[2023-06-19 06:19:08,499] [INFO] DFAST_QC pipeline started.
[2023-06-19 06:19:08,501] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 06:19:08,501] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b5fc9dd-8fc1-4442-800b-3a0cf9a8fd4e/dqc_reference
[2023-06-19 06:19:09,788] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 06:19:09,789] [INFO] Task started: Prodigal
[2023-06-19 06:19:09,790] [INFO] Running command: gunzip -c /var/lib/cwl/stg00cc789b-eff1-43a5-bb6b-4c4318e9f034/GCA_013378385.1_ASM1337838v1_genomic.fna.gz | prodigal -d GCA_013378385.1_ASM1337838v1_genomic.fna/cds.fna -a GCA_013378385.1_ASM1337838v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 06:19:11,502] [INFO] Task succeeded: Prodigal
[2023-06-19 06:19:11,502] [INFO] Task started: HMMsearch
[2023-06-19 06:19:11,502] [INFO] Running command: hmmsearch --tblout GCA_013378385.1_ASM1337838v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b5fc9dd-8fc1-4442-800b-3a0cf9a8fd4e/dqc_reference/reference_markers.hmm GCA_013378385.1_ASM1337838v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 06:19:11,696] [INFO] Task succeeded: HMMsearch
[2023-06-19 06:19:11,699] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg00cc789b-eff1-43a5-bb6b-4c4318e9f034/GCA_013378385.1_ASM1337838v1_genomic.fna.gz]
[2023-06-19 06:19:11,720] [INFO] Query marker FASTA was written to GCA_013378385.1_ASM1337838v1_genomic.fna/markers.fasta
[2023-06-19 06:19:11,720] [INFO] Task started: Blastn
[2023-06-19 06:19:11,720] [INFO] Running command: blastn -query GCA_013378385.1_ASM1337838v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b5fc9dd-8fc1-4442-800b-3a0cf9a8fd4e/dqc_reference/reference_markers.fasta -out GCA_013378385.1_ASM1337838v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 06:19:13,687] [INFO] Task succeeded: Blastn
[2023-06-19 06:19:13,692] [INFO] Selected 0 target genomes.
[2023-06-19 06:19:13,692] [INFO] Target genome list was writen to GCA_013378385.1_ASM1337838v1_genomic.fna/target_genomes.txt
[2023-06-19 06:19:13,693] [ERROR] File is empty. [GCA_013378385.1_ASM1337838v1_genomic.fna/target_genomes.txt]
[2023-06-19 06:19:13,693] [ERROR] Task failed. No target genome found.
[2023-06-19 06:19:13,693] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 06:19:13,694] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b5fc9dd-8fc1-4442-800b-3a0cf9a8fd4e/dqc_reference/checkm_data
[2023-06-19 06:19:13,698] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 06:19:13,714] [INFO] Task started: CheckM
[2023-06-19 06:19:13,715] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013378385.1_ASM1337838v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013378385.1_ASM1337838v1_genomic.fna/checkm_input GCA_013378385.1_ASM1337838v1_genomic.fna/checkm_result
[2023-06-19 06:19:30,024] [INFO] Task succeeded: CheckM
[2023-06-19 06:19:30,026] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 06:19:30,055] [INFO] ===== Completeness check finished =====
[2023-06-19 06:19:30,056] [INFO] ===== Start GTDB Search =====
[2023-06-19 06:19:30,056] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013378385.1_ASM1337838v1_genomic.fna/markers.fasta)
[2023-06-19 06:19:30,057] [INFO] Task started: Blastn
[2023-06-19 06:19:30,057] [INFO] Running command: blastn -query GCA_013378385.1_ASM1337838v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b5fc9dd-8fc1-4442-800b-3a0cf9a8fd4e/dqc_reference/reference_markers_gtdb.fasta -out GCA_013378385.1_ASM1337838v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 06:19:30,608] [INFO] Task succeeded: Blastn
[2023-06-19 06:19:30,614] [INFO] Selected 5 target genomes.
[2023-06-19 06:19:30,615] [INFO] Target genome list was writen to GCA_013378385.1_ASM1337838v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 06:19:30,622] [INFO] Task started: fastANI
[2023-06-19 06:19:30,622] [INFO] Running command: fastANI --query /var/lib/cwl/stg00cc789b-eff1-43a5-bb6b-4c4318e9f034/GCA_013378385.1_ASM1337838v1_genomic.fna.gz --refList GCA_013378385.1_ASM1337838v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013378385.1_ASM1337838v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 06:19:31,750] [INFO] Task succeeded: fastANI
[2023-06-19 06:19:31,759] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 06:19:31,759] [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_013378385.1	s__UBA57 sp013378385	100.0	280	284	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__UBA57;g__UBA57	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013306035.1	s__UBA57 sp002494565	94.7038	232	284	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__UBA57;g__UBA57	95.0	98.92	96.91	0.92	0.82	6	-
GCA_002693165.1	s__UBA57 sp002693165	83.0954	115	284	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__UBA57;g__UBA57	95.0	98.59	98.59	0.69	0.69	2	-
GCA_002495905.1	s__UBA57 sp002495905	81.8198	201	284	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__UBA57;g__UBA57	95.0	98.98	98.92	0.81	0.77	4	-
--------------------------------------------------------------------------------
[2023-06-19 06:19:31,762] [INFO] GTDB search result was written to GCA_013378385.1_ASM1337838v1_genomic.fna/result_gtdb.tsv
[2023-06-19 06:19:31,762] [INFO] ===== GTDB Search completed =====
[2023-06-19 06:19:31,766] [INFO] DFAST_QC result json was written to GCA_013378385.1_ASM1337838v1_genomic.fna/dqc_result.json
[2023-06-19 06:19:31,767] [INFO] DFAST_QC completed!
[2023-06-19 06:19:31,767] [INFO] Total running time: 0h0m23s