[2023-03-15 05:00:03,353] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:00:03,353] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:00:03,353] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ae24318-a77f-446c-a96f-9690ad39991e/dqc_reference
[2023-03-15 05:00:04,474] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:00:04,474] [INFO] Task started: Prodigal
[2023-03-15 05:00:04,474] [INFO] Running command: cat /var/lib/cwl/stga34f68dc-540d-423e-b0da-3f51c53e5a8d/OceanDNA-b30636.fa | prodigal -d OceanDNA-b30636/cds.fna -a OceanDNA-b30636/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:00:20,273] [INFO] Task succeeded: Prodigal
[2023-03-15 05:00:20,273] [INFO] Task started: HMMsearch
[2023-03-15 05:00:20,273] [INFO] Running command: hmmsearch --tblout OceanDNA-b30636/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ae24318-a77f-446c-a96f-9690ad39991e/dqc_reference/reference_markers.hmm OceanDNA-b30636/protein.faa > /dev/null
[2023-03-15 05:00:20,445] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:00:20,445] [INFO] Found 6/6 markers.
[2023-03-15 05:00:20,469] [INFO] Query marker FASTA was written to OceanDNA-b30636/markers.fasta
[2023-03-15 05:00:20,471] [INFO] Task started: Blastn
[2023-03-15 05:00:20,471] [INFO] Running command: blastn -query OceanDNA-b30636/markers.fasta -db /var/lib/cwl/stg0ae24318-a77f-446c-a96f-9690ad39991e/dqc_reference/reference_markers.fasta -out OceanDNA-b30636/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:00:21,029] [INFO] Task succeeded: Blastn
[2023-03-15 05:00:21,031] [INFO] Selected 28 target genomes.
[2023-03-15 05:00:21,031] [INFO] Target genome list was writen to OceanDNA-b30636/target_genomes.txt
[2023-03-15 05:00:21,051] [INFO] Task started: fastANI
[2023-03-15 05:00:21,051] [INFO] Running command: fastANI --query /var/lib/cwl/stga34f68dc-540d-423e-b0da-3f51c53e5a8d/OceanDNA-b30636.fa --refList OceanDNA-b30636/target_genomes.txt --output OceanDNA-b30636/fastani_result.tsv --threads 1
[2023-03-15 05:00:37,590] [INFO] Task succeeded: fastANI
[2023-03-15 05:00:37,591] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ae24318-a77f-446c-a96f-9690ad39991e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:00:37,591] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ae24318-a77f-446c-a96f-9690ad39991e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:00:37,595] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:00:37,595] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 05:00:37,595] [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
Actibacterium lipolyticum	strain=CECT 8621	GCA_900184935.1	1524263	1524263	type	True	76.1393	59	843	95	below_threshold
Profundibacter amoris	strain=BAR1	GCA_003544895.1	2171755	2171755	type	True	75.9515	69	843	95	below_threshold
Litoreibacter arenae	strain=DSM 19593	GCA_000442275.2	491388	491388	type	True	75.7745	50	843	95	below_threshold
Aliiroseovarius pelagivivens	strain=CECT 8811	GCA_900302485.1	1639690	1639690	type	True	75.7369	58	843	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 05:00:37,597] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30636/tc_result.tsv
[2023-03-15 05:00:37,602] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:00:37,602] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:00:37,602] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ae24318-a77f-446c-a96f-9690ad39991e/dqc_reference/checkm_data
[2023-03-15 05:00:37,603] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:00:37,626] [INFO] Task started: CheckM
[2023-03-15 05:00:37,626] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30636/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30636/checkm_input OceanDNA-b30636/checkm_result
[2023-03-15 05:01:19,209] [INFO] Task succeeded: CheckM
[2023-03-15 05:01:19,210] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:01:19,238] [INFO] ===== Completeness check finished =====
[2023-03-15 05:01:19,238] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:01:19,238] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30636/markers.fasta)
[2023-03-15 05:01:19,239] [INFO] Task started: Blastn
[2023-03-15 05:01:19,239] [INFO] Running command: blastn -query OceanDNA-b30636/markers.fasta -db /var/lib/cwl/stg0ae24318-a77f-446c-a96f-9690ad39991e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30636/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:01:20,057] [INFO] Task succeeded: Blastn
[2023-03-15 05:01:20,064] [INFO] Selected 17 target genomes.
[2023-03-15 05:01:20,064] [INFO] Target genome list was writen to OceanDNA-b30636/target_genomes_gtdb.txt
[2023-03-15 05:01:20,156] [INFO] Task started: fastANI
[2023-03-15 05:01:20,156] [INFO] Running command: fastANI --query /var/lib/cwl/stga34f68dc-540d-423e-b0da-3f51c53e5a8d/OceanDNA-b30636.fa --refList OceanDNA-b30636/target_genomes_gtdb.txt --output OceanDNA-b30636/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:01:30,403] [INFO] Task succeeded: fastANI
[2023-03-15 05:01:30,408] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 05:01:30,408] [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_016765235.1	s__UBA3077 sp016765235	80.1086	373	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3077	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002746395.1	s__UBA3077 sp002746395	80.0018	391	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3077	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162875.1	s__UBA3077 sp002162875	79.8116	396	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3077	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002367255.1	s__UBA3077 sp002367255	79.6368	260	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3077	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002366645.1	s__UBA3077 sp002366645	78.7056	195	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3077	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015485375.1	s__UBA3077 sp015485375	77.0632	128	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3077	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016764785.1	s__UBA3077 sp016764785	76.1957	62	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3077	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:01:30,411] [INFO] GTDB search result was written to OceanDNA-b30636/result_gtdb.tsv
[2023-03-15 05:01:30,416] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:01:30,420] [INFO] DFAST_QC result json was written to OceanDNA-b30636/dqc_result.json
[2023-03-15 05:01:30,420] [INFO] DFAST_QC completed!
[2023-03-15 05:01:30,420] [INFO] Total running time: 0h1m27s