[2023-06-29 00:46:52,935] [INFO] DFAST_QC pipeline started.
[2023-06-29 00:46:52,937] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 00:46:52,937] [INFO] DQC Reference Directory: /var/lib/cwl/stg5019aade-3ee3-4804-944b-0aaebd37c698/dqc_reference
[2023-06-29 00:46:54,287] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 00:46:54,288] [INFO] Task started: Prodigal
[2023-06-29 00:46:54,288] [INFO] Running command: gunzip -c /var/lib/cwl/stgbaf898f4-7a70-4f81-8ae9-8ff4eb3e0696/GCA_015522645.1_ASM1552264v1_genomic.fna.gz | prodigal -d GCA_015522645.1_ASM1552264v1_genomic.fna/cds.fna -a GCA_015522645.1_ASM1552264v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 00:46:57,256] [INFO] Task succeeded: Prodigal
[2023-06-29 00:46:57,256] [INFO] Task started: HMMsearch
[2023-06-29 00:46:57,256] [INFO] Running command: hmmsearch --tblout GCA_015522645.1_ASM1552264v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5019aade-3ee3-4804-944b-0aaebd37c698/dqc_reference/reference_markers.hmm GCA_015522645.1_ASM1552264v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 00:46:57,487] [INFO] Task succeeded: HMMsearch
[2023-06-29 00:46:57,488] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgbaf898f4-7a70-4f81-8ae9-8ff4eb3e0696/GCA_015522645.1_ASM1552264v1_genomic.fna.gz]
[2023-06-29 00:46:57,510] [INFO] Query marker FASTA was written to GCA_015522645.1_ASM1552264v1_genomic.fna/markers.fasta
[2023-06-29 00:46:57,510] [INFO] Task started: Blastn
[2023-06-29 00:46:57,510] [INFO] Running command: blastn -query GCA_015522645.1_ASM1552264v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5019aade-3ee3-4804-944b-0aaebd37c698/dqc_reference/reference_markers.fasta -out GCA_015522645.1_ASM1552264v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:46:58,014] [INFO] Task succeeded: Blastn
[2023-06-29 00:46:58,018] [INFO] Selected 0 target genomes.
[2023-06-29 00:46:58,018] [INFO] Target genome list was writen to GCA_015522645.1_ASM1552264v1_genomic.fna/target_genomes.txt
[2023-06-29 00:46:58,018] [ERROR] File is empty. [GCA_015522645.1_ASM1552264v1_genomic.fna/target_genomes.txt]
[2023-06-29 00:46:58,019] [ERROR] Task failed. No target genome found.
[2023-06-29 00:46:58,019] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 00:46:58,019] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5019aade-3ee3-4804-944b-0aaebd37c698/dqc_reference/checkm_data
[2023-06-29 00:46:58,022] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 00:46:58,041] [INFO] Task started: CheckM
[2023-06-29 00:46:58,042] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015522645.1_ASM1552264v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015522645.1_ASM1552264v1_genomic.fna/checkm_input GCA_015522645.1_ASM1552264v1_genomic.fna/checkm_result
[2023-06-29 00:47:15,172] [INFO] Task succeeded: CheckM
[2023-06-29 00:47:15,174] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 00:47:15,200] [INFO] ===== Completeness check finished =====
[2023-06-29 00:47:15,201] [INFO] ===== Start GTDB Search =====
[2023-06-29 00:47:15,201] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015522645.1_ASM1552264v1_genomic.fna/markers.fasta)
[2023-06-29 00:47:15,201] [INFO] Task started: Blastn
[2023-06-29 00:47:15,202] [INFO] Running command: blastn -query GCA_015522645.1_ASM1552264v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5019aade-3ee3-4804-944b-0aaebd37c698/dqc_reference/reference_markers_gtdb.fasta -out GCA_015522645.1_ASM1552264v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:47:15,671] [INFO] Task succeeded: Blastn
[2023-06-29 00:47:15,676] [INFO] Selected 2 target genomes.
[2023-06-29 00:47:15,676] [INFO] Target genome list was writen to GCA_015522645.1_ASM1552264v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 00:47:15,764] [INFO] Task started: fastANI
[2023-06-29 00:47:15,765] [INFO] Running command: fastANI --query /var/lib/cwl/stgbaf898f4-7a70-4f81-8ae9-8ff4eb3e0696/GCA_015522645.1_ASM1552264v1_genomic.fna.gz --refList GCA_015522645.1_ASM1552264v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015522645.1_ASM1552264v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 00:47:16,634] [INFO] Task succeeded: fastANI
[2023-06-29 00:47:16,638] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 00:47:16,638] [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_015522645.1	s__WALW01 sp015522645	100.0	475	478	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Acidilobaceae;g__WALW01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015522635.1	s__WALW01 sp015522635	79.3851	215	478	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Acidilobaceae;g__WALW01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 00:47:16,641] [INFO] GTDB search result was written to GCA_015522645.1_ASM1552264v1_genomic.fna/result_gtdb.tsv
[2023-06-29 00:47:16,642] [INFO] ===== GTDB Search completed =====
[2023-06-29 00:47:16,649] [INFO] DFAST_QC result json was written to GCA_015522645.1_ASM1552264v1_genomic.fna/dqc_result.json
[2023-06-29 00:47:16,650] [INFO] DFAST_QC completed!
[2023-06-29 00:47:16,650] [INFO] Total running time: 0h0m24s