[2023-06-08 19:01:04,078] [INFO] DFAST_QC pipeline started.
[2023-06-08 19:01:04,080] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 19:01:04,080] [INFO] DQC Reference Directory: /var/lib/cwl/stg68437e25-48e8-4d2a-9b51-c0e2bb1ee8b5/dqc_reference
[2023-06-08 19:01:05,559] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 19:01:05,565] [INFO] Task started: Prodigal
[2023-06-08 19:01:05,566] [INFO] Running command: gunzip -c /var/lib/cwl/stgec29f808-a683-4b00-8df2-0f64bebb0221/GCA_000990045.1_ASM99004v1_genomic.fna.gz | prodigal -d GCA_000990045.1_ASM99004v1_genomic.fna/cds.fna -a GCA_000990045.1_ASM99004v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 19:01:06,426] [INFO] Task succeeded: Prodigal
[2023-06-08 19:01:06,427] [INFO] Task started: HMMsearch
[2023-06-08 19:01:06,427] [INFO] Running command: hmmsearch --tblout GCA_000990045.1_ASM99004v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68437e25-48e8-4d2a-9b51-c0e2bb1ee8b5/dqc_reference/reference_markers.hmm GCA_000990045.1_ASM99004v1_genomic.fna/protein.faa > /dev/null
[2023-06-08 19:01:06,647] [INFO] Task succeeded: HMMsearch
[2023-06-08 19:01:06,648] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgec29f808-a683-4b00-8df2-0f64bebb0221/GCA_000990045.1_ASM99004v1_genomic.fna.gz]
[2023-06-08 19:01:06,657] [INFO] Query marker FASTA was written to GCA_000990045.1_ASM99004v1_genomic.fna/markers.fasta
[2023-06-08 19:01:06,657] [INFO] Task started: Blastn
[2023-06-08 19:01:06,657] [INFO] Running command: blastn -query GCA_000990045.1_ASM99004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68437e25-48e8-4d2a-9b51-c0e2bb1ee8b5/dqc_reference/reference_markers.fasta -out GCA_000990045.1_ASM99004v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 19:01:07,191] [INFO] Task succeeded: Blastn
[2023-06-08 19:01:07,195] [INFO] Selected 0 target genomes.
[2023-06-08 19:01:07,195] [INFO] Target genome list was writen to GCA_000990045.1_ASM99004v1_genomic.fna/target_genomes.txt
[2023-06-08 19:01:07,195] [ERROR] File is empty. [GCA_000990045.1_ASM99004v1_genomic.fna/target_genomes.txt]
[2023-06-08 19:01:07,196] [ERROR] Task failed. No target genome found.
[2023-06-08 19:01:07,196] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 19:01:07,196] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68437e25-48e8-4d2a-9b51-c0e2bb1ee8b5/dqc_reference/checkm_data
[2023-06-08 19:01:07,199] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 19:01:07,208] [INFO] Task started: CheckM
[2023-06-08 19:01:07,208] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_000990045.1_ASM99004v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_000990045.1_ASM99004v1_genomic.fna/checkm_input GCA_000990045.1_ASM99004v1_genomic.fna/checkm_result
[2023-06-08 19:01:18,703] [INFO] Task succeeded: CheckM
[2023-06-08 19:01:18,704] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 38.93%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 19:01:18,721] [INFO] ===== Completeness check finished =====
[2023-06-08 19:01:18,722] [INFO] ===== Start GTDB Search =====
[2023-06-08 19:01:18,722] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_000990045.1_ASM99004v1_genomic.fna/markers.fasta)
[2023-06-08 19:01:18,723] [INFO] Task started: Blastn
[2023-06-08 19:01:18,723] [INFO] Running command: blastn -query GCA_000990045.1_ASM99004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68437e25-48e8-4d2a-9b51-c0e2bb1ee8b5/dqc_reference/reference_markers_gtdb.fasta -out GCA_000990045.1_ASM99004v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 19:01:19,194] [INFO] Task succeeded: Blastn
[2023-06-08 19:01:19,198] [INFO] Selected 4 target genomes.
[2023-06-08 19:01:19,198] [INFO] Target genome list was writen to GCA_000990045.1_ASM99004v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 19:01:19,204] [INFO] Task started: fastANI
[2023-06-08 19:01:19,205] [INFO] Running command: fastANI --query /var/lib/cwl/stgec29f808-a683-4b00-8df2-0f64bebb0221/GCA_000990045.1_ASM99004v1_genomic.fna.gz --refList GCA_000990045.1_ASM99004v1_genomic.fna/target_genomes_gtdb.txt --output GCA_000990045.1_ASM99004v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 19:01:19,872] [INFO] Task succeeded: fastANI
[2023-06-08 19:01:19,876] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 19:01:19,877] [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_001820215.1	s__GWA2-33-14 sp001820215	99.5494	63	67	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__Paceibacterales;f__Staskawiczbacteraceae;g__GWA2-33-14	95.0	99.80	99.73	0.87	0.83	3	conclusive
--------------------------------------------------------------------------------
[2023-06-08 19:01:19,879] [INFO] GTDB search result was written to GCA_000990045.1_ASM99004v1_genomic.fna/result_gtdb.tsv
[2023-06-08 19:01:19,879] [INFO] ===== GTDB Search completed =====
[2023-06-08 19:01:19,882] [INFO] DFAST_QC result json was written to GCA_000990045.1_ASM99004v1_genomic.fna/dqc_result.json
[2023-06-08 19:01:19,882] [INFO] DFAST_QC completed!
[2023-06-08 19:01:19,882] [INFO] Total running time: 0h0m16s