[2023-06-05 08:20:14,400] [INFO] DFAST_QC pipeline started.
[2023-06-05 08:20:14,402] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 08:20:14,402] [INFO] DQC Reference Directory: /var/lib/cwl/stg69c375be-149a-4552-b75e-f0b2d2519a84/dqc_reference
[2023-06-05 08:20:16,648] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 08:20:16,649] [INFO] Task started: Prodigal
[2023-06-05 08:20:16,650] [INFO] Running command: gunzip -c /var/lib/cwl/stg1db8730e-1782-407d-a91b-2b7b962d30e6/GCA_902525595.1_AG-337-G05_genomic.fna.gz | prodigal -d GCA_902525595.1_AG-337-G05_genomic.fna/cds.fna -a GCA_902525595.1_AG-337-G05_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 08:20:18,383] [INFO] Task succeeded: Prodigal
[2023-06-05 08:20:18,383] [INFO] Task started: HMMsearch
[2023-06-05 08:20:18,383] [INFO] Running command: hmmsearch --tblout GCA_902525595.1_AG-337-G05_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69c375be-149a-4552-b75e-f0b2d2519a84/dqc_reference/reference_markers.hmm GCA_902525595.1_AG-337-G05_genomic.fna/protein.faa > /dev/null
[2023-06-05 08:20:18,565] [INFO] Task succeeded: HMMsearch
[2023-06-05 08:20:18,567] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg1db8730e-1782-407d-a91b-2b7b962d30e6/GCA_902525595.1_AG-337-G05_genomic.fna.gz]
[2023-06-05 08:20:18,586] [INFO] Query marker FASTA was written to GCA_902525595.1_AG-337-G05_genomic.fna/markers.fasta
[2023-06-05 08:20:18,586] [INFO] Task started: Blastn
[2023-06-05 08:20:18,586] [INFO] Running command: blastn -query GCA_902525595.1_AG-337-G05_genomic.fna/markers.fasta -db /var/lib/cwl/stg69c375be-149a-4552-b75e-f0b2d2519a84/dqc_reference/reference_markers.fasta -out GCA_902525595.1_AG-337-G05_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 08:20:20,062] [INFO] Task succeeded: Blastn
[2023-06-05 08:20:20,067] [INFO] Selected 9 target genomes.
[2023-06-05 08:20:20,067] [INFO] Target genome list was writen to GCA_902525595.1_AG-337-G05_genomic.fna/target_genomes.txt
[2023-06-05 08:20:20,099] [INFO] Task started: fastANI
[2023-06-05 08:20:20,099] [INFO] Running command: fastANI --query /var/lib/cwl/stg1db8730e-1782-407d-a91b-2b7b962d30e6/GCA_902525595.1_AG-337-G05_genomic.fna.gz --refList GCA_902525595.1_AG-337-G05_genomic.fna/target_genomes.txt --output GCA_902525595.1_AG-337-G05_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 08:20:24,883] [INFO] Task succeeded: fastANI
[2023-06-05 08:20:24,883] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69c375be-149a-4552-b75e-f0b2d2519a84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 08:20:24,884] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69c375be-149a-4552-b75e-f0b2d2519a84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 08:20:24,886] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 08:20:24,886] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 08:20:24,887] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-06-05 08:20:24,889] [INFO] DFAST Taxonomy check result was written to GCA_902525595.1_AG-337-G05_genomic.fna/tc_result.tsv
[2023-06-05 08:20:24,890] [INFO] ===== Taxonomy check completed =====
[2023-06-05 08:20:24,890] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 08:20:24,890] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69c375be-149a-4552-b75e-f0b2d2519a84/dqc_reference/checkm_data
[2023-06-05 08:20:24,895] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 08:20:24,912] [INFO] Task started: CheckM
[2023-06-05 08:20:24,912] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902525595.1_AG-337-G05_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902525595.1_AG-337-G05_genomic.fna/checkm_input GCA_902525595.1_AG-337-G05_genomic.fna/checkm_result
[2023-06-05 08:20:38,868] [INFO] Task succeeded: CheckM
[2023-06-05 08:20:38,870] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 08:20:38,889] [INFO] ===== Completeness check finished =====
[2023-06-05 08:20:38,890] [INFO] ===== Start GTDB Search =====
[2023-06-05 08:20:38,890] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902525595.1_AG-337-G05_genomic.fna/markers.fasta)
[2023-06-05 08:20:38,891] [INFO] Task started: Blastn
[2023-06-05 08:20:38,891] [INFO] Running command: blastn -query GCA_902525595.1_AG-337-G05_genomic.fna/markers.fasta -db /var/lib/cwl/stg69c375be-149a-4552-b75e-f0b2d2519a84/dqc_reference/reference_markers_gtdb.fasta -out GCA_902525595.1_AG-337-G05_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 08:20:39,500] [INFO] Task succeeded: Blastn
[2023-06-05 08:20:39,505] [INFO] Selected 13 target genomes.
[2023-06-05 08:20:39,505] [INFO] Target genome list was writen to GCA_902525595.1_AG-337-G05_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 08:20:39,563] [INFO] Task started: fastANI
[2023-06-05 08:20:39,563] [INFO] Running command: fastANI --query /var/lib/cwl/stg1db8730e-1782-407d-a91b-2b7b962d30e6/GCA_902525595.1_AG-337-G05_genomic.fna.gz --refList GCA_902525595.1_AG-337-G05_genomic.fna/target_genomes_gtdb.txt --output GCA_902525595.1_AG-337-G05_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 08:20:42,055] [INFO] Task succeeded: fastANI
[2023-06-05 08:20:42,070] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 08:20:42,070] [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_902525595.1	s__AG-422-B15 sp902525595	100.0	310	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902570675.1	s__AG-422-B15 sp902570675	94.4224	214	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	98.46	98.46	0.72	0.72	2	-
GCA_902524285.1	s__AG-422-B15 sp902524285	80.4523	107	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902578305.1	s__AG-422-B15 sp902578305	80.1959	128	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003213515.1	s__AG-422-B15 sp003213515	80.1263	140	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902580665.1	s__AG-422-B15 sp902580665	80.1019	67	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902565955.1	s__AG-422-B15 sp902565955	79.9892	94	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902524795.1	s__AG-422-B15 sp902524795	79.8466	100	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902571005.1	s__AG-422-B15 sp902571005	79.816	145	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902546615.1	s__AG-422-B15 sp902546615	79.7744	93	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	99.01	98.34	0.72	0.68	3	-
GCA_902533965.1	s__AG-422-B15 sp902533965	79.4553	70	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 08:20:42,072] [INFO] GTDB search result was written to GCA_902525595.1_AG-337-G05_genomic.fna/result_gtdb.tsv
[2023-06-05 08:20:42,072] [INFO] ===== GTDB Search completed =====
[2023-06-05 08:20:42,076] [INFO] DFAST_QC result json was written to GCA_902525595.1_AG-337-G05_genomic.fna/dqc_result.json
[2023-06-05 08:20:42,077] [INFO] DFAST_QC completed!
[2023-06-05 08:20:42,077] [INFO] Total running time: 0h0m28s