[2023-06-27 01:56:42,882] [INFO] DFAST_QC pipeline started.
[2023-06-27 01:56:42,885] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 01:56:42,885] [INFO] DQC Reference Directory: /var/lib/cwl/stgd65a536c-02b5-49b2-bff9-84cf977bd251/dqc_reference
[2023-06-27 01:56:45,107] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 01:56:45,108] [INFO] Task started: Prodigal
[2023-06-27 01:56:45,108] [INFO] Running command: gunzip -c /var/lib/cwl/stg86675e3a-294f-46c3-a382-cd2c3c8d1ef7/GCA_027491815.1_ASM2749181v1_genomic.fna.gz | prodigal -d GCA_027491815.1_ASM2749181v1_genomic.fna/cds.fna -a GCA_027491815.1_ASM2749181v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 01:56:46,857] [INFO] Task succeeded: Prodigal
[2023-06-27 01:56:46,858] [INFO] Task started: HMMsearch
[2023-06-27 01:56:46,858] [INFO] Running command: hmmsearch --tblout GCA_027491815.1_ASM2749181v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd65a536c-02b5-49b2-bff9-84cf977bd251/dqc_reference/reference_markers.hmm GCA_027491815.1_ASM2749181v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 01:56:47,027] [INFO] Task succeeded: HMMsearch
[2023-06-27 01:56:47,029] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg86675e3a-294f-46c3-a382-cd2c3c8d1ef7/GCA_027491815.1_ASM2749181v1_genomic.fna.gz]
[2023-06-27 01:56:47,049] [INFO] Query marker FASTA was written to GCA_027491815.1_ASM2749181v1_genomic.fna/markers.fasta
[2023-06-27 01:56:47,049] [INFO] Task started: Blastn
[2023-06-27 01:56:47,049] [INFO] Running command: blastn -query GCA_027491815.1_ASM2749181v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd65a536c-02b5-49b2-bff9-84cf977bd251/dqc_reference/reference_markers.fasta -out GCA_027491815.1_ASM2749181v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 01:56:48,691] [INFO] Task succeeded: Blastn
[2023-06-27 01:56:48,695] [INFO] Selected 0 target genomes.
[2023-06-27 01:56:48,696] [INFO] Target genome list was writen to GCA_027491815.1_ASM2749181v1_genomic.fna/target_genomes.txt
[2023-06-27 01:56:48,696] [ERROR] File is empty. [GCA_027491815.1_ASM2749181v1_genomic.fna/target_genomes.txt]
[2023-06-27 01:56:48,696] [ERROR] Task failed. No target genome found.
[2023-06-27 01:56:48,696] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 01:56:48,696] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd65a536c-02b5-49b2-bff9-84cf977bd251/dqc_reference/checkm_data
[2023-06-27 01:56:48,700] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 01:56:48,715] [INFO] Task started: CheckM
[2023-06-27 01:56:48,715] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027491815.1_ASM2749181v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027491815.1_ASM2749181v1_genomic.fna/checkm_input GCA_027491815.1_ASM2749181v1_genomic.fna/checkm_result
[2023-06-27 01:57:03,961] [INFO] Task succeeded: CheckM
[2023-06-27 01:57:03,962] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 01:57:03,989] [INFO] ===== Completeness check finished =====
[2023-06-27 01:57:03,990] [INFO] ===== Start GTDB Search =====
[2023-06-27 01:57:03,990] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027491815.1_ASM2749181v1_genomic.fna/markers.fasta)
[2023-06-27 01:57:03,990] [INFO] Task started: Blastn
[2023-06-27 01:57:03,991] [INFO] Running command: blastn -query GCA_027491815.1_ASM2749181v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd65a536c-02b5-49b2-bff9-84cf977bd251/dqc_reference/reference_markers_gtdb.fasta -out GCA_027491815.1_ASM2749181v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 01:57:04,489] [INFO] Task succeeded: Blastn
[2023-06-27 01:57:04,493] [INFO] Selected 1 target genomes.
[2023-06-27 01:57:04,493] [INFO] Target genome list was writen to GCA_027491815.1_ASM2749181v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 01:57:04,502] [INFO] Task started: fastANI
[2023-06-27 01:57:04,502] [INFO] Running command: fastANI --query /var/lib/cwl/stg86675e3a-294f-46c3-a382-cd2c3c8d1ef7/GCA_027491815.1_ASM2749181v1_genomic.fna.gz --refList GCA_027491815.1_ASM2749181v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027491815.1_ASM2749181v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 01:57:04,791] [INFO] Task succeeded: fastANI
[2023-06-27 01:57:04,796] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 01:57:04,796] [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_015522685.1	s__WALU01 sp015522685	78.1507	85	285	d__Archaea;p__Thermoproteota;c__Korarchaeia;o__Korarchaeales;f__Korarchaeaceae;g__WALU01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 01:57:04,799] [INFO] GTDB search result was written to GCA_027491815.1_ASM2749181v1_genomic.fna/result_gtdb.tsv
[2023-06-27 01:57:04,800] [INFO] ===== GTDB Search completed =====
[2023-06-27 01:57:04,820] [INFO] DFAST_QC result json was written to GCA_027491815.1_ASM2749181v1_genomic.fna/dqc_result.json
[2023-06-27 01:57:04,820] [INFO] DFAST_QC completed!
[2023-06-27 01:57:04,821] [INFO] Total running time: 0h0m22s