[2023-06-13 05:12:33,873] [INFO] DFAST_QC pipeline started.
[2023-06-13 05:12:33,875] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 05:12:33,876] [INFO] DQC Reference Directory: /var/lib/cwl/stgca086c8a-4b3c-45db-b62f-735e934fa400/dqc_reference
[2023-06-13 05:12:35,100] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 05:12:35,101] [INFO] Task started: Prodigal
[2023-06-13 05:12:35,101] [INFO] Running command: gunzip -c /var/lib/cwl/stg3b569d0f-1160-429e-b06d-ad1c709844ad/GCA_022564175.1_ASM2256417v1_genomic.fna.gz | prodigal -d GCA_022564175.1_ASM2256417v1_genomic.fna/cds.fna -a GCA_022564175.1_ASM2256417v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 05:12:38,266] [INFO] Task succeeded: Prodigal
[2023-06-13 05:12:38,266] [INFO] Task started: HMMsearch
[2023-06-13 05:12:38,266] [INFO] Running command: hmmsearch --tblout GCA_022564175.1_ASM2256417v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca086c8a-4b3c-45db-b62f-735e934fa400/dqc_reference/reference_markers.hmm GCA_022564175.1_ASM2256417v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 05:12:38,498] [INFO] Task succeeded: HMMsearch
[2023-06-13 05:12:38,500] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg3b569d0f-1160-429e-b06d-ad1c709844ad/GCA_022564175.1_ASM2256417v1_genomic.fna.gz]
[2023-06-13 05:12:38,516] [INFO] Query marker FASTA was written to GCA_022564175.1_ASM2256417v1_genomic.fna/markers.fasta
[2023-06-13 05:12:38,516] [INFO] Task started: Blastn
[2023-06-13 05:12:38,517] [INFO] Running command: blastn -query GCA_022564175.1_ASM2256417v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca086c8a-4b3c-45db-b62f-735e934fa400/dqc_reference/reference_markers.fasta -out GCA_022564175.1_ASM2256417v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 05:12:40,682] [INFO] Task succeeded: Blastn
[2023-06-13 05:12:40,686] [INFO] Selected 0 target genomes.
[2023-06-13 05:12:40,686] [INFO] Target genome list was writen to GCA_022564175.1_ASM2256417v1_genomic.fna/target_genomes.txt
[2023-06-13 05:12:40,686] [ERROR] File is empty. [GCA_022564175.1_ASM2256417v1_genomic.fna/target_genomes.txt]
[2023-06-13 05:12:40,686] [ERROR] Task failed. No target genome found.
[2023-06-13 05:12:40,687] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 05:12:40,687] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca086c8a-4b3c-45db-b62f-735e934fa400/dqc_reference/checkm_data
[2023-06-13 05:12:40,689] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 05:12:40,703] [INFO] Task started: CheckM
[2023-06-13 05:12:40,703] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022564175.1_ASM2256417v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022564175.1_ASM2256417v1_genomic.fna/checkm_input GCA_022564175.1_ASM2256417v1_genomic.fna/checkm_result
[2023-06-13 05:13:00,054] [INFO] Task succeeded: CheckM
[2023-06-13 05:13:00,055] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 42.27%
Contamintation: 5.21%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 05:13:00,082] [INFO] ===== Completeness check finished =====
[2023-06-13 05:13:00,083] [INFO] ===== Start GTDB Search =====
[2023-06-13 05:13:00,083] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022564175.1_ASM2256417v1_genomic.fna/markers.fasta)
[2023-06-13 05:13:00,083] [INFO] Task started: Blastn
[2023-06-13 05:13:00,083] [INFO] Running command: blastn -query GCA_022564175.1_ASM2256417v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca086c8a-4b3c-45db-b62f-735e934fa400/dqc_reference/reference_markers_gtdb.fasta -out GCA_022564175.1_ASM2256417v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 05:13:00,540] [INFO] Task succeeded: Blastn
[2023-06-13 05:13:00,544] [INFO] Selected 1 target genomes.
[2023-06-13 05:13:00,544] [INFO] Target genome list was writen to GCA_022564175.1_ASM2256417v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 05:13:00,547] [INFO] Task started: fastANI
[2023-06-13 05:13:00,548] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b569d0f-1160-429e-b06d-ad1c709844ad/GCA_022564175.1_ASM2256417v1_genomic.fna.gz --refList GCA_022564175.1_ASM2256417v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022564175.1_ASM2256417v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 05:13:00,863] [INFO] Task succeeded: fastANI
[2023-06-13 05:13:00,972] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 05:13:00,972] [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_011055585.1	s__DRGT01 sp011055585	93.0548	114	165	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__DRGT01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 05:13:00,974] [INFO] GTDB search result was written to GCA_022564175.1_ASM2256417v1_genomic.fna/result_gtdb.tsv
[2023-06-13 05:13:00,975] [INFO] ===== GTDB Search completed =====
[2023-06-13 05:13:00,977] [INFO] DFAST_QC result json was written to GCA_022564175.1_ASM2256417v1_genomic.fna/dqc_result.json
[2023-06-13 05:13:00,978] [INFO] DFAST_QC completed!
[2023-06-13 05:13:00,978] [INFO] Total running time: 0h0m27s