[2023-03-17 00:17:04,655] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:17:04,656] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:17:04,656] [INFO] DQC Reference Directory: /var/lib/cwl/stg5cfd7afa-fcbe-4502-8969-9b65531339be/dqc_reference
[2023-03-17 00:17:05,752] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:17:05,752] [INFO] Task started: Prodigal
[2023-03-17 00:17:05,752] [INFO] Running command: cat /var/lib/cwl/stgfb8004ab-a9a0-4aa2-8f7e-fccb8ec7706a/OceanDNA-b4499.fa | prodigal -d OceanDNA-b4499/cds.fna -a OceanDNA-b4499/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:17:39,170] [INFO] Task succeeded: Prodigal
[2023-03-17 00:17:39,171] [INFO] Task started: HMMsearch
[2023-03-17 00:17:39,171] [INFO] Running command: hmmsearch --tblout OceanDNA-b4499/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5cfd7afa-fcbe-4502-8969-9b65531339be/dqc_reference/reference_markers.hmm OceanDNA-b4499/protein.faa > /dev/null
[2023-03-17 00:17:39,571] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:17:39,572] [INFO] Found 6/6 markers.
[2023-03-17 00:17:39,603] [INFO] Query marker FASTA was written to OceanDNA-b4499/markers.fasta
[2023-03-17 00:17:39,604] [INFO] Task started: Blastn
[2023-03-17 00:17:39,604] [INFO] Running command: blastn -query OceanDNA-b4499/markers.fasta -db /var/lib/cwl/stg5cfd7afa-fcbe-4502-8969-9b65531339be/dqc_reference/reference_markers.fasta -out OceanDNA-b4499/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:17:43,499] [INFO] Task succeeded: Blastn
[2023-03-17 00:17:43,500] [INFO] Selected 31 target genomes.
[2023-03-17 00:17:43,500] [INFO] Target genome list was writen to OceanDNA-b4499/target_genomes.txt
[2023-03-17 00:17:43,521] [INFO] Task started: fastANI
[2023-03-17 00:17:43,521] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb8004ab-a9a0-4aa2-8f7e-fccb8ec7706a/OceanDNA-b4499.fa --refList OceanDNA-b4499/target_genomes.txt --output OceanDNA-b4499/fastani_result.tsv --threads 1
[2023-03-17 00:18:07,738] [INFO] Task succeeded: fastANI
[2023-03-17 00:18:07,739] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5cfd7afa-fcbe-4502-8969-9b65531339be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:18:07,739] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5cfd7afa-fcbe-4502-8969-9b65531339be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:18:07,743] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:18:07,743] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 00:18:07,743] [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
Jiulongibacter sediminis	strain=JN14-9	GCA_001306455.1	1605367	1605367	type	True	77.3018	254	1532	95	below_threshold
Jiulongibacter sediminis	strain=JN14-9	GCA_004329705.1	1605367	1605367	type	True	77.2918	255	1532	95	below_threshold
Marinilongibacter aquaticus	strain=YYF0007	GCA_020149935.1	2975157	2975157	type	True	76.1221	102	1532	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 00:18:07,743] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4499/tc_result.tsv
[2023-03-17 00:18:07,744] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:18:07,744] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:18:07,744] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5cfd7afa-fcbe-4502-8969-9b65531339be/dqc_reference/checkm_data
[2023-03-17 00:18:07,744] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:18:07,761] [INFO] Task started: CheckM
[2023-03-17 00:18:07,761] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4499/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4499/checkm_input OceanDNA-b4499/checkm_result
[2023-03-17 00:19:30,161] [INFO] Task succeeded: CheckM
[2023-03-17 00:19:30,162] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:19:30,165] [INFO] ===== Completeness check finished =====
[2023-03-17 00:19:30,165] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:19:30,165] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4499/markers.fasta)
[2023-03-17 00:19:30,166] [INFO] Task started: Blastn
[2023-03-17 00:19:30,166] [INFO] Running command: blastn -query OceanDNA-b4499/markers.fasta -db /var/lib/cwl/stg5cfd7afa-fcbe-4502-8969-9b65531339be/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4499/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:19:30,873] [INFO] Task succeeded: Blastn
[2023-03-17 00:19:30,889] [INFO] Selected 32 target genomes.
[2023-03-17 00:19:30,889] [INFO] Target genome list was writen to OceanDNA-b4499/target_genomes_gtdb.txt
[2023-03-17 00:19:30,937] [INFO] Task started: fastANI
[2023-03-17 00:19:30,938] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb8004ab-a9a0-4aa2-8f7e-fccb8ec7706a/OceanDNA-b4499.fa --refList OceanDNA-b4499/target_genomes_gtdb.txt --output OceanDNA-b4499/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:19:56,396] [INFO] Task succeeded: fastANI
[2023-03-17 00:19:56,399] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 00:19:56,399] [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
GCF_001306455.1	s__Jiulongibacter sediminis	77.2918	255	1532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Jiulongibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009905725.1	s__Leadbetterella sp002483125	75.8315	55	1532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Leadbetterella	95.0	98.11	98.11	0.94	0.94	2	-
GCA_016722655.1	s__Leadbetterella sp016722655	75.7038	53	1532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Leadbetterella	95.0	99.38	99.07	0.96	0.94	5	-
--------------------------------------------------------------------------------
[2023-03-17 00:19:56,399] [INFO] GTDB search result was written to OceanDNA-b4499/result_gtdb.tsv
[2023-03-17 00:19:56,400] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:19:56,400] [INFO] DFAST_QC result json was written to OceanDNA-b4499/dqc_result.json
[2023-03-17 00:19:56,400] [INFO] DFAST_QC completed!
[2023-03-17 00:19:56,400] [INFO] Total running time: 0h2m52s