[2023-06-13 18:25:47,643] [INFO] DFAST_QC pipeline started.
[2023-06-13 18:25:47,645] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 18:25:47,645] [INFO] DQC Reference Directory: /var/lib/cwl/stg22cd9489-7b59-47a7-9b1c-1bc50e558bf8/dqc_reference
[2023-06-13 18:25:48,894] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 18:25:48,894] [INFO] Task started: Prodigal
[2023-06-13 18:25:48,895] [INFO] Running command: gunzip -c /var/lib/cwl/stg76ecd86b-93df-42a1-bd5e-8a82c77307ea/GCA_003332035.1_ASM333203v1_genomic.fna.gz | prodigal -d GCA_003332035.1_ASM333203v1_genomic.fna/cds.fna -a GCA_003332035.1_ASM333203v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 18:25:51,314] [INFO] Task succeeded: Prodigal
[2023-06-13 18:25:51,314] [INFO] Task started: HMMsearch
[2023-06-13 18:25:51,314] [INFO] Running command: hmmsearch --tblout GCA_003332035.1_ASM333203v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg22cd9489-7b59-47a7-9b1c-1bc50e558bf8/dqc_reference/reference_markers.hmm GCA_003332035.1_ASM333203v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 18:25:51,491] [INFO] Task succeeded: HMMsearch
[2023-06-13 18:25:51,492] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg76ecd86b-93df-42a1-bd5e-8a82c77307ea/GCA_003332035.1_ASM333203v1_genomic.fna.gz]
[2023-06-13 18:25:51,512] [INFO] Query marker FASTA was written to GCA_003332035.1_ASM333203v1_genomic.fna/markers.fasta
[2023-06-13 18:25:51,512] [INFO] Task started: Blastn
[2023-06-13 18:25:51,512] [INFO] Running command: blastn -query GCA_003332035.1_ASM333203v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22cd9489-7b59-47a7-9b1c-1bc50e558bf8/dqc_reference/reference_markers.fasta -out GCA_003332035.1_ASM333203v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 18:25:51,990] [INFO] Task succeeded: Blastn
[2023-06-13 18:25:51,994] [INFO] Selected 11 target genomes.
[2023-06-13 18:25:51,994] [INFO] Target genome list was writen to GCA_003332035.1_ASM333203v1_genomic.fna/target_genomes.txt
[2023-06-13 18:25:51,998] [INFO] Task started: fastANI
[2023-06-13 18:25:51,998] [INFO] Running command: fastANI --query /var/lib/cwl/stg76ecd86b-93df-42a1-bd5e-8a82c77307ea/GCA_003332035.1_ASM333203v1_genomic.fna.gz --refList GCA_003332035.1_ASM333203v1_genomic.fna/target_genomes.txt --output GCA_003332035.1_ASM333203v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 18:25:57,953] [INFO] Task succeeded: fastANI
[2023-06-13 18:25:57,954] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg22cd9489-7b59-47a7-9b1c-1bc50e558bf8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 18:25:57,954] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg22cd9489-7b59-47a7-9b1c-1bc50e558bf8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 18:25:57,955] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 18:25:57,955] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 18:25:57,955] [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 18:25:57,957] [INFO] DFAST Taxonomy check result was written to GCA_003332035.1_ASM333203v1_genomic.fna/tc_result.tsv
[2023-06-13 18:25:57,958] [INFO] ===== Taxonomy check completed =====
[2023-06-13 18:25:57,958] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 18:25:57,958] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg22cd9489-7b59-47a7-9b1c-1bc50e558bf8/dqc_reference/checkm_data
[2023-06-13 18:25:57,961] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 18:25:57,978] [INFO] Task started: CheckM
[2023-06-13 18:25:57,978] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003332035.1_ASM333203v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003332035.1_ASM333203v1_genomic.fna/checkm_input GCA_003332035.1_ASM333203v1_genomic.fna/checkm_result
[2023-06-13 18:26:12,059] [INFO] Task succeeded: CheckM
[2023-06-13 18:26:12,060] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.08%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 18:26:12,088] [INFO] ===== Completeness check finished =====
[2023-06-13 18:26:12,089] [INFO] ===== Start GTDB Search =====
[2023-06-13 18:26:12,089] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003332035.1_ASM333203v1_genomic.fna/markers.fasta)
[2023-06-13 18:26:12,089] [INFO] Task started: Blastn
[2023-06-13 18:26:12,089] [INFO] Running command: blastn -query GCA_003332035.1_ASM333203v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22cd9489-7b59-47a7-9b1c-1bc50e558bf8/dqc_reference/reference_markers_gtdb.fasta -out GCA_003332035.1_ASM333203v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 18:26:12,709] [INFO] Task succeeded: Blastn
[2023-06-13 18:26:12,713] [INFO] Selected 9 target genomes.
[2023-06-13 18:26:12,713] [INFO] Target genome list was writen to GCA_003332035.1_ASM333203v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 18:26:12,719] [INFO] Task started: fastANI
[2023-06-13 18:26:12,719] [INFO] Running command: fastANI --query /var/lib/cwl/stg76ecd86b-93df-42a1-bd5e-8a82c77307ea/GCA_003332035.1_ASM333203v1_genomic.fna.gz --refList GCA_003332035.1_ASM333203v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003332035.1_ASM333203v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 18:26:16,089] [INFO] Task succeeded: fastANI
[2023-06-13 18:26:16,095] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 18:26:16,095] [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_003332035.1	s__MED-G52 sp003332035	100.0	439	443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MED-G52	95.0	96.52	96.52	0.74	0.74	2	conclusive
GCA_902554705.1	s__MED-G52 sp902554705	84.7439	262	443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MED-G52	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902573175.1	s__MED-G52 sp902573175	84.1013	215	443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MED-G52	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902606585.1	s__MED-G52 sp902606585	83.7371	245	443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MED-G52	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902543185.1	s__MED-G52 sp902543185	83.5359	324	443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MED-G52	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012270125.1	s__MED-G52 sp001627375	79.1207	288	443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MED-G52	95.0	97.90	95.50	0.79	0.63	16	-
--------------------------------------------------------------------------------
[2023-06-13 18:26:16,099] [INFO] GTDB search result was written to GCA_003332035.1_ASM333203v1_genomic.fna/result_gtdb.tsv
[2023-06-13 18:26:16,100] [INFO] ===== GTDB Search completed =====
[2023-06-13 18:26:16,103] [INFO] DFAST_QC result json was written to GCA_003332035.1_ASM333203v1_genomic.fna/dqc_result.json
[2023-06-13 18:26:16,103] [INFO] DFAST_QC completed!
[2023-06-13 18:26:16,103] [INFO] Total running time: 0h0m28s