[2023-06-08 13:32:57,094] [INFO] DFAST_QC pipeline started.
[2023-06-08 13:32:57,097] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 13:32:57,097] [INFO] DQC Reference Directory: /var/lib/cwl/stgad8ef6ba-f8d5-4884-be43-410cc78a9011/dqc_reference
[2023-06-08 13:32:58,178] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 13:32:58,179] [INFO] Task started: Prodigal
[2023-06-08 13:32:58,179] [INFO] Running command: gunzip -c /var/lib/cwl/stg84feead0-fca7-48be-901d-4ac3b77405fe/GCA_902614585.1_AG-919-B17_genomic.fna.gz | prodigal -d GCA_902614585.1_AG-919-B17_genomic.fna/cds.fna -a GCA_902614585.1_AG-919-B17_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 13:32:58,987] [INFO] Task succeeded: Prodigal
[2023-06-08 13:32:58,987] [INFO] Task started: HMMsearch
[2023-06-08 13:32:58,987] [INFO] Running command: hmmsearch --tblout GCA_902614585.1_AG-919-B17_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad8ef6ba-f8d5-4884-be43-410cc78a9011/dqc_reference/reference_markers.hmm GCA_902614585.1_AG-919-B17_genomic.fna/protein.faa > /dev/null
[2023-06-08 13:32:59,085] [INFO] Task succeeded: HMMsearch
[2023-06-08 13:32:59,086] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg84feead0-fca7-48be-901d-4ac3b77405fe/GCA_902614585.1_AG-919-B17_genomic.fna.gz]
[2023-06-08 13:32:59,093] [INFO] Query marker FASTA was written to GCA_902614585.1_AG-919-B17_genomic.fna/markers.fasta
[2023-06-08 13:32:59,093] [INFO] Task started: Blastn
[2023-06-08 13:32:59,093] [INFO] Running command: blastn -query GCA_902614585.1_AG-919-B17_genomic.fna/markers.fasta -db /var/lib/cwl/stgad8ef6ba-f8d5-4884-be43-410cc78a9011/dqc_reference/reference_markers.fasta -out GCA_902614585.1_AG-919-B17_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:32:59,537] [INFO] Task succeeded: Blastn
[2023-06-08 13:32:59,540] [INFO] Selected 0 target genomes.
[2023-06-08 13:32:59,540] [INFO] Target genome list was writen to GCA_902614585.1_AG-919-B17_genomic.fna/target_genomes.txt
[2023-06-08 13:32:59,540] [ERROR] File is empty. [GCA_902614585.1_AG-919-B17_genomic.fna/target_genomes.txt]
[2023-06-08 13:32:59,540] [ERROR] Task failed. No target genome found.
[2023-06-08 13:32:59,540] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 13:32:59,541] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad8ef6ba-f8d5-4884-be43-410cc78a9011/dqc_reference/checkm_data
[2023-06-08 13:32:59,543] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 13:32:59,550] [INFO] Task started: CheckM
[2023-06-08 13:32:59,551] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902614585.1_AG-919-B17_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902614585.1_AG-919-B17_genomic.fna/checkm_input GCA_902614585.1_AG-919-B17_genomic.fna/checkm_result
[2023-06-08 13:33:08,844] [INFO] Task succeeded: CheckM
[2023-06-08 13:33:08,845] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 16.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 13:33:08,858] [INFO] ===== Completeness check finished =====
[2023-06-08 13:33:08,858] [INFO] ===== Start GTDB Search =====
[2023-06-08 13:33:08,859] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902614585.1_AG-919-B17_genomic.fna/markers.fasta)
[2023-06-08 13:33:08,859] [INFO] Task started: Blastn
[2023-06-08 13:33:08,859] [INFO] Running command: blastn -query GCA_902614585.1_AG-919-B17_genomic.fna/markers.fasta -db /var/lib/cwl/stgad8ef6ba-f8d5-4884-be43-410cc78a9011/dqc_reference/reference_markers_gtdb.fasta -out GCA_902614585.1_AG-919-B17_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:33:09,341] [INFO] Task succeeded: Blastn
[2023-06-08 13:33:09,347] [INFO] Selected 8 target genomes.
[2023-06-08 13:33:09,347] [INFO] Target genome list was writen to GCA_902614585.1_AG-919-B17_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 13:33:09,350] [INFO] Task started: fastANI
[2023-06-08 13:33:09,350] [INFO] Running command: fastANI --query /var/lib/cwl/stg84feead0-fca7-48be-901d-4ac3b77405fe/GCA_902614585.1_AG-919-B17_genomic.fna.gz --refList GCA_902614585.1_AG-919-B17_genomic.fna/target_genomes_gtdb.txt --output GCA_902614585.1_AG-919-B17_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 13:33:10,611] [INFO] Task succeeded: fastANI
[2023-06-08 13:33:10,616] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 13:33:10,616] [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_003209915.1	s__Pelagibacter sp003209915	97.6907	87	109	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	96.70	95.04	0.84	0.76	80	conclusive
GCA_902540595.1	s__Pelagibacter sp902540595	94.2901	75	109	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.43	95.31	0.77	0.75	3	-
GCA_014653985.1	s__Pelagibacter sp014653985	92.7839	88	109	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902590915.1	s__Pelagibacter sp902590915	90.4239	74	109	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902604525.1	s__Pelagibacter sp902604525	89.5866	74	109	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902622795.1	s__Pelagibacter sp902622795	88.979	64	109	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.61	99.61	0.85	0.85	2	-
GCA_902604355.1	s__Pelagibacter sp902604355	87.6212	69	109	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 13:33:10,617] [INFO] GTDB search result was written to GCA_902614585.1_AG-919-B17_genomic.fna/result_gtdb.tsv
[2023-06-08 13:33:10,618] [INFO] ===== GTDB Search completed =====
[2023-06-08 13:33:10,621] [INFO] DFAST_QC result json was written to GCA_902614585.1_AG-919-B17_genomic.fna/dqc_result.json
[2023-06-08 13:33:10,621] [INFO] DFAST_QC completed!
[2023-06-08 13:33:10,621] [INFO] Total running time: 0h0m14s