[2023-06-08 11:16:42,106] [INFO] DFAST_QC pipeline started.
[2023-06-08 11:16:42,108] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 11:16:42,109] [INFO] DQC Reference Directory: /var/lib/cwl/stg8606de77-18cc-4545-9d92-29970499f51d/dqc_reference
[2023-06-08 11:16:44,187] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 11:16:44,188] [INFO] Task started: Prodigal
[2023-06-08 11:16:44,188] [INFO] Running command: gunzip -c /var/lib/cwl/stge5c7cc52-6df9-46f3-b452-216a9063e23b/GCA_000997665.1_ASM99766v1_genomic.fna.gz | prodigal -d GCA_000997665.1_ASM99766v1_genomic.fna/cds.fna -a GCA_000997665.1_ASM99766v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 11:16:46,440] [INFO] Task succeeded: Prodigal
[2023-06-08 11:16:46,441] [INFO] Task started: HMMsearch
[2023-06-08 11:16:46,441] [INFO] Running command: hmmsearch --tblout GCA_000997665.1_ASM99766v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8606de77-18cc-4545-9d92-29970499f51d/dqc_reference/reference_markers.hmm GCA_000997665.1_ASM99766v1_genomic.fna/protein.faa > /dev/null
[2023-06-08 11:16:46,536] [INFO] Task succeeded: HMMsearch
[2023-06-08 11:16:46,537] [WARNING] Found 1/6 markers. [/var/lib/cwl/stge5c7cc52-6df9-46f3-b452-216a9063e23b/GCA_000997665.1_ASM99766v1_genomic.fna.gz]
[2023-06-08 11:16:46,547] [INFO] Query marker FASTA was written to GCA_000997665.1_ASM99766v1_genomic.fna/markers.fasta
[2023-06-08 11:16:46,547] [INFO] Task started: Blastn
[2023-06-08 11:16:46,547] [INFO] Running command: blastn -query GCA_000997665.1_ASM99766v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8606de77-18cc-4545-9d92-29970499f51d/dqc_reference/reference_markers.fasta -out GCA_000997665.1_ASM99766v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:16:47,668] [INFO] Task succeeded: Blastn
[2023-06-08 11:16:47,671] [INFO] Selected 0 target genomes.
[2023-06-08 11:16:47,672] [INFO] Target genome list was writen to GCA_000997665.1_ASM99766v1_genomic.fna/target_genomes.txt
[2023-06-08 11:16:47,672] [ERROR] File is empty. [GCA_000997665.1_ASM99766v1_genomic.fna/target_genomes.txt]
[2023-06-08 11:16:47,672] [ERROR] Task failed. No target genome found.
[2023-06-08 11:16:47,672] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 11:16:47,672] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8606de77-18cc-4545-9d92-29970499f51d/dqc_reference/checkm_data
[2023-06-08 11:16:47,675] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 11:16:47,683] [INFO] Task started: CheckM
[2023-06-08 11:16:47,683] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_000997665.1_ASM99766v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_000997665.1_ASM99766v1_genomic.fna/checkm_input GCA_000997665.1_ASM99766v1_genomic.fna/checkm_result
[2023-06-08 11:17:01,061] [INFO] Task succeeded: CheckM
[2023-06-08 11:17:01,062] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.04%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 11:17:01,081] [INFO] ===== Completeness check finished =====
[2023-06-08 11:17:01,081] [INFO] ===== Start GTDB Search =====
[2023-06-08 11:17:01,081] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_000997665.1_ASM99766v1_genomic.fna/markers.fasta)
[2023-06-08 11:17:01,082] [INFO] Task started: Blastn
[2023-06-08 11:17:01,082] [INFO] Running command: blastn -query GCA_000997665.1_ASM99766v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8606de77-18cc-4545-9d92-29970499f51d/dqc_reference/reference_markers_gtdb.fasta -out GCA_000997665.1_ASM99766v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:17:01,483] [INFO] Task succeeded: Blastn
[2023-06-08 11:17:01,486] [INFO] Selected 5 target genomes.
[2023-06-08 11:17:01,486] [INFO] Target genome list was writen to GCA_000997665.1_ASM99766v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 11:17:01,487] [INFO] Task started: fastANI
[2023-06-08 11:17:01,487] [INFO] Running command: fastANI --query /var/lib/cwl/stge5c7cc52-6df9-46f3-b452-216a9063e23b/GCA_000997665.1_ASM99766v1_genomic.fna.gz --refList GCA_000997665.1_ASM99766v1_genomic.fna/target_genomes_gtdb.txt --output GCA_000997665.1_ASM99766v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 11:17:02,098] [INFO] Task succeeded: fastANI
[2023-06-08 11:17:02,102] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 11:17:02,102] [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_001795975.1	s__2-01-FULL-44-22 sp001795975	98.6059	122	162	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__2-02-FULL-40-12;f__GWA2-44-9;g__2-01-FULL-44-22	95.0	99.30	99.22	0.76	0.75	3	conclusive
GCA_001794205.1	s__2-01-FULL-44-22 sp001794205	82.2543	50	162	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__2-02-FULL-40-12;f__GWA2-44-9;g__2-01-FULL-44-22	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 11:17:02,104] [INFO] GTDB search result was written to GCA_000997665.1_ASM99766v1_genomic.fna/result_gtdb.tsv
[2023-06-08 11:17:02,104] [INFO] ===== GTDB Search completed =====
[2023-06-08 11:17:02,107] [INFO] DFAST_QC result json was written to GCA_000997665.1_ASM99766v1_genomic.fna/dqc_result.json
[2023-06-08 11:17:02,107] [INFO] DFAST_QC completed!
[2023-06-08 11:17:02,107] [INFO] Total running time: 0h0m20s