[2023-03-18 08:36:16,001] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:36:16,001] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:36:16,001] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8f9b3ea-8c3c-423e-b62b-24a9e370d1b0/dqc_reference
[2023-03-18 08:36:17,831] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:36:17,831] [INFO] Task started: Prodigal
[2023-03-18 08:36:17,831] [INFO] Running command: cat /var/lib/cwl/stg234bba91-9171-43f4-b766-e64a6513e7a0/OceanDNA-b16193.fa | prodigal -d OceanDNA-b16193/cds.fna -a OceanDNA-b16193/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:36:52,296] [INFO] Task succeeded: Prodigal
[2023-03-18 08:36:52,297] [INFO] Task started: HMMsearch
[2023-03-18 08:36:52,297] [INFO] Running command: hmmsearch --tblout OceanDNA-b16193/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8f9b3ea-8c3c-423e-b62b-24a9e370d1b0/dqc_reference/reference_markers.hmm OceanDNA-b16193/protein.faa > /dev/null
[2023-03-18 08:36:52,585] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:36:52,585] [INFO] Found 6/6 markers.
[2023-03-18 08:36:52,648] [INFO] Query marker FASTA was written to OceanDNA-b16193/markers.fasta
[2023-03-18 08:36:52,650] [INFO] Task started: Blastn
[2023-03-18 08:36:52,650] [INFO] Running command: blastn -query OceanDNA-b16193/markers.fasta -db /var/lib/cwl/stgc8f9b3ea-8c3c-423e-b62b-24a9e370d1b0/dqc_reference/reference_markers.fasta -out OceanDNA-b16193/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:36:53,183] [INFO] Task succeeded: Blastn
[2023-03-18 08:36:53,184] [INFO] Selected 25 target genomes.
[2023-03-18 08:36:53,184] [INFO] Target genome list was writen to OceanDNA-b16193/target_genomes.txt
[2023-03-18 08:36:53,250] [INFO] Task started: fastANI
[2023-03-18 08:36:53,250] [INFO] Running command: fastANI --query /var/lib/cwl/stg234bba91-9171-43f4-b766-e64a6513e7a0/OceanDNA-b16193.fa --refList OceanDNA-b16193/target_genomes.txt --output OceanDNA-b16193/fastani_result.tsv --threads 1
[2023-03-18 08:37:15,038] [INFO] Task succeeded: fastANI
[2023-03-18 08:37:15,039] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8f9b3ea-8c3c-423e-b62b-24a9e370d1b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:37:15,039] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8f9b3ea-8c3c-423e-b62b-24a9e370d1b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:37:15,042] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:37:15,042] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:37:15,042] [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
Spirulina major	strain=PCC 6313	GCA_001890765.1	270636	270636	type	True	75.3784	57	1914	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:37:15,044] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16193/tc_result.tsv
[2023-03-18 08:37:15,045] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:37:15,045] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:37:15,045] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8f9b3ea-8c3c-423e-b62b-24a9e370d1b0/dqc_reference/checkm_data
[2023-03-18 08:37:15,046] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:37:15,057] [INFO] Task started: CheckM
[2023-03-18 08:37:15,058] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16193/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16193/checkm_input OceanDNA-b16193/checkm_result
[2023-03-18 08:38:36,685] [INFO] Task succeeded: CheckM
[2023-03-18 08:38:36,686] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:38:36,704] [INFO] ===== Completeness check finished =====
[2023-03-18 08:38:36,704] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:38:36,704] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16193/markers.fasta)
[2023-03-18 08:38:36,705] [INFO] Task started: Blastn
[2023-03-18 08:38:36,705] [INFO] Running command: blastn -query OceanDNA-b16193/markers.fasta -db /var/lib/cwl/stgc8f9b3ea-8c3c-423e-b62b-24a9e370d1b0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16193/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:38:37,394] [INFO] Task succeeded: Blastn
[2023-03-18 08:38:37,414] [INFO] Selected 34 target genomes.
[2023-03-18 08:38:37,414] [INFO] Target genome list was writen to OceanDNA-b16193/target_genomes_gtdb.txt
[2023-03-18 08:38:37,435] [INFO] Task started: fastANI
[2023-03-18 08:38:37,435] [INFO] Running command: fastANI --query /var/lib/cwl/stg234bba91-9171-43f4-b766-e64a6513e7a0/OceanDNA-b16193.fa --refList OceanDNA-b16193/target_genomes_gtdb.txt --output OceanDNA-b16193/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:39:08,015] [INFO] Task succeeded: fastANI
[2023-03-18 08:39:08,025] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:39:08,025] [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_015207365.1	s__FACHB-8 sp015207365	76.0896	71	1914	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__FACHB-8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014697375.1	s__Nodosilinea sp014697375	75.8395	72	1914	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000763385.1	s__Nodosilinea sp000763385	75.7547	82	1914	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012032425.1	s__PCC-6406 sp012032425	75.7301	60	1914	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__PCC-6406	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003249105.1	s__Nodosilinea sp003249105	75.721	51	1914	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016403105.1	s__Nodosilinea sp016403105	75.7206	71	1914	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015295945.1	s__DVED01 sp003695795	75.5791	52	1914	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Geitlerinemaceae;g__DVED01	95.0	99.89	99.88	0.96	0.93	3	-
GCA_014695345.1	s__JAAUTN01 sp014695345	75.56	55	1914	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__JAAUTN01	95.0	97.27	96.86	0.89	0.88	4	-
GCA_016743235.1	s__Pantanalinema sp016743235	75.5163	59	1914	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__Pantanalinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014696135.1	s__Nodosilinea sp014696135	75.5139	57	1914	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	95.07	95.07	0.90	0.90	2	-
GCF_000332335.1	s__PCC-10802 sp000332335	75.4582	56	1914	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Oscillatoriaceae_A;g__PCC-10802	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001939115.1	s__GCF-001939115 sp001939115	75.4138	52	1914	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__GCF-001939115;f__GCF-001939115;g__GCF-001939115	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001890765.1	s__Spirulina major	75.3784	57	1914	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Spirulinaceae;g__Spirulina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012295525.1	s__Oxynema aestuarii	75.357	69	1914	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Oscillatoriaceae;g__Oxynema	95.0	97.71	95.88	0.95	0.91	3	-
GCF_000317125.1	s__Chroococcidiopsis thermalis	75.1558	50	1914	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Chroococcidiopsidaceae;g__Chroococcidiopsis	95.0	97.58	95.17	0.86	0.79	7	-
GCA_003249025.1	s__ULC077BIN1 sp003249025	75.0895	52	1914	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__ULC077BIN1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:39:08,033] [INFO] GTDB search result was written to OceanDNA-b16193/result_gtdb.tsv
[2023-03-18 08:39:08,046] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:39:08,050] [INFO] DFAST_QC result json was written to OceanDNA-b16193/dqc_result.json
[2023-03-18 08:39:08,051] [INFO] DFAST_QC completed!
[2023-03-18 08:39:08,051] [INFO] Total running time: 0h2m52s