[2023-06-05 18:05:11,260] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:05:11,265] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:05:11,265] [INFO] DQC Reference Directory: /var/lib/cwl/stgeabf53b0-2106-4390-af96-da0c56ed3338/dqc_reference
[2023-06-05 18:05:12,396] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:05:12,396] [INFO] Task started: Prodigal
[2023-06-05 18:05:12,397] [INFO] Running command: gunzip -c /var/lib/cwl/stgb1f96392-7b87-47a9-a7ce-ab4b3666e5e3/GCA_902628055.1_AH-321-O04_genomic.fna.gz | prodigal -d GCA_902628055.1_AH-321-O04_genomic.fna/cds.fna -a GCA_902628055.1_AH-321-O04_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:05:13,162] [INFO] Task succeeded: Prodigal
[2023-06-05 18:05:13,162] [INFO] Task started: HMMsearch
[2023-06-05 18:05:13,162] [INFO] Running command: hmmsearch --tblout GCA_902628055.1_AH-321-O04_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeabf53b0-2106-4390-af96-da0c56ed3338/dqc_reference/reference_markers.hmm GCA_902628055.1_AH-321-O04_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:05:13,696] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:05:13,697] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgb1f96392-7b87-47a9-a7ce-ab4b3666e5e3/GCA_902628055.1_AH-321-O04_genomic.fna.gz]
[2023-06-05 18:05:13,704] [INFO] Query marker FASTA was written to GCA_902628055.1_AH-321-O04_genomic.fna/markers.fasta
[2023-06-05 18:05:13,704] [INFO] Task started: Blastn
[2023-06-05 18:05:13,704] [INFO] Running command: blastn -query GCA_902628055.1_AH-321-O04_genomic.fna/markers.fasta -db /var/lib/cwl/stgeabf53b0-2106-4390-af96-da0c56ed3338/dqc_reference/reference_markers.fasta -out GCA_902628055.1_AH-321-O04_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:05:14,131] [INFO] Task succeeded: Blastn
[2023-06-05 18:05:14,571] [INFO] Selected 0 target genomes.
[2023-06-05 18:05:14,571] [INFO] Target genome list was writen to GCA_902628055.1_AH-321-O04_genomic.fna/target_genomes.txt
[2023-06-05 18:05:14,572] [ERROR] File is empty. [GCA_902628055.1_AH-321-O04_genomic.fna/target_genomes.txt]
[2023-06-05 18:05:14,572] [ERROR] Task failed. No target genome found.
[2023-06-05 18:05:14,572] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:05:14,572] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeabf53b0-2106-4390-af96-da0c56ed3338/dqc_reference/checkm_data
[2023-06-05 18:05:14,574] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:05:14,580] [INFO] Task started: CheckM
[2023-06-05 18:05:14,581] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902628055.1_AH-321-O04_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902628055.1_AH-321-O04_genomic.fna/checkm_input GCA_902628055.1_AH-321-O04_genomic.fna/checkm_result
[2023-06-05 18:05:25,586] [INFO] Task succeeded: CheckM
[2023-06-05 18:05:25,587] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 16.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:05:25,604] [INFO] ===== Completeness check finished =====
[2023-06-05 18:05:25,604] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:05:25,605] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902628055.1_AH-321-O04_genomic.fna/markers.fasta)
[2023-06-05 18:05:25,605] [INFO] Task started: Blastn
[2023-06-05 18:05:25,605] [INFO] Running command: blastn -query GCA_902628055.1_AH-321-O04_genomic.fna/markers.fasta -db /var/lib/cwl/stgeabf53b0-2106-4390-af96-da0c56ed3338/dqc_reference/reference_markers_gtdb.fasta -out GCA_902628055.1_AH-321-O04_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:05:26,150] [INFO] Task succeeded: Blastn
[2023-06-05 18:05:26,152] [INFO] Selected 7 target genomes.
[2023-06-05 18:05:26,153] [INFO] Target genome list was writen to GCA_902628055.1_AH-321-O04_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:05:26,162] [INFO] Task started: fastANI
[2023-06-05 18:05:26,162] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1f96392-7b87-47a9-a7ce-ab4b3666e5e3/GCA_902628055.1_AH-321-O04_genomic.fna.gz --refList GCA_902628055.1_AH-321-O04_genomic.fna/target_genomes_gtdb.txt --output GCA_902628055.1_AH-321-O04_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:05:27,372] [INFO] Task succeeded: fastANI
[2023-06-05 18:05:27,376] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:05:27,376] [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_902625715.1	s__Pelagibacter sp902625715	95.4839	61	72	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.20	95.77	0.80	0.79	3	conclusive
GCF_002101295.1	s__Pelagibacter sp002101295	91.8312	62	72	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.97	95.60	0.92	0.90	4	-
GCA_902601315.1	s__Pelagibacter sp902601315	90.6985	55	72	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902614125.1	s__Pelagibacter sp902614125	90.5119	60	72	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 18:05:27,378] [INFO] GTDB search result was written to GCA_902628055.1_AH-321-O04_genomic.fna/result_gtdb.tsv
[2023-06-05 18:05:27,379] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:05:27,455] [INFO] DFAST_QC result json was written to GCA_902628055.1_AH-321-O04_genomic.fna/dqc_result.json
[2023-06-05 18:05:27,455] [INFO] DFAST_QC completed!
[2023-06-05 18:05:27,455] [INFO] Total running time: 0h0m16s