[2023-03-16 10:20:34,796] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:20:34,797] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:20:34,797] [INFO] DQC Reference Directory: /var/lib/cwl/stg43498608-0b6a-4228-a69f-6103fff56f06/dqc_reference
[2023-03-16 10:20:36,027] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:20:36,027] [INFO] Task started: Prodigal
[2023-03-16 10:20:36,027] [INFO] Running command: cat /var/lib/cwl/stg5b74ba90-8a0e-4848-9137-795ad82c48c6/OceanDNA-b38370.fa | prodigal -d OceanDNA-b38370/cds.fna -a OceanDNA-b38370/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:21:00,678] [INFO] Task succeeded: Prodigal
[2023-03-16 10:21:00,678] [INFO] Task started: HMMsearch
[2023-03-16 10:21:00,678] [INFO] Running command: hmmsearch --tblout OceanDNA-b38370/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43498608-0b6a-4228-a69f-6103fff56f06/dqc_reference/reference_markers.hmm OceanDNA-b38370/protein.faa > /dev/null
[2023-03-16 10:21:00,998] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:21:00,999] [INFO] Found 6/6 markers.
[2023-03-16 10:21:01,024] [INFO] Query marker FASTA was written to OceanDNA-b38370/markers.fasta
[2023-03-16 10:21:01,025] [INFO] Task started: Blastn
[2023-03-16 10:21:01,025] [INFO] Running command: blastn -query OceanDNA-b38370/markers.fasta -db /var/lib/cwl/stg43498608-0b6a-4228-a69f-6103fff56f06/dqc_reference/reference_markers.fasta -out OceanDNA-b38370/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:21:01,628] [INFO] Task succeeded: Blastn
[2023-03-16 10:21:01,629] [INFO] Selected 30 target genomes.
[2023-03-16 10:21:01,629] [INFO] Target genome list was writen to OceanDNA-b38370/target_genomes.txt
[2023-03-16 10:21:01,657] [INFO] Task started: fastANI
[2023-03-16 10:21:01,657] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b74ba90-8a0e-4848-9137-795ad82c48c6/OceanDNA-b38370.fa --refList OceanDNA-b38370/target_genomes.txt --output OceanDNA-b38370/fastani_result.tsv --threads 1
[2023-03-16 10:21:21,820] [INFO] Task succeeded: fastANI
[2023-03-16 10:21:21,820] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43498608-0b6a-4228-a69f-6103fff56f06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:21:21,821] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43498608-0b6a-4228-a69f-6103fff56f06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:21:21,824] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:21:21,824] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 10:21:21,824] [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
Alcanivorax profundi	strain=MTEO17	GCA_003597125.1	2338368	2338368	type	True	76.28	58	1313	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 10:21:21,824] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38370/tc_result.tsv
[2023-03-16 10:21:21,824] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:21:21,824] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:21:21,824] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43498608-0b6a-4228-a69f-6103fff56f06/dqc_reference/checkm_data
[2023-03-16 10:21:21,825] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:21:21,831] [INFO] Task started: CheckM
[2023-03-16 10:21:21,831] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38370/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38370/checkm_input OceanDNA-b38370/checkm_result
[2023-03-16 10:22:23,790] [INFO] Task succeeded: CheckM
[2023-03-16 10:22:23,791] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:22:23,793] [INFO] ===== Completeness check finished =====
[2023-03-16 10:22:23,794] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:22:23,794] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38370/markers.fasta)
[2023-03-16 10:22:23,795] [INFO] Task started: Blastn
[2023-03-16 10:22:23,795] [INFO] Running command: blastn -query OceanDNA-b38370/markers.fasta -db /var/lib/cwl/stg43498608-0b6a-4228-a69f-6103fff56f06/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38370/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:22:24,617] [INFO] Task succeeded: Blastn
[2023-03-16 10:22:24,618] [INFO] Selected 30 target genomes.
[2023-03-16 10:22:24,618] [INFO] Target genome list was writen to OceanDNA-b38370/target_genomes_gtdb.txt
[2023-03-16 10:22:24,768] [INFO] Task started: fastANI
[2023-03-16 10:22:24,769] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b74ba90-8a0e-4848-9137-795ad82c48c6/OceanDNA-b38370.fa --refList OceanDNA-b38370/target_genomes_gtdb.txt --output OceanDNA-b38370/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:22:44,202] [INFO] Task succeeded: fastANI
[2023-03-16 10:22:44,206] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:22:44,206] [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_003597125.1	s__Alcanivorax profundi	76.28	58	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	99.31	99.31	0.96	0.96	2	-
GCA_002701845.1	s__Ketobacter sp002701845	76.181	104	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706085.1	s__Alcanivorax sp002706085	76.181	50	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.88	97.88	0.86	0.86	2	-
GCA_003671495.1	s__Ketobacter sp003671495	76.1646	107	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002471665.1	s__Ketobacter sp002471665	75.9614	103	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	99.82	99.43	0.96	0.93	14	-
--------------------------------------------------------------------------------
[2023-03-16 10:22:44,207] [INFO] GTDB search result was written to OceanDNA-b38370/result_gtdb.tsv
[2023-03-16 10:22:44,207] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:22:44,207] [INFO] DFAST_QC result json was written to OceanDNA-b38370/dqc_result.json
[2023-03-16 10:22:44,207] [INFO] DFAST_QC completed!
[2023-03-16 10:22:44,208] [INFO] Total running time: 0h2m9s