[2023-06-04 23:35:00,043] [INFO] DFAST_QC pipeline started.
[2023-06-04 23:35:00,045] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 23:35:00,046] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0635753-3a71-4a17-8ce6-f30afa5edb3c/dqc_reference
[2023-06-04 23:35:02,449] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 23:35:02,450] [INFO] Task started: Prodigal
[2023-06-04 23:35:02,450] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c0e25d7-9168-4055-a91e-ca2fdb618e60/GCA_902519085.1_AG-333-D20_genomic.fna.gz | prodigal -d GCA_902519085.1_AG-333-D20_genomic.fna/cds.fna -a GCA_902519085.1_AG-333-D20_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 23:35:03,386] [INFO] Task succeeded: Prodigal
[2023-06-04 23:35:03,386] [INFO] Task started: HMMsearch
[2023-06-04 23:35:03,387] [INFO] Running command: hmmsearch --tblout GCA_902519085.1_AG-333-D20_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0635753-3a71-4a17-8ce6-f30afa5edb3c/dqc_reference/reference_markers.hmm GCA_902519085.1_AG-333-D20_genomic.fna/protein.faa > /dev/null
[2023-06-04 23:35:03,545] [INFO] Task succeeded: HMMsearch
[2023-06-04 23:35:03,547] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg6c0e25d7-9168-4055-a91e-ca2fdb618e60/GCA_902519085.1_AG-333-D20_genomic.fna.gz]
[2023-06-04 23:35:03,568] [INFO] Query marker FASTA was written to GCA_902519085.1_AG-333-D20_genomic.fna/markers.fasta
[2023-06-04 23:35:03,568] [INFO] Task started: Blastn
[2023-06-04 23:35:03,568] [INFO] Running command: blastn -query GCA_902519085.1_AG-333-D20_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0635753-3a71-4a17-8ce6-f30afa5edb3c/dqc_reference/reference_markers.fasta -out GCA_902519085.1_AG-333-D20_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 23:35:05,749] [INFO] Task succeeded: Blastn
[2023-06-04 23:35:05,754] [INFO] Selected 9 target genomes.
[2023-06-04 23:35:05,755] [INFO] Target genome list was writen to GCA_902519085.1_AG-333-D20_genomic.fna/target_genomes.txt
[2023-06-04 23:35:05,758] [INFO] Task started: fastANI
[2023-06-04 23:35:05,758] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c0e25d7-9168-4055-a91e-ca2fdb618e60/GCA_902519085.1_AG-333-D20_genomic.fna.gz --refList GCA_902519085.1_AG-333-D20_genomic.fna/target_genomes.txt --output GCA_902519085.1_AG-333-D20_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 23:35:10,306] [INFO] Task succeeded: fastANI
[2023-06-04 23:35:10,307] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0635753-3a71-4a17-8ce6-f30afa5edb3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 23:35:10,307] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0635753-3a71-4a17-8ce6-f30afa5edb3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 23:35:10,309] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 23:35:10,309] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 23:35:10,309] [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
--------------------------------------------------------------------------------
[2023-06-04 23:35:10,312] [INFO] DFAST Taxonomy check result was written to GCA_902519085.1_AG-333-D20_genomic.fna/tc_result.tsv
[2023-06-04 23:35:10,312] [INFO] ===== Taxonomy check completed =====
[2023-06-04 23:35:10,313] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 23:35:10,313] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0635753-3a71-4a17-8ce6-f30afa5edb3c/dqc_reference/checkm_data
[2023-06-04 23:35:10,318] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 23:35:10,337] [INFO] Task started: CheckM
[2023-06-04 23:35:10,337] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902519085.1_AG-333-D20_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902519085.1_AG-333-D20_genomic.fna/checkm_input GCA_902519085.1_AG-333-D20_genomic.fna/checkm_result
[2023-06-04 23:35:21,382] [INFO] Task succeeded: CheckM
[2023-06-04 23:35:21,384] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 30.21%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 23:35:21,402] [INFO] ===== Completeness check finished =====
[2023-06-04 23:35:21,402] [INFO] ===== Start GTDB Search =====
[2023-06-04 23:35:21,403] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902519085.1_AG-333-D20_genomic.fna/markers.fasta)
[2023-06-04 23:35:21,403] [INFO] Task started: Blastn
[2023-06-04 23:35:21,403] [INFO] Running command: blastn -query GCA_902519085.1_AG-333-D20_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0635753-3a71-4a17-8ce6-f30afa5edb3c/dqc_reference/reference_markers_gtdb.fasta -out GCA_902519085.1_AG-333-D20_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 23:35:22,030] [INFO] Task succeeded: Blastn
[2023-06-04 23:35:22,040] [INFO] Selected 7 target genomes.
[2023-06-04 23:35:22,040] [INFO] Target genome list was writen to GCA_902519085.1_AG-333-D20_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 23:35:22,081] [INFO] Task started: fastANI
[2023-06-04 23:35:22,082] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c0e25d7-9168-4055-a91e-ca2fdb618e60/GCA_902519085.1_AG-333-D20_genomic.fna.gz --refList GCA_902519085.1_AG-333-D20_genomic.fna/target_genomes_gtdb.txt --output GCA_902519085.1_AG-333-D20_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 23:35:23,482] [INFO] Task succeeded: fastANI
[2023-06-04 23:35:23,492] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 23:35:23,493] [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_902609025.1	s__AG-430-B22 sp902609025	98.0468	106	163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__AG-430-B22	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902533755.1	s__AG-430-B22 sp902533755	93.9646	110	163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__AG-430-B22	95.0	99.48	99.48	0.87	0.87	3	-
GCA_003212795.1	s__AG-430-B22 sp003212795	93.2192	146	163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__AG-430-B22	95.0	98.52	95.66	0.95	0.87	7	-
GCA_003209955.1	s__AG-430-B22 sp003209955	92.3504	127	163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__AG-430-B22	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902608415.1	s__AG-430-B22 sp902608415	91.7452	109	163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__AG-430-B22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002726005.1	s__AG-430-B22 sp002726005	90.6068	124	163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__AG-430-B22	95.0	98.76	98.76	0.74	0.74	2	-
GCA_002728335.1	s__AG-430-B22 sp002728335	83.2639	105	163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__AG-430-B22	95.0	97.53	96.38	0.78	0.71	4	-
--------------------------------------------------------------------------------
[2023-06-04 23:35:23,495] [INFO] GTDB search result was written to GCA_902519085.1_AG-333-D20_genomic.fna/result_gtdb.tsv
[2023-06-04 23:35:23,495] [INFO] ===== GTDB Search completed =====
[2023-06-04 23:35:23,498] [INFO] DFAST_QC result json was written to GCA_902519085.1_AG-333-D20_genomic.fna/dqc_result.json
[2023-06-04 23:35:23,498] [INFO] DFAST_QC completed!
[2023-06-04 23:35:23,499] [INFO] Total running time: 0h0m23s