[2023-03-14 11:33:34,948] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:33:34,948] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:33:34,948] [INFO] DQC Reference Directory: /var/lib/cwl/stgf89d57a1-2c78-4c91-88d6-46fa4c399384/dqc_reference
[2023-03-14 11:33:36,229] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:33:36,229] [INFO] Task started: Prodigal
[2023-03-14 11:33:36,230] [INFO] Running command: cat /var/lib/cwl/stg7bcd4351-c86b-4db0-a467-279ff30c84e4/OceanDNA-b259.fa | prodigal -d OceanDNA-b259/cds.fna -a OceanDNA-b259/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:33:50,397] [INFO] Task succeeded: Prodigal
[2023-03-14 11:33:50,397] [INFO] Task started: HMMsearch
[2023-03-14 11:33:50,397] [INFO] Running command: hmmsearch --tblout OceanDNA-b259/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf89d57a1-2c78-4c91-88d6-46fa4c399384/dqc_reference/reference_markers.hmm OceanDNA-b259/protein.faa > /dev/null
[2023-03-14 11:33:50,596] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:33:50,597] [INFO] Found 6/6 markers.
[2023-03-14 11:33:50,613] [INFO] Query marker FASTA was written to OceanDNA-b259/markers.fasta
[2023-03-14 11:33:50,613] [INFO] Task started: Blastn
[2023-03-14 11:33:50,613] [INFO] Running command: blastn -query OceanDNA-b259/markers.fasta -db /var/lib/cwl/stgf89d57a1-2c78-4c91-88d6-46fa4c399384/dqc_reference/reference_markers.fasta -out OceanDNA-b259/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:33:51,165] [INFO] Task succeeded: Blastn
[2023-03-14 11:33:51,166] [INFO] Selected 23 target genomes.
[2023-03-14 11:33:51,166] [INFO] Target genome list was writen to OceanDNA-b259/target_genomes.txt
[2023-03-14 11:33:51,180] [INFO] Task started: fastANI
[2023-03-14 11:33:51,180] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bcd4351-c86b-4db0-a467-279ff30c84e4/OceanDNA-b259.fa --refList OceanDNA-b259/target_genomes.txt --output OceanDNA-b259/fastani_result.tsv --threads 1
[2023-03-14 11:34:09,234] [INFO] Task succeeded: fastANI
[2023-03-14 11:34:09,234] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf89d57a1-2c78-4c91-88d6-46fa4c399384/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:34:09,234] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf89d57a1-2c78-4c91-88d6-46fa4c399384/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:34:09,235] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:34:09,235] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:34:09,235] [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
--------------------------------------------------------------------------------
[2023-03-14 11:34:09,297] [INFO] DFAST Taxonomy check result was written to OceanDNA-b259/tc_result.tsv
[2023-03-14 11:34:09,297] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:34:09,297] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:34:09,297] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf89d57a1-2c78-4c91-88d6-46fa4c399384/dqc_reference/checkm_data
[2023-03-14 11:34:09,300] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:34:09,320] [INFO] Task started: CheckM
[2023-03-14 11:34:09,320] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b259/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b259/checkm_input OceanDNA-b259/checkm_result
[2023-03-14 11:34:48,100] [INFO] Task succeeded: CheckM
[2023-03-14 11:34:48,101] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:34:48,103] [INFO] ===== Completeness check finished =====
[2023-03-14 11:34:48,103] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:34:48,103] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b259/markers.fasta)
[2023-03-14 11:34:48,103] [INFO] Task started: Blastn
[2023-03-14 11:34:48,103] [INFO] Running command: blastn -query OceanDNA-b259/markers.fasta -db /var/lib/cwl/stgf89d57a1-2c78-4c91-88d6-46fa4c399384/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b259/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:34:48,866] [INFO] Task succeeded: Blastn
[2023-03-14 11:34:48,867] [INFO] Selected 20 target genomes.
[2023-03-14 11:34:48,867] [INFO] Target genome list was writen to OceanDNA-b259/target_genomes_gtdb.txt
[2023-03-14 11:34:48,908] [INFO] Task started: fastANI
[2023-03-14 11:34:48,908] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bcd4351-c86b-4db0-a467-279ff30c84e4/OceanDNA-b259.fa --refList OceanDNA-b259/target_genomes_gtdb.txt --output OceanDNA-b259/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:35:02,242] [INFO] Task succeeded: fastANI
[2023-03-14 11:35:02,247] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:35:02,247] [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_009838525.1	s__VXRJ01 sp009838525	76.4198	63	765	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__VXRJ01	95.0	98.98	98.07	0.95	0.93	4	-
GCA_012271165.1	s__JAAXGX01 sp012271165	76.3725	80	765	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__JAAXGX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002730525.1	s__UBA2161 sp002730525	76.3658	54	765	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA823;g__UBA2161	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523845.1	s__WTFV01 sp011523845	76.2136	119	765	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523485.1	s__WTFV01 sp011523485	76.1956	59	765	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009861545.1	s__WTFV01 sp009861545	76.0562	99	765	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	96.15	96.15	0.82	0.82	2	-
GCA_001767525.1	s__Gp6-AA40 sp001767525	75.824	53	765	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	99.96	99.96	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-03-14 11:35:02,247] [INFO] GTDB search result was written to OceanDNA-b259/result_gtdb.tsv
[2023-03-14 11:35:02,248] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:35:02,248] [INFO] DFAST_QC result json was written to OceanDNA-b259/dqc_result.json
[2023-03-14 11:35:02,248] [INFO] DFAST_QC completed!
[2023-03-14 11:35:02,248] [INFO] Total running time: 0h1m27s