[2023-03-15 13:20:51,586] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:20:51,586] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:20:51,586] [INFO] DQC Reference Directory: /var/lib/cwl/stg9bf07121-a7e0-43c7-a112-e0176345ec83/dqc_reference
[2023-03-15 13:20:52,735] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:20:52,735] [INFO] Task started: Prodigal
[2023-03-15 13:20:52,736] [INFO] Running command: cat /var/lib/cwl/stg10e52432-9d4e-45d7-8550-c3ffedbccef5/OceanDNA-b10577.fa | prodigal -d OceanDNA-b10577/cds.fna -a OceanDNA-b10577/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:21:00,703] [INFO] Task succeeded: Prodigal
[2023-03-15 13:21:00,703] [INFO] Task started: HMMsearch
[2023-03-15 13:21:00,704] [INFO] Running command: hmmsearch --tblout OceanDNA-b10577/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9bf07121-a7e0-43c7-a112-e0176345ec83/dqc_reference/reference_markers.hmm OceanDNA-b10577/protein.faa > /dev/null
[2023-03-15 13:21:00,933] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:21:00,934] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg10e52432-9d4e-45d7-8550-c3ffedbccef5/OceanDNA-b10577.fa]
[2023-03-15 13:21:00,952] [INFO] Query marker FASTA was written to OceanDNA-b10577/markers.fasta
[2023-03-15 13:21:00,953] [INFO] Task started: Blastn
[2023-03-15 13:21:00,953] [INFO] Running command: blastn -query OceanDNA-b10577/markers.fasta -db /var/lib/cwl/stg9bf07121-a7e0-43c7-a112-e0176345ec83/dqc_reference/reference_markers.fasta -out OceanDNA-b10577/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:21:01,564] [INFO] Task succeeded: Blastn
[2023-03-15 13:21:01,565] [INFO] Selected 30 target genomes.
[2023-03-15 13:21:01,565] [INFO] Target genome list was writen to OceanDNA-b10577/target_genomes.txt
[2023-03-15 13:21:01,591] [INFO] Task started: fastANI
[2023-03-15 13:21:01,591] [INFO] Running command: fastANI --query /var/lib/cwl/stg10e52432-9d4e-45d7-8550-c3ffedbccef5/OceanDNA-b10577.fa --refList OceanDNA-b10577/target_genomes.txt --output OceanDNA-b10577/fastani_result.tsv --threads 1
[2023-03-15 13:21:18,085] [INFO] Task succeeded: fastANI
[2023-03-15 13:21:18,085] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9bf07121-a7e0-43c7-a112-e0176345ec83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:21:18,085] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9bf07121-a7e0-43c7-a112-e0176345ec83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:21:18,090] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:21:18,090] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 13:21:18,090] [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
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	75.7745	56	324	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	75.5601	51	324	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:21:18,090] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10577/tc_result.tsv
[2023-03-15 13:21:18,091] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:21:18,091] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:21:18,091] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9bf07121-a7e0-43c7-a112-e0176345ec83/dqc_reference/checkm_data
[2023-03-15 13:21:18,092] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:21:18,097] [INFO] Task started: CheckM
[2023-03-15 13:21:18,097] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10577/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10577/checkm_input OceanDNA-b10577/checkm_result
[2023-03-15 13:21:43,536] [INFO] Task succeeded: CheckM
[2023-03-15 13:21:43,537] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 13:21:43,539] [INFO] ===== Completeness check finished =====
[2023-03-15 13:21:43,539] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:21:43,539] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10577/markers.fasta)
[2023-03-15 13:21:43,540] [INFO] Task started: Blastn
[2023-03-15 13:21:43,541] [INFO] Running command: blastn -query OceanDNA-b10577/markers.fasta -db /var/lib/cwl/stg9bf07121-a7e0-43c7-a112-e0176345ec83/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10577/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:21:44,368] [INFO] Task succeeded: Blastn
[2023-03-15 13:21:44,370] [INFO] Selected 27 target genomes.
[2023-03-15 13:21:44,370] [INFO] Target genome list was writen to OceanDNA-b10577/target_genomes_gtdb.txt
[2023-03-15 13:21:44,390] [INFO] Task started: fastANI
[2023-03-15 13:21:44,390] [INFO] Running command: fastANI --query /var/lib/cwl/stg10e52432-9d4e-45d7-8550-c3ffedbccef5/OceanDNA-b10577.fa --refList OceanDNA-b10577/target_genomes_gtdb.txt --output OceanDNA-b10577/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:21:56,282] [INFO] Task succeeded: fastANI
[2023-03-15 13:21:56,290] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 13:21:56,290] [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_001735715.1	s__GCA001735715 sp001735715	79.0284	196	324	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA001735715	95.0	98.19	98.19	0.84	0.84	2	-
GCA_018673215.1	s__Hel1-33-131 sp018673215	77.5285	92	324	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608725.1	s__Hel1-33-131 sp018608725	77.0672	72	324	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001735745.1	s__Hel1-33-131 sp001735745	77.0008	87	324	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002725015.1	s__UBA3537 sp002725015	76.9205	71	324	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	96.56	95.66	0.77	0.72	3	-
GCA_002698705.1	s__UBA3537 sp002698705	76.7276	89	324	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181825.1	s__Hel1-33-131 sp905181825	76.6898	56	324	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	99.01	99.01	0.77	0.77	2	-
GCA_018608765.1	s__Hel1-33-131 sp018608765	76.6774	84	324	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608625.1	s__Hel1-33-131 sp018608625	76.6606	73	324	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	98.93	97.98	0.88	0.82	3	-
GCA_018608705.1	s__Hel1-33-131 sp018608705	76.1569	64	324	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	99.44	99.44	0.94	0.94	2	-
GCA_013042715.1	s__Site-B15 sp013042715	76.1359	53	324	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Site-B15	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008084905.1	s__Xanthomarina maritima	75.9929	57	324	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608735.1	s__Hel1-33-131 sp018608735	75.9151	76	324	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:21:56,291] [INFO] GTDB search result was written to OceanDNA-b10577/result_gtdb.tsv
[2023-03-15 13:21:56,291] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:21:56,293] [INFO] DFAST_QC result json was written to OceanDNA-b10577/dqc_result.json
[2023-03-15 13:21:56,293] [INFO] DFAST_QC completed!
[2023-03-15 13:21:56,293] [INFO] Total running time: 0h1m5s