[2023-03-18 09:27:55,579] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:27:55,579] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:27:55,579] [INFO] DQC Reference Directory: /var/lib/cwl/stg3b893ca4-b663-465b-9350-8f11c68de989/dqc_reference
[2023-03-18 09:27:56,657] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:27:56,658] [INFO] Task started: Prodigal
[2023-03-18 09:27:56,659] [INFO] Running command: cat /var/lib/cwl/stg691e8561-3655-475c-acb1-5d868fcec6e1/OceanDNA-b10869.fa | prodigal -d OceanDNA-b10869/cds.fna -a OceanDNA-b10869/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:28:08,771] [INFO] Task succeeded: Prodigal
[2023-03-18 09:28:08,771] [INFO] Task started: HMMsearch
[2023-03-18 09:28:08,771] [INFO] Running command: hmmsearch --tblout OceanDNA-b10869/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3b893ca4-b663-465b-9350-8f11c68de989/dqc_reference/reference_markers.hmm OceanDNA-b10869/protein.faa > /dev/null
[2023-03-18 09:28:08,962] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:28:08,962] [INFO] Found 6/6 markers.
[2023-03-18 09:28:08,976] [INFO] Query marker FASTA was written to OceanDNA-b10869/markers.fasta
[2023-03-18 09:28:08,977] [INFO] Task started: Blastn
[2023-03-18 09:28:08,978] [INFO] Running command: blastn -query OceanDNA-b10869/markers.fasta -db /var/lib/cwl/stg3b893ca4-b663-465b-9350-8f11c68de989/dqc_reference/reference_markers.fasta -out OceanDNA-b10869/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:28:09,542] [INFO] Task succeeded: Blastn
[2023-03-18 09:28:09,543] [INFO] Selected 33 target genomes.
[2023-03-18 09:28:09,543] [INFO] Target genome list was writen to OceanDNA-b10869/target_genomes.txt
[2023-03-18 09:28:09,561] [INFO] Task started: fastANI
[2023-03-18 09:28:09,561] [INFO] Running command: fastANI --query /var/lib/cwl/stg691e8561-3655-475c-acb1-5d868fcec6e1/OceanDNA-b10869.fa --refList OceanDNA-b10869/target_genomes.txt --output OceanDNA-b10869/fastani_result.tsv --threads 1
[2023-03-18 09:28:27,792] [INFO] Task succeeded: fastANI
[2023-03-18 09:28:27,792] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3b893ca4-b663-465b-9350-8f11c68de989/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:28:27,792] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3b893ca4-b663-465b-9350-8f11c68de989/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:28:27,796] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:28:27,796] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 09:28:27,796] [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
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	75.841	52	634	95	below_threshold
Lutibacter citreus	strain=1KV19	GCA_003260195.1	2138210	2138210	type	True	75.7687	56	634	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 09:28:27,796] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10869/tc_result.tsv
[2023-03-18 09:28:27,796] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:28:27,796] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:28:27,796] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3b893ca4-b663-465b-9350-8f11c68de989/dqc_reference/checkm_data
[2023-03-18 09:28:27,797] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:28:27,801] [INFO] Task started: CheckM
[2023-03-18 09:28:27,801] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10869/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10869/checkm_input OceanDNA-b10869/checkm_result
[2023-03-18 09:29:01,885] [INFO] Task succeeded: CheckM
[2023-03-18 09:29:01,886] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.48%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 09:29:01,887] [INFO] ===== Completeness check finished =====
[2023-03-18 09:29:01,887] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:29:01,888] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10869/markers.fasta)
[2023-03-18 09:29:01,889] [INFO] Task started: Blastn
[2023-03-18 09:29:01,889] [INFO] Running command: blastn -query OceanDNA-b10869/markers.fasta -db /var/lib/cwl/stg3b893ca4-b663-465b-9350-8f11c68de989/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10869/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:29:02,670] [INFO] Task succeeded: Blastn
[2023-03-18 09:29:02,670] [INFO] Selected 17 target genomes.
[2023-03-18 09:29:02,670] [INFO] Target genome list was writen to OceanDNA-b10869/target_genomes_gtdb.txt
[2023-03-18 09:29:02,733] [INFO] Task started: fastANI
[2023-03-18 09:29:02,733] [INFO] Running command: fastANI --query /var/lib/cwl/stg691e8561-3655-475c-acb1-5d868fcec6e1/OceanDNA-b10869.fa --refList OceanDNA-b10869/target_genomes_gtdb.txt --output OceanDNA-b10869/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:29:08,574] [INFO] Task succeeded: fastANI
[2023-03-18 09:29:08,579] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 09:29:08,579] [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_905181615.1	s__UBA7428 sp905181615	99.7866	619	634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	99.59	99.59	0.98	0.98	2	conclusive
GCA_003023645.1	s__UBA7428 sp003023645	78.9572	294	634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	99.50	99.50	0.87	0.87	2	-
GCA_018608425.1	s__UBA7428 sp018608425	78.9275	222	634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002477625.1	s__UBA7428 sp002477625	78.5837	224	634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	98.28	97.25	0.74	0.68	4	-
GCA_002708445.1	s__UBA7428 sp002708445	77.5602	176	634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480425.1	s__MS024-2A sp905480425	76.4866	74	634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	95.11	95.11	0.87	0.87	2	-
GCA_009886625.1	s__MS024-2A sp009886625	76.3654	63	634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000173095.1	s__MS024-2A sp000173095	76.3036	62	634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.61	99.48	0.88	0.84	16	-
--------------------------------------------------------------------------------
[2023-03-18 09:29:08,579] [INFO] GTDB search result was written to OceanDNA-b10869/result_gtdb.tsv
[2023-03-18 09:29:08,580] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:29:08,580] [INFO] DFAST_QC result json was written to OceanDNA-b10869/dqc_result.json
[2023-03-18 09:29:08,581] [INFO] DFAST_QC completed!
[2023-03-18 09:29:08,581] [INFO] Total running time: 0h1m13s