[2023-06-29 07:11:24,363] [INFO] DFAST_QC pipeline started.
[2023-06-29 07:11:24,365] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 07:11:24,365] [INFO] DQC Reference Directory: /var/lib/cwl/stgfec49caf-878f-40e8-a9e2-532b39eab4bb/dqc_reference
[2023-06-29 07:11:25,525] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 07:11:25,525] [INFO] Task started: Prodigal
[2023-06-29 07:11:25,526] [INFO] Running command: gunzip -c /var/lib/cwl/stgdde9ded4-7529-42e5-a0eb-31438533d717/GCA_005883755.1_ASM588375v1_genomic.fna.gz | prodigal -d GCA_005883755.1_ASM588375v1_genomic.fna/cds.fna -a GCA_005883755.1_ASM588375v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 07:11:32,508] [INFO] Task succeeded: Prodigal
[2023-06-29 07:11:32,508] [INFO] Task started: HMMsearch
[2023-06-29 07:11:32,509] [INFO] Running command: hmmsearch --tblout GCA_005883755.1_ASM588375v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfec49caf-878f-40e8-a9e2-532b39eab4bb/dqc_reference/reference_markers.hmm GCA_005883755.1_ASM588375v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 07:11:32,700] [INFO] Task succeeded: HMMsearch
[2023-06-29 07:11:32,702] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgdde9ded4-7529-42e5-a0eb-31438533d717/GCA_005883755.1_ASM588375v1_genomic.fna.gz]
[2023-06-29 07:11:32,721] [INFO] Query marker FASTA was written to GCA_005883755.1_ASM588375v1_genomic.fna/markers.fasta
[2023-06-29 07:11:32,722] [INFO] Task started: Blastn
[2023-06-29 07:11:32,722] [INFO] Running command: blastn -query GCA_005883755.1_ASM588375v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfec49caf-878f-40e8-a9e2-532b39eab4bb/dqc_reference/reference_markers.fasta -out GCA_005883755.1_ASM588375v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 07:11:33,214] [INFO] Task succeeded: Blastn
[2023-06-29 07:11:33,218] [INFO] Selected 0 target genomes.
[2023-06-29 07:11:33,219] [INFO] Target genome list was writen to GCA_005883755.1_ASM588375v1_genomic.fna/target_genomes.txt
[2023-06-29 07:11:33,219] [ERROR] File is empty. [GCA_005883755.1_ASM588375v1_genomic.fna/target_genomes.txt]
[2023-06-29 07:11:33,220] [ERROR] Task failed. No target genome found.
[2023-06-29 07:11:33,220] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 07:11:33,220] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfec49caf-878f-40e8-a9e2-532b39eab4bb/dqc_reference/checkm_data
[2023-06-29 07:11:33,224] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 07:11:33,247] [INFO] Task started: CheckM
[2023-06-29 07:11:33,247] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_005883755.1_ASM588375v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_005883755.1_ASM588375v1_genomic.fna/checkm_input GCA_005883755.1_ASM588375v1_genomic.fna/checkm_result
[2023-06-29 07:11:59,588] [INFO] Task succeeded: CheckM
[2023-06-29 07:11:59,589] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.98%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 07:11:59,612] [INFO] ===== Completeness check finished =====
[2023-06-29 07:11:59,612] [INFO] ===== Start GTDB Search =====
[2023-06-29 07:11:59,613] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_005883755.1_ASM588375v1_genomic.fna/markers.fasta)
[2023-06-29 07:11:59,613] [INFO] Task started: Blastn
[2023-06-29 07:11:59,613] [INFO] Running command: blastn -query GCA_005883755.1_ASM588375v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfec49caf-878f-40e8-a9e2-532b39eab4bb/dqc_reference/reference_markers_gtdb.fasta -out GCA_005883755.1_ASM588375v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 07:12:00,137] [INFO] Task succeeded: Blastn
[2023-06-29 07:12:00,141] [INFO] Selected 5 target genomes.
[2023-06-29 07:12:00,142] [INFO] Target genome list was writen to GCA_005883755.1_ASM588375v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 07:12:00,208] [INFO] Task started: fastANI
[2023-06-29 07:12:00,209] [INFO] Running command: fastANI --query /var/lib/cwl/stgdde9ded4-7529-42e5-a0eb-31438533d717/GCA_005883755.1_ASM588375v1_genomic.fna.gz --refList GCA_005883755.1_ASM588375v1_genomic.fna/target_genomes_gtdb.txt --output GCA_005883755.1_ASM588375v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 07:12:01,817] [INFO] Task succeeded: fastANI
[2023-06-29 07:12:01,826] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 07:12:01,827] [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_001915065.1	s__40CM-2-53-6 sp001915065	99.396	399	468	d__Archaea;p__Thermoproteota;c__Bathyarchaeia;o__40CM-2-53-6;f__40CM-2-53-6;g__40CM-2-53-6	95.0	99.61	99.44	0.84	0.76	4	conclusive
GCA_005882905.1	s__40CM-2-53-6 sp005882905	92.9094	297	468	d__Archaea;p__Thermoproteota;c__Bathyarchaeia;o__40CM-2-53-6;f__40CM-2-53-6;g__40CM-2-53-6	95.0	97.53	96.88	0.75	0.75	3	-
GCA_005888635.1	s__40CM-2-53-6 sp005888635	78.216	123	468	d__Archaea;p__Thermoproteota;c__Bathyarchaeia;o__40CM-2-53-6;f__40CM-2-53-6;g__40CM-2-53-6	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002495485.1	s__40CM-2-53-6 sp002495485	77.6678	108	468	d__Archaea;p__Thermoproteota;c__Bathyarchaeia;o__40CM-2-53-6;f__40CM-2-53-6;g__40CM-2-53-6	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 07:12:01,829] [INFO] GTDB search result was written to GCA_005883755.1_ASM588375v1_genomic.fna/result_gtdb.tsv
[2023-06-29 07:12:01,829] [INFO] ===== GTDB Search completed =====
[2023-06-29 07:12:01,831] [INFO] DFAST_QC result json was written to GCA_005883755.1_ASM588375v1_genomic.fna/dqc_result.json
[2023-06-29 07:12:01,832] [INFO] DFAST_QC completed!
[2023-06-29 07:12:01,832] [INFO] Total running time: 0h0m37s