[2023-06-17 04:56:35,293] [INFO] DFAST_QC pipeline started.
[2023-06-17 04:56:35,296] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 04:56:35,296] [INFO] DQC Reference Directory: /var/lib/cwl/stgbefb3aaa-3281-433b-8d03-fdce5b857d52/dqc_reference
[2023-06-17 04:56:37,065] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 04:56:37,066] [INFO] Task started: Prodigal
[2023-06-17 04:56:37,066] [INFO] Running command: gunzip -c /var/lib/cwl/stg54c7a2eb-81dd-4560-b2c1-474a879a46e7/GCA_003151815.1_20120700_P3D_genomic.fna.gz | prodigal -d GCA_003151815.1_20120700_P3D_genomic.fna/cds.fna -a GCA_003151815.1_20120700_P3D_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 04:56:46,495] [INFO] Task succeeded: Prodigal
[2023-06-17 04:56:46,496] [INFO] Task started: HMMsearch
[2023-06-17 04:56:46,496] [INFO] Running command: hmmsearch --tblout GCA_003151815.1_20120700_P3D_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbefb3aaa-3281-433b-8d03-fdce5b857d52/dqc_reference/reference_markers.hmm GCA_003151815.1_20120700_P3D_genomic.fna/protein.faa > /dev/null
[2023-06-17 04:56:46,757] [INFO] Task succeeded: HMMsearch
[2023-06-17 04:56:46,758] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg54c7a2eb-81dd-4560-b2c1-474a879a46e7/GCA_003151815.1_20120700_P3D_genomic.fna.gz]
[2023-06-17 04:56:46,787] [INFO] Query marker FASTA was written to GCA_003151815.1_20120700_P3D_genomic.fna/markers.fasta
[2023-06-17 04:56:46,787] [INFO] Task started: Blastn
[2023-06-17 04:56:46,788] [INFO] Running command: blastn -query GCA_003151815.1_20120700_P3D_genomic.fna/markers.fasta -db /var/lib/cwl/stgbefb3aaa-3281-433b-8d03-fdce5b857d52/dqc_reference/reference_markers.fasta -out GCA_003151815.1_20120700_P3D_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 04:56:47,412] [INFO] Task succeeded: Blastn
[2023-06-17 04:56:47,418] [INFO] Selected 23 target genomes.
[2023-06-17 04:56:47,419] [INFO] Target genome list was writen to GCA_003151815.1_20120700_P3D_genomic.fna/target_genomes.txt
[2023-06-17 04:56:47,428] [INFO] Task started: fastANI
[2023-06-17 04:56:47,428] [INFO] Running command: fastANI --query /var/lib/cwl/stg54c7a2eb-81dd-4560-b2c1-474a879a46e7/GCA_003151815.1_20120700_P3D_genomic.fna.gz --refList GCA_003151815.1_20120700_P3D_genomic.fna/target_genomes.txt --output GCA_003151815.1_20120700_P3D_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 04:57:03,787] [INFO] Task succeeded: fastANI
[2023-06-17 04:57:03,787] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbefb3aaa-3281-433b-8d03-fdce5b857d52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 04:57:03,788] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbefb3aaa-3281-433b-8d03-fdce5b857d52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 04:57:03,795] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 04:57:03,795] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 04:57:03,795] [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
--------------------------------------------------------------------------------
[2023-06-17 04:57:03,798] [INFO] DFAST Taxonomy check result was written to GCA_003151815.1_20120700_P3D_genomic.fna/tc_result.tsv
[2023-06-17 04:57:03,799] [INFO] ===== Taxonomy check completed =====
[2023-06-17 04:57:03,799] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 04:57:03,799] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbefb3aaa-3281-433b-8d03-fdce5b857d52/dqc_reference/checkm_data
[2023-06-17 04:57:03,803] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 04:57:03,836] [INFO] Task started: CheckM
[2023-06-17 04:57:03,836] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003151815.1_20120700_P3D_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003151815.1_20120700_P3D_genomic.fna/checkm_input GCA_003151815.1_20120700_P3D_genomic.fna/checkm_result
[2023-06-17 04:57:36,501] [INFO] Task succeeded: CheckM
[2023-06-17 04:57:36,502] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 04:57:36,523] [INFO] ===== Completeness check finished =====
[2023-06-17 04:57:36,523] [INFO] ===== Start GTDB Search =====
[2023-06-17 04:57:36,524] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003151815.1_20120700_P3D_genomic.fna/markers.fasta)
[2023-06-17 04:57:36,524] [INFO] Task started: Blastn
[2023-06-17 04:57:36,525] [INFO] Running command: blastn -query GCA_003151815.1_20120700_P3D_genomic.fna/markers.fasta -db /var/lib/cwl/stgbefb3aaa-3281-433b-8d03-fdce5b857d52/dqc_reference/reference_markers_gtdb.fasta -out GCA_003151815.1_20120700_P3D_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 04:57:37,324] [INFO] Task succeeded: Blastn
[2023-06-17 04:57:37,330] [INFO] Selected 11 target genomes.
