[2023-06-27 07:43:04,197] [INFO] DFAST_QC pipeline started.
[2023-06-27 07:43:04,200] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 07:43:04,200] [INFO] DQC Reference Directory: /var/lib/cwl/stge9cb099f-7cc9-438e-8a0f-93e1ee6fdbf8/dqc_reference
[2023-06-27 07:43:05,472] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 07:43:05,473] [INFO] Task started: Prodigal
[2023-06-27 07:43:05,473] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ff234a6-1003-4c7d-ad2d-99ca73ab12a5/GCA_026014845.1_ASM2601484v1_genomic.fna.gz | prodigal -d GCA_026014845.1_ASM2601484v1_genomic.fna/cds.fna -a GCA_026014845.1_ASM2601484v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 07:43:08,055] [INFO] Task succeeded: Prodigal
[2023-06-27 07:43:08,056] [INFO] Task started: HMMsearch
[2023-06-27 07:43:08,056] [INFO] Running command: hmmsearch --tblout GCA_026014845.1_ASM2601484v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9cb099f-7cc9-438e-8a0f-93e1ee6fdbf8/dqc_reference/reference_markers.hmm GCA_026014845.1_ASM2601484v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 07:43:08,271] [INFO] Task succeeded: HMMsearch
[2023-06-27 07:43:08,273] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg9ff234a6-1003-4c7d-ad2d-99ca73ab12a5/GCA_026014845.1_ASM2601484v1_genomic.fna.gz]
[2023-06-27 07:43:08,304] [INFO] Query marker FASTA was written to GCA_026014845.1_ASM2601484v1_genomic.fna/markers.fasta
[2023-06-27 07:43:08,304] [INFO] Task started: Blastn
[2023-06-27 07:43:08,305] [INFO] Running command: blastn -query GCA_026014845.1_ASM2601484v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9cb099f-7cc9-438e-8a0f-93e1ee6fdbf8/dqc_reference/reference_markers.fasta -out GCA_026014845.1_ASM2601484v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 07:43:08,806] [INFO] Task succeeded: Blastn
[2023-06-27 07:43:08,822] [INFO] Selected 0 target genomes.
[2023-06-27 07:43:08,823] [INFO] Target genome list was writen to GCA_026014845.1_ASM2601484v1_genomic.fna/target_genomes.txt
[2023-06-27 07:43:08,824] [ERROR] File is empty. [GCA_026014845.1_ASM2601484v1_genomic.fna/target_genomes.txt]
[2023-06-27 07:43:08,824] [ERROR] Task failed. No target genome found.
[2023-06-27 07:43:08,824] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 07:43:08,825] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9cb099f-7cc9-438e-8a0f-93e1ee6fdbf8/dqc_reference/checkm_data
[2023-06-27 07:43:08,829] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 07:43:08,851] [INFO] Task started: CheckM
[2023-06-27 07:43:08,852] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026014845.1_ASM2601484v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026014845.1_ASM2601484v1_genomic.fna/checkm_input GCA_026014845.1_ASM2601484v1_genomic.fna/checkm_result
[2023-06-27 07:43:24,730] [INFO] Task succeeded: CheckM
[2023-06-27 07:43:24,732] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 07:43:24,750] [INFO] ===== Completeness check finished =====
[2023-06-27 07:43:24,750] [INFO] ===== Start GTDB Search =====
[2023-06-27 07:43:24,751] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026014845.1_ASM2601484v1_genomic.fna/markers.fasta)
[2023-06-27 07:43:24,751] [INFO] Task started: Blastn
[2023-06-27 07:43:24,751] [INFO] Running command: blastn -query GCA_026014845.1_ASM2601484v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9cb099f-7cc9-438e-8a0f-93e1ee6fdbf8/dqc_reference/reference_markers_gtdb.fasta -out GCA_026014845.1_ASM2601484v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 07:43:25,284] [INFO] Task succeeded: Blastn
[2023-06-27 07:43:25,289] [INFO] Selected 3 target genomes.
[2023-06-27 07:43:25,290] [INFO] Target genome list was writen to GCA_026014845.1_ASM2601484v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 07:43:25,328] [INFO] Task started: fastANI
[2023-06-27 07:43:25,328] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ff234a6-1003-4c7d-ad2d-99ca73ab12a5/GCA_026014845.1_ASM2601484v1_genomic.fna.gz --refList GCA_026014845.1_ASM2601484v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026014845.1_ASM2601484v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 07:43:26,205] [INFO] Task succeeded: fastANI
[2023-06-27 07:43:26,212] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 07:43:26,213] [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_014859805.1	s__SOJA01 sp014859805	89.9565	158	291	d__Archaea;p__Thermoproteota;c__Bathyarchaeia;o__B26-1;f__UBA233;g__SOJA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004376975.1	s__SOJA01 sp004376975	80.4456	156	291	d__Archaea;p__Thermoproteota;c__Bathyarchaeia;o__B26-1;f__UBA233;g__SOJA01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 07:43:26,215] [INFO] GTDB search result was written to GCA_026014845.1_ASM2601484v1_genomic.fna/result_gtdb.tsv
[2023-06-27 07:43:26,216] [INFO] ===== GTDB Search completed =====
[2023-06-27 07:43:26,219] [INFO] DFAST_QC result json was written to GCA_026014845.1_ASM2601484v1_genomic.fna/dqc_result.json
[2023-06-27 07:43:26,219] [INFO] DFAST_QC completed!
[2023-06-27 07:43:26,219] [INFO] Total running time: 0h0m22s