[2023-03-16 04:24:46,335] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:24:46,335] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:24:46,335] [INFO] DQC Reference Directory: /var/lib/cwl/stg03afc90f-a18d-4eba-badc-8df55055456f/dqc_reference
[2023-03-16 04:24:48,115] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:24:48,115] [INFO] Task started: Prodigal
[2023-03-16 04:24:48,115] [INFO] Running command: cat /var/lib/cwl/stgef4211fd-cb10-4d45-897a-eaed44abfb09/OceanDNA-b41358.fa | prodigal -d OceanDNA-b41358/cds.fna -a OceanDNA-b41358/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:25:08,894] [INFO] Task succeeded: Prodigal
[2023-03-16 04:25:08,894] [INFO] Task started: HMMsearch
[2023-03-16 04:25:08,894] [INFO] Running command: hmmsearch --tblout OceanDNA-b41358/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03afc90f-a18d-4eba-badc-8df55055456f/dqc_reference/reference_markers.hmm OceanDNA-b41358/protein.faa > /dev/null
[2023-03-16 04:25:09,179] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:25:09,179] [INFO] Found 6/6 markers.
[2023-03-16 04:25:09,201] [INFO] Query marker FASTA was written to OceanDNA-b41358/markers.fasta
[2023-03-16 04:25:09,201] [INFO] Task started: Blastn
[2023-03-16 04:25:09,201] [INFO] Running command: blastn -query OceanDNA-b41358/markers.fasta -db /var/lib/cwl/stg03afc90f-a18d-4eba-badc-8df55055456f/dqc_reference/reference_markers.fasta -out OceanDNA-b41358/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:25:09,864] [INFO] Task succeeded: Blastn
[2023-03-16 04:25:09,865] [INFO] Selected 23 target genomes.
[2023-03-16 04:25:09,865] [INFO] Target genome list was writen to OceanDNA-b41358/target_genomes.txt
[2023-03-16 04:25:09,877] [INFO] Task started: fastANI
[2023-03-16 04:25:09,877] [INFO] Running command: fastANI --query /var/lib/cwl/stgef4211fd-cb10-4d45-897a-eaed44abfb09/OceanDNA-b41358.fa --refList OceanDNA-b41358/target_genomes.txt --output OceanDNA-b41358/fastani_result.tsv --threads 1
[2023-03-16 04:25:27,073] [INFO] Task succeeded: fastANI
[2023-03-16 04:25:27,073] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03afc90f-a18d-4eba-badc-8df55055456f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:25:27,073] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03afc90f-a18d-4eba-badc-8df55055456f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:25:27,079] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:25:27,080] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:25:27,080] [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
Oleibacter marinus	strain=DSM 24913	GCA_900156675.1	484498	484498	type	True	87.0135	954	1176	95	below_threshold
Thalassolituus marinus	strain=IMCC1826	GCA_020320395.1	671053	671053	type	True	78.5698	221	1176	95	below_threshold
Bacterioplanes sanyensis	strain=KCTC 32220	GCA_014652515.1	1249553	1249553	type	True	77.9753	118	1176	95	below_threshold
Thalassolituus oleivorans	strain=MIL-1	GCA_000355675.1	187493	187493	type	True	77.9428	158	1176	95	below_threshold
Oceanobacter kriegii	strain=DSM 6294	GCA_000422845.1	64972	64972	type	True	77.9104	158	1176	95	below_threshold
Oceanobacter mangrovi	strain=SM2-42	GCA_019740315.1	2862510	2862510	type	True	77.6692	145	1176	95	below_threshold
Amphritea spongicola	strain=JCM 16668	GCA_017051665.1	707589	707589	type	True	76.455	57	1176	95	below_threshold
Marinobacterium lutimaris	strain=DSM 22012	GCA_900108065.1	568106	568106	type	True	76.2972	63	1176	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:25:27,080] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41358/tc_result.tsv
[2023-03-16 04:25:27,080] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:25:27,080] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:25:27,080] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03afc90f-a18d-4eba-badc-8df55055456f/dqc_reference/checkm_data
[2023-03-16 04:25:27,081] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:25:27,086] [INFO] Task started: CheckM
[2023-03-16 04:25:27,087] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41358/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41358/checkm_input OceanDNA-b41358/checkm_result
[2023-03-16 04:26:20,198] [INFO] Task succeeded: CheckM
[2023-03-16 04:26:20,198] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:26:20,201] [INFO] ===== Completeness check finished =====
[2023-03-16 04:26:20,201] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:26:20,201] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41358/markers.fasta)
[2023-03-16 04:26:20,202] [INFO] Task started: Blastn
[2023-03-16 04:26:20,202] [INFO] Running command: blastn -query OceanDNA-b41358/markers.fasta -db /var/lib/cwl/stg03afc90f-a18d-4eba-badc-8df55055456f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41358/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:26:21,313] [INFO] Task succeeded: Blastn
[2023-03-16 04:26:21,314] [INFO] Selected 10 target genomes.
[2023-03-16 04:26:21,314] [INFO] Target genome list was writen to OceanDNA-b41358/target_genomes_gtdb.txt
[2023-03-16 04:26:21,346] [INFO] Task started: fastANI
[2023-03-16 04:26:21,346] [INFO] Running command: fastANI --query /var/lib/cwl/stgef4211fd-cb10-4d45-897a-eaed44abfb09/OceanDNA-b41358.fa --refList OceanDNA-b41358/target_genomes_gtdb.txt --output OceanDNA-b41358/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:26:28,498] [INFO] Task succeeded: fastANI
[2023-03-16 04:26:28,504] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 04:26:28,504] [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_002724925.1	s__Oleibacter sp002724925	99.9891	1164	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	98.64	97.85	0.94	0.89	5	conclusive
GCA_002331105.1	s__Oleibacter sp002331105	87.6207	832	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	98.96	97.07	0.90	0.84	7	-
GCF_900156675.1	s__Oleibacter marinus	87.0135	954	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	98.96	98.96	0.99	0.99	2	-
GCA_006212115.1	s__Oleibacter sp006212115	81.0745	446	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007785795.1	s__UBA2009 sp002335285	78.3511	221	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	97.54	97.44	0.92	0.92	6	-
GCA_002314145.1	s__UBA2009 sp002314145	77.8985	182	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	99.98	99.96	0.95	0.88	5	-
GCA_016132445.1	s__UBA2009 sp016132445	77.8933	169	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	97.98	97.98	0.94	0.94	2	-
GCA_014859445.1	s__Bacterioplanes sp014859445	77.5351	78	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Bacterioplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:26:28,504] [INFO] GTDB search result was written to OceanDNA-b41358/result_gtdb.tsv
[2023-03-16 04:26:28,504] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:26:28,505] [INFO] DFAST_QC result json was written to OceanDNA-b41358/dqc_result.json
[2023-03-16 04:26:28,505] [INFO] DFAST_QC completed!
[2023-03-16 04:26:28,505] [INFO] Total running time: 0h1m42s