[2023-03-16 23:05:03,880] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:05:03,880] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:05:03,880] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f86181d-a1fd-47f1-b96b-3716225b524e/dqc_reference
[2023-03-16 23:05:05,095] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:05:05,096] [INFO] Task started: Prodigal
[2023-03-16 23:05:05,096] [INFO] Running command: cat /var/lib/cwl/stgb3dcba3d-3daa-4a30-a1bc-6ae1dfd30351/OceanDNA-b12063.fa | prodigal -d OceanDNA-b12063/cds.fna -a OceanDNA-b12063/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:05:15,741] [INFO] Task succeeded: Prodigal
[2023-03-16 23:05:15,741] [INFO] Task started: HMMsearch
[2023-03-16 23:05:15,741] [INFO] Running command: hmmsearch --tblout OceanDNA-b12063/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f86181d-a1fd-47f1-b96b-3716225b524e/dqc_reference/reference_markers.hmm OceanDNA-b12063/protein.faa > /dev/null
[2023-03-16 23:05:15,915] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:05:15,915] [INFO] Found 6/6 markers.
[2023-03-16 23:05:15,926] [INFO] Query marker FASTA was written to OceanDNA-b12063/markers.fasta
[2023-03-16 23:05:15,926] [INFO] Task started: Blastn
[2023-03-16 23:05:15,926] [INFO] Running command: blastn -query OceanDNA-b12063/markers.fasta -db /var/lib/cwl/stg3f86181d-a1fd-47f1-b96b-3716225b524e/dqc_reference/reference_markers.fasta -out OceanDNA-b12063/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:05:16,504] [INFO] Task succeeded: Blastn
[2023-03-16 23:05:16,505] [INFO] Selected 25 target genomes.
[2023-03-16 23:05:16,505] [INFO] Target genome list was writen to OceanDNA-b12063/target_genomes.txt
[2023-03-16 23:05:16,518] [INFO] Task started: fastANI
[2023-03-16 23:05:16,518] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3dcba3d-3daa-4a30-a1bc-6ae1dfd30351/OceanDNA-b12063.fa --refList OceanDNA-b12063/target_genomes.txt --output OceanDNA-b12063/fastani_result.tsv --threads 1
[2023-03-16 23:05:31,486] [INFO] Task succeeded: fastANI
[2023-03-16 23:05:31,486] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f86181d-a1fd-47f1-b96b-3716225b524e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:05:31,487] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f86181d-a1fd-47f1-b96b-3716225b524e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:05:31,487] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:05:31,487] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 23:05:31,487] [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
--------------------------------------------------------------------------------
[2023-03-16 23:05:31,487] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12063/tc_result.tsv
[2023-03-16 23:05:31,487] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:05:31,487] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:05:31,488] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f86181d-a1fd-47f1-b96b-3716225b524e/dqc_reference/checkm_data
[2023-03-16 23:05:31,490] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:05:31,494] [INFO] Task started: CheckM
[2023-03-16 23:05:31,494] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12063/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12063/checkm_input OceanDNA-b12063/checkm_result
[2023-03-16 23:06:02,386] [INFO] Task succeeded: CheckM
[2023-03-16 23:06:02,387] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.76%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 23:06:02,389] [INFO] ===== Completeness check finished =====
[2023-03-16 23:06:02,389] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:06:02,389] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12063/markers.fasta)
[2023-03-16 23:06:02,389] [INFO] Task started: Blastn
[2023-03-16 23:06:02,390] [INFO] Running command: blastn -query OceanDNA-b12063/markers.fasta -db /var/lib/cwl/stg3f86181d-a1fd-47f1-b96b-3716225b524e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12063/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:06:03,113] [INFO] Task succeeded: Blastn
[2023-03-16 23:06:03,114] [INFO] Selected 25 target genomes.
[2023-03-16 23:06:03,114] [INFO] Target genome list was writen to OceanDNA-b12063/target_genomes_gtdb.txt
[2023-03-16 23:06:03,643] [INFO] Task started: fastANI
[2023-03-16 23:06:03,643] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3dcba3d-3daa-4a30-a1bc-6ae1dfd30351/OceanDNA-b12063.fa --refList OceanDNA-b12063/target_genomes_gtdb.txt --output OceanDNA-b12063/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:06:16,028] [INFO] Task succeeded: fastANI
[2023-03-16 23:06:16,032] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 23:06:16,032] [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_002693775.1	s__UBA974 sp002693775	76.8462	67	518	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480095.1	s__UBA974 sp905480095	76.5921	53	518	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700285.1	s__UBA974 sp002700285	76.578	61	518	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	99.89	99.89	0.95	0.95	2	-
GCA_002722795.1	s__UBA974 sp002722795	76.3399	52	518	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 23:06:16,032] [INFO] GTDB search result was written to OceanDNA-b12063/result_gtdb.tsv
[2023-03-16 23:06:16,033] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:06:16,033] [INFO] DFAST_QC result json was written to OceanDNA-b12063/dqc_result.json
[2023-03-16 23:06:16,033] [INFO] DFAST_QC completed!
[2023-03-16 23:06:16,033] [INFO] Total running time: 0h1m12s