[2023-03-16 23:35:13,188] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:35:13,188] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:35:13,188] [INFO] DQC Reference Directory: /var/lib/cwl/stg56b37769-ad19-44b8-bf33-7b01577f2e3e/dqc_reference
[2023-03-16 23:35:14,948] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:35:14,948] [INFO] Task started: Prodigal
[2023-03-16 23:35:14,948] [INFO] Running command: cat /var/lib/cwl/stg02f9ee8a-1c9f-4531-a460-4f210f9d2ced/OceanDNA-b4134.fa | prodigal -d OceanDNA-b4134/cds.fna -a OceanDNA-b4134/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:35:46,236] [INFO] Task succeeded: Prodigal
[2023-03-16 23:35:46,236] [INFO] Task started: HMMsearch
[2023-03-16 23:35:46,237] [INFO] Running command: hmmsearch --tblout OceanDNA-b4134/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56b37769-ad19-44b8-bf33-7b01577f2e3e/dqc_reference/reference_markers.hmm OceanDNA-b4134/protein.faa > /dev/null
[2023-03-16 23:35:46,467] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:35:46,468] [INFO] Found 6/6 markers.
[2023-03-16 23:35:46,493] [INFO] Query marker FASTA was written to OceanDNA-b4134/markers.fasta
[2023-03-16 23:35:46,493] [INFO] Task started: Blastn
[2023-03-16 23:35:46,493] [INFO] Running command: blastn -query OceanDNA-b4134/markers.fasta -db /var/lib/cwl/stg56b37769-ad19-44b8-bf33-7b01577f2e3e/dqc_reference/reference_markers.fasta -out OceanDNA-b4134/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:35:47,030] [INFO] Task succeeded: Blastn
[2023-03-16 23:35:47,031] [INFO] Selected 10 target genomes.
[2023-03-16 23:35:47,031] [INFO] Target genome list was writen to OceanDNA-b4134/target_genomes.txt
[2023-03-16 23:35:47,037] [INFO] Task started: fastANI
[2023-03-16 23:35:47,038] [INFO] Running command: fastANI --query /var/lib/cwl/stg02f9ee8a-1c9f-4531-a460-4f210f9d2ced/OceanDNA-b4134.fa --refList OceanDNA-b4134/target_genomes.txt --output OceanDNA-b4134/fastani_result.tsv --threads 1
[2023-03-16 23:35:55,407] [INFO] Task succeeded: fastANI
[2023-03-16 23:35:55,408] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56b37769-ad19-44b8-bf33-7b01577f2e3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:35:55,408] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56b37769-ad19-44b8-bf33-7b01577f2e3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:35:55,412] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:35:55,413] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 23:35:55,413] [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
Roseivirga ehrenbergii	strain=DSM 102268	GCA_004340805.1	279360	279360	type	True	87.1709	1079	1478	95	below_threshold
Roseivirga ehrenbergii	strain=KMM 6017	GCA_001593005.1	279360	279360	type	True	87.1684	1081	1478	95	below_threshold
Roseivirga seohaensis	strain=SW-152	GCA_001592945.1	1914963	1914963	type	True	86.9682	1097	1478	95	below_threshold
Roseivirga seohaensis subsp. aquiponti	strain=D-25	GCA_001267955.1	1566026	1914963	type	True	86.6441	1070	1478	95	below_threshold
Roseivirga echinicomitans	strain=KMM 6058	GCA_001592935.1	296218	296218	type	True	85.3758	1067	1478	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 23:35:55,413] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4134/tc_result.tsv
[2023-03-16 23:35:55,413] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:35:55,413] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:35:55,413] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56b37769-ad19-44b8-bf33-7b01577f2e3e/dqc_reference/checkm_data
[2023-03-16 23:35:55,414] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:35:55,503] [INFO] Task started: CheckM
[2023-03-16 23:35:55,503] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4134/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4134/checkm_input OceanDNA-b4134/checkm_result
[2023-03-16 23:37:12,245] [INFO] Task succeeded: CheckM
[2023-03-16 23:37:12,246] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 23:37:12,248] [INFO] ===== Completeness check finished =====
[2023-03-16 23:37:12,248] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:37:12,249] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4134/markers.fasta)
[2023-03-16 23:37:12,250] [INFO] Task started: Blastn
[2023-03-16 23:37:12,250] [INFO] Running command: blastn -query OceanDNA-b4134/markers.fasta -db /var/lib/cwl/stg56b37769-ad19-44b8-bf33-7b01577f2e3e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4134/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:37:12,984] [INFO] Task succeeded: Blastn
[2023-03-16 23:37:12,985] [INFO] Selected 10 target genomes.
[2023-03-16 23:37:12,985] [INFO] Target genome list was writen to OceanDNA-b4134/target_genomes_gtdb.txt
[2023-03-16 23:37:13,168] [INFO] Task started: fastANI
[2023-03-16 23:37:13,168] [INFO] Running command: fastANI --query /var/lib/cwl/stg02f9ee8a-1c9f-4531-a460-4f210f9d2ced/OceanDNA-b4134.fa --refList OceanDNA-b4134/target_genomes_gtdb.txt --output OceanDNA-b4134/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:37:20,916] [INFO] Task succeeded: fastANI
[2023-03-16 23:37:20,922] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 23:37:20,922] [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_001593005.1	s__Roseivirga ehrenbergii	87.1801	1080	1478	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Roseivirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001592945.1	s__Roseivirga seohaensis	86.9682	1097	1478	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Roseivirga	95.0	97.29	97.29	0.91	0.91	2	-
GCF_001592935.1	s__Roseivirga echinicomitans	85.3793	1067	1478	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Roseivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002786855.1	s__Roseivirga sp002786855	77.9075	367	1478	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Roseivirga	95.0	99.94	99.94	0.97	0.97	2	-
GCA_002477595.1	s__Fabibacter sp002477595	77.048	66	1478	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	99.68	99.60	0.84	0.83	4	-
GCF_900111145.1	s__Fabibacter pacificus	76.9528	171	1478	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002427755.1	s__Fabibacter sp002427755	76.6787	100	1478	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001747095.1	s__Fabibacter sp001747095	76.3748	109	1478	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 23:37:20,922] [INFO] GTDB search result was written to OceanDNA-b4134/result_gtdb.tsv
[2023-03-16 23:37:20,922] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:37:20,923] [INFO] DFAST_QC result json was written to OceanDNA-b4134/dqc_result.json
[2023-03-16 23:37:20,923] [INFO] DFAST_QC completed!
[2023-03-16 23:37:20,923] [INFO] Total running time: 0h2m8s