[2023-03-18 03:45:10,282] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:45:10,282] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:45:10,283] [INFO] DQC Reference Directory: /var/lib/cwl/stg84097e14-def5-4364-9571-8405fef03874/dqc_reference
[2023-03-18 03:45:12,144] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:45:12,144] [INFO] Task started: Prodigal
[2023-03-18 03:45:12,144] [INFO] Running command: cat /var/lib/cwl/stga072e41b-96b5-4661-84db-3fe086157a46/OceanDNA-b5399.fa | prodigal -d OceanDNA-b5399/cds.fna -a OceanDNA-b5399/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:45:29,621] [INFO] Task succeeded: Prodigal
[2023-03-18 03:45:29,621] [INFO] Task started: HMMsearch
[2023-03-18 03:45:29,622] [INFO] Running command: hmmsearch --tblout OceanDNA-b5399/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84097e14-def5-4364-9571-8405fef03874/dqc_reference/reference_markers.hmm OceanDNA-b5399/protein.faa > /dev/null
[2023-03-18 03:45:29,942] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:45:29,942] [INFO] Found 6/6 markers.
[2023-03-18 03:45:29,965] [INFO] Query marker FASTA was written to OceanDNA-b5399/markers.fasta
[2023-03-18 03:45:29,965] [INFO] Task started: Blastn
[2023-03-18 03:45:29,965] [INFO] Running command: blastn -query OceanDNA-b5399/markers.fasta -db /var/lib/cwl/stg84097e14-def5-4364-9571-8405fef03874/dqc_reference/reference_markers.fasta -out OceanDNA-b5399/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:45:30,535] [INFO] Task succeeded: Blastn
[2023-03-18 03:45:30,576] [INFO] Selected 23 target genomes.
[2023-03-18 03:45:30,577] [INFO] Target genome list was writen to OceanDNA-b5399/target_genomes.txt
[2023-03-18 03:45:30,588] [INFO] Task started: fastANI
[2023-03-18 03:45:30,588] [INFO] Running command: fastANI --query /var/lib/cwl/stga072e41b-96b5-4661-84db-3fe086157a46/OceanDNA-b5399.fa --refList OceanDNA-b5399/target_genomes.txt --output OceanDNA-b5399/fastani_result.tsv --threads 1
[2023-03-18 03:45:42,724] [INFO] Task succeeded: fastANI
[2023-03-18 03:45:42,725] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84097e14-def5-4364-9571-8405fef03874/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:45:42,725] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84097e14-def5-4364-9571-8405fef03874/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:45:42,725] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:45:42,725] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 03:45:42,725] [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
--------------------------------------------------------------------------------
[2023-03-18 03:45:42,725] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5399/tc_result.tsv
[2023-03-18 03:45:42,725] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:45:42,726] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:45:42,726] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84097e14-def5-4364-9571-8405fef03874/dqc_reference/checkm_data
[2023-03-18 03:45:42,728] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:45:42,737] [INFO] Task started: CheckM
[2023-03-18 03:45:42,738] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5399/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5399/checkm_input OceanDNA-b5399/checkm_result
[2023-03-18 03:46:29,825] [INFO] Task succeeded: CheckM
[2023-03-18 03:46:29,826] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:46:29,828] [INFO] ===== Completeness check finished =====
[2023-03-18 03:46:29,828] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:46:29,828] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5399/markers.fasta)
[2023-03-18 03:46:29,829] [INFO] Task started: Blastn
[2023-03-18 03:46:29,829] [INFO] Running command: blastn -query OceanDNA-b5399/markers.fasta -db /var/lib/cwl/stg84097e14-def5-4364-9571-8405fef03874/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5399/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:46:30,566] [INFO] Task succeeded: Blastn
[2023-03-18 03:46:30,567] [INFO] Selected 21 target genomes.
[2023-03-18 03:46:30,567] [INFO] Target genome list was writen to OceanDNA-b5399/target_genomes_gtdb.txt
[2023-03-18 03:46:30,728] [INFO] Task started: fastANI
[2023-03-18 03:46:30,729] [INFO] Running command: fastANI --query /var/lib/cwl/stga072e41b-96b5-4661-84db-3fe086157a46/OceanDNA-b5399.fa --refList OceanDNA-b5399/target_genomes_gtdb.txt --output OceanDNA-b5399/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:46:41,472] [INFO] Task succeeded: fastANI
[2023-03-18 03:46:41,477] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 03:46:41,477] [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_002471375.1	s__UBA4466 sp002471375	98.5691	727	795	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002733985.1	s__UBA4466 sp002733985	76.769	88	795	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	96.56	96.56	0.90	0.90	2	-
GCA_013373595.1	s__UBA4466 sp013373595	76.5219	75	795	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182335.1	s__UBA4466 sp905182335	76.5016	57	795	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	99.88	99.88	0.98	0.98	2	-
GCA_905478665.1	s__UBA4466 sp905478665	76.2799	69	795	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002427735.1	s__UBA4466 sp002427735	76.0825	50	795	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:46:41,477] [INFO] GTDB search result was written to OceanDNA-b5399/result_gtdb.tsv
[2023-03-18 03:46:41,477] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:46:41,478] [INFO] DFAST_QC result json was written to OceanDNA-b5399/dqc_result.json
[2023-03-18 03:46:41,478] [INFO] DFAST_QC completed!
[2023-03-18 03:46:41,478] [INFO] Total running time: 0h1m31s