[2023-06-19 08:45:32,370] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:45:32,374] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:45:32,374] [INFO] DQC Reference Directory: /var/lib/cwl/stg43e9dafe-6dc1-491d-985f-196ecb29f832/dqc_reference
[2023-06-19 08:45:35,362] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:45:35,363] [INFO] Task started: Prodigal
[2023-06-19 08:45:35,364] [INFO] Running command: gunzip -c /var/lib/cwl/stg6065362c-7589-46f7-966a-c293de1329f6/GCA_018694835.1_ASM1869483v1_genomic.fna.gz | prodigal -d GCA_018694835.1_ASM1869483v1_genomic.fna/cds.fna -a GCA_018694835.1_ASM1869483v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:45:44,293] [INFO] Task succeeded: Prodigal
[2023-06-19 08:45:44,294] [INFO] Task started: HMMsearch
[2023-06-19 08:45:44,294] [INFO] Running command: hmmsearch --tblout GCA_018694835.1_ASM1869483v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43e9dafe-6dc1-491d-985f-196ecb29f832/dqc_reference/reference_markers.hmm GCA_018694835.1_ASM1869483v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:45:44,576] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:45:44,578] [INFO] Found 6/6 markers.
[2023-06-19 08:45:44,612] [INFO] Query marker FASTA was written to GCA_018694835.1_ASM1869483v1_genomic.fna/markers.fasta
[2023-06-19 08:45:44,612] [INFO] Task started: Blastn
[2023-06-19 08:45:44,612] [INFO] Running command: blastn -query GCA_018694835.1_ASM1869483v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43e9dafe-6dc1-491d-985f-196ecb29f832/dqc_reference/reference_markers.fasta -out GCA_018694835.1_ASM1869483v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:45:45,226] [INFO] Task succeeded: Blastn
[2023-06-19 08:45:45,235] [INFO] Selected 20 target genomes.
[2023-06-19 08:45:45,236] [INFO] Target genome list was writen to GCA_018694835.1_ASM1869483v1_genomic.fna/target_genomes.txt
[2023-06-19 08:45:45,238] [INFO] Task started: fastANI
[2023-06-19 08:45:45,238] [INFO] Running command: fastANI --query /var/lib/cwl/stg6065362c-7589-46f7-966a-c293de1329f6/GCA_018694835.1_ASM1869483v1_genomic.fna.gz --refList GCA_018694835.1_ASM1869483v1_genomic.fna/target_genomes.txt --output GCA_018694835.1_ASM1869483v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:45:59,243] [INFO] Task succeeded: fastANI
[2023-06-19 08:45:59,243] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43e9dafe-6dc1-491d-985f-196ecb29f832/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:45:59,244] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43e9dafe-6dc1-491d-985f-196ecb29f832/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:45:59,246] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:45:59,246] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 08:45:59,247] [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
--------------------------------------------------------------------------------
[2023-06-19 08:45:59,258] [INFO] DFAST Taxonomy check result was written to GCA_018694835.1_ASM1869483v1_genomic.fna/tc_result.tsv
[2023-06-19 08:45:59,259] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:45:59,260] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:45:59,260] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43e9dafe-6dc1-491d-985f-196ecb29f832/dqc_reference/checkm_data
[2023-06-19 08:45:59,264] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:45:59,294] [INFO] Task started: CheckM
[2023-06-19 08:45:59,294] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018694835.1_ASM1869483v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018694835.1_ASM1869483v1_genomic.fna/checkm_input GCA_018694835.1_ASM1869483v1_genomic.fna/checkm_result
[2023-06-19 08:46:30,584] [INFO] Task succeeded: CheckM
[2023-06-19 08:46:30,586] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:46:30,606] [INFO] ===== Completeness check finished =====
[2023-06-19 08:46:30,606] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:46:30,607] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018694835.1_ASM1869483v1_genomic.fna/markers.fasta)
[2023-06-19 08:46:30,607] [INFO] Task started: Blastn
[2023-06-19 08:46:30,607] [INFO] Running command: blastn -query GCA_018694835.1_ASM1869483v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43e9dafe-6dc1-491d-985f-196ecb29f832/dqc_reference/reference_markers_gtdb.fasta -out GCA_018694835.1_ASM1869483v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:46:31,430] [INFO] Task succeeded: Blastn
[2023-06-19 08:46:31,437] [INFO] Selected 8 target genomes.
[2023-06-19 08:46:31,438] [INFO] Target genome list was writen to GCA_018694835.1_ASM1869483v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:46:31,439] [INFO] Task started: fastANI
[2023-06-19 08:46:31,439] [INFO] Running command: fastANI --query /var/lib/cwl/stg6065362c-7589-46f7-966a-c293de1329f6/GCA_018694835.1_ASM1869483v1_genomic.fna.gz --refList GCA_018694835.1_ASM1869483v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018694835.1_ASM1869483v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:46:36,717] [INFO] Task succeeded: fastANI
[2023-06-19 08:46:36,729] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 08:46:36,729] [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_018694835.1	s__QNYK01 sp018694835	100.0	953	962	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA1146;f__UBA1146;g__QNYK01	95.0	99.80	99.78	0.93	0.92	8	conclusive
GCA_012960845.1	s__QNYK01 sp012960845	94.4799	847	962	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA1146;f__UBA1146;g__QNYK01	95.0	99.73	99.73	0.93	0.93	2	-
GCA_014240375.1	s__QNYK01 sp014240375	93.3037	918	962	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA1146;f__UBA1146;g__QNYK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003973385.1	s__QNYK01 sp003973385	79.5523	382	962	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA1146;f__UBA1146;g__QNYK01	95.0	99.67	99.67	0.93	0.93	2	-
GCA_002711105.1	s__UBA1146 sp002711105	77.9309	215	962	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA1146;f__UBA1146;g__UBA1146	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911165.1	s__UBA12191 sp013911165	76.846	84	962	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA1146;f__UBA1146;g__UBA12191	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012269595.1	s__UBA12191 sp012269595	76.8255	97	962	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA1146;f__UBA1146;g__UBA12191	95.0	99.68	99.68	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-06-19 08:46:36,733] [INFO] GTDB search result was written to GCA_018694835.1_ASM1869483v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:46:36,733] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:46:36,736] [INFO] DFAST_QC result json was written to GCA_018694835.1_ASM1869483v1_genomic.fna/dqc_result.json
[2023-06-19 08:46:36,737] [INFO] DFAST_QC completed!
[2023-06-19 08:46:36,737] [INFO] Total running time: 0h1m4s