[2023-06-05 12:22:33,236] [INFO] DFAST_QC pipeline started.
[2023-06-05 12:22:33,245] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 12:22:33,245] [INFO] DQC Reference Directory: /var/lib/cwl/stg2cfcc133-5b58-4343-9e78-7a4ef0dbcadf/dqc_reference
[2023-06-05 12:22:34,890] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 12:22:34,891] [INFO] Task started: Prodigal
[2023-06-05 12:22:34,891] [INFO] Running command: gunzip -c /var/lib/cwl/stg0a1b9f02-277a-44cb-8093-541bdca2dc34/GCA_902517675.1_AG-333-A17_genomic.fna.gz | prodigal -d GCA_902517675.1_AG-333-A17_genomic.fna/cds.fna -a GCA_902517675.1_AG-333-A17_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 12:22:36,088] [INFO] Task succeeded: Prodigal
[2023-06-05 12:22:36,089] [INFO] Task started: HMMsearch
[2023-06-05 12:22:36,089] [INFO] Running command: hmmsearch --tblout GCA_902517675.1_AG-333-A17_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2cfcc133-5b58-4343-9e78-7a4ef0dbcadf/dqc_reference/reference_markers.hmm GCA_902517675.1_AG-333-A17_genomic.fna/protein.faa > /dev/null
[2023-06-05 12:22:36,192] [INFO] Task succeeded: HMMsearch
[2023-06-05 12:22:36,194] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg0a1b9f02-277a-44cb-8093-541bdca2dc34/GCA_902517675.1_AG-333-A17_genomic.fna.gz]
[2023-06-05 12:22:36,203] [INFO] Query marker FASTA was written to GCA_902517675.1_AG-333-A17_genomic.fna/markers.fasta
[2023-06-05 12:22:36,204] [INFO] Task started: Blastn
[2023-06-05 12:22:36,204] [INFO] Running command: blastn -query GCA_902517675.1_AG-333-A17_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cfcc133-5b58-4343-9e78-7a4ef0dbcadf/dqc_reference/reference_markers.fasta -out GCA_902517675.1_AG-333-A17_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 12:22:36,705] [INFO] Task succeeded: Blastn
[2023-06-05 12:22:36,708] [INFO] Selected 0 target genomes.
[2023-06-05 12:22:36,709] [INFO] Target genome list was writen to GCA_902517675.1_AG-333-A17_genomic.fna/target_genomes.txt
[2023-06-05 12:22:36,709] [ERROR] File is empty. [GCA_902517675.1_AG-333-A17_genomic.fna/target_genomes.txt]
[2023-06-05 12:22:36,709] [ERROR] Task failed. No target genome found.
[2023-06-05 12:22:36,709] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 12:22:36,709] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2cfcc133-5b58-4343-9e78-7a4ef0dbcadf/dqc_reference/checkm_data
[2023-06-05 12:22:36,712] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 12:22:36,720] [INFO] Task started: CheckM
[2023-06-05 12:22:36,720] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902517675.1_AG-333-A17_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902517675.1_AG-333-A17_genomic.fna/checkm_input GCA_902517675.1_AG-333-A17_genomic.fna/checkm_result
[2023-06-05 12:22:47,920] [INFO] Task succeeded: CheckM
[2023-06-05 12:22:47,921] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 12.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 12:22:47,938] [INFO] ===== Completeness check finished =====
[2023-06-05 12:22:47,939] [INFO] ===== Start GTDB Search =====
[2023-06-05 12:22:47,939] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902517675.1_AG-333-A17_genomic.fna/markers.fasta)
[2023-06-05 12:22:47,939] [INFO] Task started: Blastn
[2023-06-05 12:22:47,939] [INFO] Running command: blastn -query GCA_902517675.1_AG-333-A17_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cfcc133-5b58-4343-9e78-7a4ef0dbcadf/dqc_reference/reference_markers_gtdb.fasta -out GCA_902517675.1_AG-333-A17_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 12:22:48,483] [INFO] Task succeeded: Blastn
[2023-06-05 12:22:48,487] [INFO] Selected 9 target genomes.
[2023-06-05 12:22:48,487] [INFO] Target genome list was writen to GCA_902517675.1_AG-333-A17_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 12:22:48,494] [INFO] Task started: fastANI
[2023-06-05 12:22:48,494] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a1b9f02-277a-44cb-8093-541bdca2dc34/GCA_902517675.1_AG-333-A17_genomic.fna.gz --refList GCA_902517675.1_AG-333-A17_genomic.fna/target_genomes_gtdb.txt --output GCA_902517675.1_AG-333-A17_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 12:22:50,230] [INFO] Task succeeded: fastANI
[2023-06-05 12:22:50,239] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 12:22:50,240] [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_902583075.1	s__Pelagibacter sp902583075	95.5661	90	114	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902518395.1	s__Pelagibacter sp902518395	92.5787	70	114	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902570545.1	s__Pelagibacter sp902570545	91.9196	54	114	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902524635.1	s__Pelagibacter sp902524635	91.3255	81	114	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902604975.1	s__Pelagibacter sp902604975	91.2364	78	114	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902592715.1	s__Pelagibacter sp902592715	90.4689	93	114	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003282205.1	s__Pelagibacter sp003282205	89.1929	106	114	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.18	98.36	0.96	0.92	3	-
GCA_014654115.1	s__Pelagibacter sp014654115	87.8548	72	114	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902584995.1	s__Pelagibacter sp902584995	84.2621	92	114	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.86	99.86	0.80	0.80	2	-
--------------------------------------------------------------------------------
[2023-06-05 12:22:50,242] [INFO] GTDB search result was written to GCA_902517675.1_AG-333-A17_genomic.fna/result_gtdb.tsv
[2023-06-05 12:22:50,242] [INFO] ===== GTDB Search completed =====
[2023-06-05 12:22:50,246] [INFO] DFAST_QC result json was written to GCA_902517675.1_AG-333-A17_genomic.fna/dqc_result.json
[2023-06-05 12:22:50,246] [INFO] DFAST_QC completed!
[2023-06-05 12:22:50,246] [INFO] Total running time: 0h0m17s