[2024-01-25 17:49:20,433] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:49:20,434] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:49:20,434] [INFO] DQC Reference Directory: /var/lib/cwl/stgf5a8a8a1-4d07-4f91-ba5d-bc5df2fdaa56/dqc_reference
[2024-01-25 17:49:21,567] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:49:21,568] [INFO] Task started: Prodigal
[2024-01-25 17:49:21,568] [INFO] Running command: gunzip -c /var/lib/cwl/stgfe1f364c-540a-4872-b32d-8db81bfcdfe1/GCF_022012475.1_ASM2201247v1_genomic.fna.gz | prodigal -d GCF_022012475.1_ASM2201247v1_genomic.fna/cds.fna -a GCF_022012475.1_ASM2201247v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:49:40,051] [INFO] Task succeeded: Prodigal
[2024-01-25 17:49:40,051] [INFO] Task started: HMMsearch
[2024-01-25 17:49:40,051] [INFO] Running command: hmmsearch --tblout GCF_022012475.1_ASM2201247v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf5a8a8a1-4d07-4f91-ba5d-bc5df2fdaa56/dqc_reference/reference_markers.hmm GCF_022012475.1_ASM2201247v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:49:40,283] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:49:40,284] [INFO] Found 6/6 markers.
[2024-01-25 17:49:40,322] [INFO] Query marker FASTA was written to GCF_022012475.1_ASM2201247v1_genomic.fna/markers.fasta
[2024-01-25 17:49:40,322] [INFO] Task started: Blastn
[2024-01-25 17:49:40,322] [INFO] Running command: blastn -query GCF_022012475.1_ASM2201247v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5a8a8a1-4d07-4f91-ba5d-bc5df2fdaa56/dqc_reference/reference_markers.fasta -out GCF_022012475.1_ASM2201247v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:49:40,855] [INFO] Task succeeded: Blastn
[2024-01-25 17:49:40,858] [INFO] Selected 17 target genomes.
[2024-01-25 17:49:40,858] [INFO] Target genome list was writen to GCF_022012475.1_ASM2201247v1_genomic.fna/target_genomes.txt
[2024-01-25 17:49:40,867] [INFO] Task started: fastANI
[2024-01-25 17:49:40,867] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe1f364c-540a-4872-b32d-8db81bfcdfe1/GCF_022012475.1_ASM2201247v1_genomic.fna.gz --refList GCF_022012475.1_ASM2201247v1_genomic.fna/target_genomes.txt --output GCF_022012475.1_ASM2201247v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:49:51,067] [INFO] Task succeeded: fastANI
[2024-01-25 17:49:51,067] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf5a8a8a1-4d07-4f91-ba5d-bc5df2fdaa56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:49:51,067] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf5a8a8a1-4d07-4f91-ba5d-bc5df2fdaa56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:49:51,072] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:49:51,072] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:49:51,072] [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
Rhodohalobacter mucosus	strain=8A47	GCA_003150675.1	2079485	2079485	type	True	76.6591	72	1647	95	below_threshold
Rhodohalobacter halophilus	strain=JZ3C29	GCA_001715195.1	1812810	1812810	type	True	76.2687	62	1647	95	below_threshold
Rhodohalobacter barkolensis	strain=15182	GCA_002834295.1	2053187	2053187	type	True	76.1597	80	1647	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:49:51,073] [INFO] DFAST Taxonomy check result was written to GCF_022012475.1_ASM2201247v1_genomic.fna/tc_result.tsv
[2024-01-25 17:49:51,074] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:49:51,074] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:49:51,075] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf5a8a8a1-4d07-4f91-ba5d-bc5df2fdaa56/dqc_reference/checkm_data
[2024-01-25 17:49:51,075] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:49:51,125] [INFO] Task started: CheckM
[2024-01-25 17:49:51,125] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022012475.1_ASM2201247v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022012475.1_ASM2201247v1_genomic.fna/checkm_input GCF_022012475.1_ASM2201247v1_genomic.fna/checkm_result
[2024-01-25 17:50:45,748] [INFO] Task succeeded: CheckM
[2024-01-25 17:50:45,749] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:50:45,765] [INFO] ===== Completeness check finished =====
[2024-01-25 17:50:45,765] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:50:45,766] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022012475.1_ASM2201247v1_genomic.fna/markers.fasta)
[2024-01-25 17:50:45,766] [INFO] Task started: Blastn
[2024-01-25 17:50:45,766] [INFO] Running command: blastn -query GCF_022012475.1_ASM2201247v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5a8a8a1-4d07-4f91-ba5d-bc5df2fdaa56/dqc_reference/reference_markers_gtdb.fasta -out GCF_022012475.1_ASM2201247v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:46,561] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:46,563] [INFO] Selected 24 target genomes.
[2024-01-25 17:50:46,564] [INFO] Target genome list was writen to GCF_022012475.1_ASM2201247v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:50:46,594] [INFO] Task started: fastANI
[2024-01-25 17:50:46,595] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe1f364c-540a-4872-b32d-8db81bfcdfe1/GCF_022012475.1_ASM2201247v1_genomic.fna.gz --refList GCF_022012475.1_ASM2201247v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022012475.1_ASM2201247v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:50:59,115] [INFO] Task succeeded: fastANI
[2024-01-25 17:50:59,122] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:50:59,123] [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_001564065.1	s__Rhodohalobacter sp001564065	76.3565	65	1647	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Rhodohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390325.1	s__SW132 sp003390325	76.3235	78	1647	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__SW132	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001715195.1	s__Rhodohalobacter halophilus	76.2983	61	1647	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Rhodohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002834295.1	s__Rhodohalobacter barkolensis	76.1597	80	1647	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Rhodohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002359315.1	s__UBA2664 sp002359315	76.1477	61	1647	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__UBA2664	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007134085.1	s__UBA2664 sp007134085	76.0563	67	1647	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__UBA2664	95.0	99.68	99.40	0.90	0.85	6	-
GCA_007127745.1	s__UBA2664 sp007127745	76.0369	81	1647	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__UBA2664	95.0	99.25	98.53	0.84	0.77	4	-
GCA_007131725.1	s__UBA2664 sp007131725	75.9598	84	1647	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__UBA2664	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007123985.1	s__UBA2664 sp007123985	75.8632	77	1647	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__UBA2664	95.0	99.06	99.06	0.82	0.82	2	-
GCA_007693295.1	s__QGGB01 sp007693295	75.8535	54	1647	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__QGGB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693395.1	s__UBA2664 sp007693395	75.4864	68	1647	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__UBA2664	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:50:59,124] [INFO] GTDB search result was written to GCF_022012475.1_ASM2201247v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:50:59,124] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:50:59,127] [INFO] DFAST_QC result json was written to GCF_022012475.1_ASM2201247v1_genomic.fna/dqc_result.json
[2024-01-25 17:50:59,127] [INFO] DFAST_QC completed!
[2024-01-25 17:50:59,127] [INFO] Total running time: 0h1m39s