[2023-06-17 04:57:37,330] [INFO] Target genome list was writen to GCA_003151815.1_20120700_P3D_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 04:57:37,340] [INFO] Task started: fastANI
[2023-06-17 04:57:37,340] [INFO] Running command: fastANI --query /var/lib/cwl/stg54c7a2eb-81dd-4560-b2c1-474a879a46e7/GCA_003151815.1_20120700_P3D_genomic.fna.gz --refList GCA_003151815.1_20120700_P3D_genomic.fna/target_genomes_gtdb.txt --output GCA_003151815.1_20120700_P3D_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 04:57:44,422] [INFO] Task succeeded: fastANI
[2023-06-17 04:57:44,441] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 04:57:44,441] [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_003151815.1	s__2-12-FULL-35-15 sp003151815	100.0	809	814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__2-12-FULL-35-15;g__2-12-FULL-35-15	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001769385.1	s__2-12-FULL-35-15 sp001769385	77.7752	203	814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__2-12-FULL-35-15;g__2-12-FULL-35-15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903919535.1	s__2-12-FULL-35-15 sp903919535	77.1135	150	814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__2-12-FULL-35-15;g__2-12-FULL-35-15	95.0	99.81	99.81	0.93	0.93	2	-
GCA_903847205.1	s__2-12-FULL-35-15 sp903847205	77.0737	171	814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__2-12-FULL-35-15;g__2-12-FULL-35-15	95.0	100.00	100.00	0.99	0.99	2	-
GCA_005772895.1	s__2-12-FULL-35-15 sp005772895	76.9597	125	814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__2-12-FULL-35-15;g__2-12-FULL-35-15	95.0	99.94	99.94	0.94	0.94	2	-
GCA_016707685.1	s__JAEUTT01 sp016707685	76.5947	114	814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__2-12-FULL-35-15;g__JAEUTT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903870175.1	s__2-12-FULL-35-15 sp903870175	76.5793	96	814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__2-12-FULL-35-15;g__2-12-FULL-35-15	95.0	99.44	99.36	0.89	0.82	6	-
GCA_016787165.1	s__JAEUTT01 sp016787165	76.284	79	814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__2-12-FULL-35-15;g__JAEUTT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903881065.1	s__2-12-FULL-35-15 sp903881065	76.2713	90	814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__2-12-FULL-35-15;g__2-12-FULL-35-15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013816615.1	s__UBA2475 sp013816615	76.0638	54	814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA2475	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 04:57:44,443] [INFO] GTDB search result was written to GCA_003151815.1_20120700_P3D_genomic.fna/result_gtdb.tsv
[2023-06-17 04:57:44,444] [INFO] ===== GTDB Search completed =====
[2023-06-17 04:57:44,447] [INFO] DFAST_QC result json was written to GCA_003151815.1_20120700_P3D_genomic.fna/dqc_result.json
[2023-06-17 04:57:44,447] [INFO] DFAST_QC completed!
[2023-06-17 04:57:44,447] [INFO] Total running time: 0h1m9s