-06-13 02:32:36,252] [INFO] Running command: hmmsearch --tblout GCA_022425665.1_ASM2242566v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8cd2e009-30a9-4704-b11e-8214cb0f1079/dqc_reference/reference_markers.hmm GCA_022425665.1_ASM2242566v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 02:32:36,460] [INFO] Task succeeded: HMMsearch
[2023-06-13 02:32:36,462] [INFO] Found 6/6 markers.
[2023-06-13 02:32:36,484] [INFO] Query marker FASTA was written to GCA_022425665.1_ASM2242566v1_genomic.fna/markers.fasta
[2023-06-13 02:32:36,484] [INFO] Task started: Blastn
[2023-06-13 02:32:36,485] [INFO] Running command: blastn -query GCA_022425665.1_ASM2242566v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8cd2e009-30a9-4704-b11e-8214cb0f1079/dqc_reference/reference_markers.fasta -out GCA_022425665.1_ASM2242566v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:32:37,124] [INFO] Task succeeded: Blastn
[2023-06-13 02:32:37,129] [INFO] Selected 34 target genomes.
[2023-06-13 02:32:37,130] [INFO] Target genome list was writen to GCA_022425665.1_ASM2242566v1_genomic.fna/target_genomes.txt
[2023-06-13 02:32:37,138] [INFO] Task started: fastANI
[2023-06-13 02:32:37,138] [INFO] Running command: fastANI --query /var/lib/cwl/stgaff5f534-7017-4731-ade4-2a05d3181ec5/GCA_022425665.1_ASM2242566v1_genomic.fna.gz --refList GCA_022425665.1_ASM2242566v1_genomic.fna/target_genomes.txt --output GCA_022425665.1_ASM2242566v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 02:32:57,450] [INFO] Task succeeded: fastANI
[2023-06-13 02:32:57,451] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8cd2e009-30a9-4704-b11e-8214cb0f1079/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 02:32:57,452] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8cd2e009-30a9-4704-b11e-8214cb0f1079/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 02:32:57,454] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 02:32:57,454] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 02:32:57,454] [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
--------------------------------------------------------------------------------
[2023-06-13 02:32:57,456] [INFO] DFAST Taxonomy check result was written to GCA_022425665.1_ASM2242566v1_genomic.fna/tc_result.tsv
[2023-06-13 02:32:57,457] [INFO] ===== Taxonomy check completed =====
[2023-06-13 02:32:57,457] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 02:32:57,457] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8cd2e009-30a9-4704-b11e-8214cb0f1079/dqc_reference/checkm_data
[2023-06-13 02:32:57,461] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 02:32:57,480] [INFO] Task started: CheckM
[2023-06-13 02:32:57,480] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022425665.1_ASM2242566v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022425665.1_ASM2242566v1_genomic.fna/checkm_input GCA_022425665.1_ASM2242566v1_genomic.fna/checkm_result
[2023-06-13 02:33:14,998] [INFO] Task succeeded: CheckM
[2023-06-13 02:33:15,000] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.23%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 02:33:15,059] [INFO] ===== Completeness check finished =====
[2023-06-13 02:33:15,059] [INFO] ===== Start GTDB Search =====
[2023-06-13 02:33:15,059] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022425665.1_ASM2242566v1_genomic.fna/markers.fasta)
[2023-06-13 02:33:15,060] [INFO] Task started: Blastn
[2023-06-13 02:33:15,060] [INFO] Running command: blastn -query GCA_022425665.1_ASM2242566v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8cd2e009-30a9-4704-b11e-8214cb0f1079/dqc_reference/reference_markers_gtdb.fasta -out GCA_022425665.1_ASM2242566v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:33:16,073] [INFO] Task succeeded: Blastn
[2023-06-13 02:33:16,077] [INFO] Selected 9 target genomes.
[2023-06-13 02:33:16,078] [INFO] Target genome list was writen to GCA_022425665.1_ASM2242566v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 02:33:16,083] [INFO] Task started: fastANI
[2023-06-13 02:33:16,084] [INFO] Running command: fastANI --query /var/lib/cwl/stgaff5f534-7017-4731-ade4-2a05d3181ec5/GCA_022425665.1_ASM2242566v1_genomic.fna.gz --refList GCA_022425665.1_ASM2242566v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022425665.1_ASM2242566v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 02:33:18,947] [INFO] Task succeeded: fastANI
[2023-06-13 02:33:18,961] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 02:33:18,961] [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_900197605.1	s__UBA8337 sp900197605	96.5284	252	292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA8337	95.0	96.88	95.59	0.86	0.84	6	conclusive
GCA_009920875.1	s__UBA8337 sp009920875	82.0047	180	292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA8337	95.0	97.55	97.55	0.89	0.89	2	-
GCA_016779015.1	s__UBA8337 sp016779015	81.5161	157	292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA8337	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721725.1	s__UBA8337 sp002721725	81.0328	214	292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA8337	95.0	99.29	99.29	0.93	0.93	2	-
GCA_018673175.1	s__UBA8337 sp018673175	78.0877	136	292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA8337	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018660505.1	s__UBA8337 sp018660505	78.0542	149	292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA8337	95.0	99.75	99.71	0.96	0.95	3	-
GCA_002689195.1	s__UBA7378 sp002689195	77.3135	78	292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA7378	95.0	98.73	98.05	0.85	0.80	4	-
GCA_002469805.1	s__UBA7378 sp002469805	76.2157	51	292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA7378	95.0	99.20	98.74	0.81	0.77	5	-
--------------------------------------------------------------------------------
[2023-06-13 02:33:18,963] [INFO] GTDB search result was written to GCA_022425665.1_ASM2242566v1_genomic.fna/result_gtdb.tsv
[2023-06-13 02:33:18,964] [INFO] ===== GTDB Search completed =====
[2023-06-13 02:33:18,968] [INFO] DFAST_QC result json was written to GCA_022425665.1_ASM2242566v1_genomic.fna/dqc_result.json
[2023-06-13 02:33:18,968] [INFO] DFAST_QC completed!
[2023-06-13 02:33:18,968] [INFO] Total running time: 0h0m49s