[2023-03-16 00:43:24,325] [INFO] DFAST_QC pipeline started.
[2023-03-16 00:43:24,325] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 00:43:24,325] [INFO] DQC Reference Directory: /var/lib/cwl/stg149ab1e6-7c9f-4e45-9aa8-b487dfc98ac4/dqc_reference
[2023-03-16 00:43:25,444] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 00:43:25,445] [INFO] Task started: Prodigal
[2023-03-16 00:43:25,445] [INFO] Running command: cat /var/lib/cwl/stg31f80b5e-3212-4d5e-9232-2596cac286d4/OceanDNA-b16198.fa | prodigal -d OceanDNA-b16198/cds.fna -a OceanDNA-b16198/protein.faa -g 11 -q > /dev/null
[2023-03-16 00:43:47,599] [INFO] Task succeeded: Prodigal
[2023-03-16 00:43:47,599] [INFO] Task started: HMMsearch
[2023-03-16 00:43:47,599] [INFO] Running command: hmmsearch --tblout OceanDNA-b16198/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg149ab1e6-7c9f-4e45-9aa8-b487dfc98ac4/dqc_reference/reference_markers.hmm OceanDNA-b16198/protein.faa > /dev/null
[2023-03-16 00:43:47,839] [INFO] Task succeeded: HMMsearch
[2023-03-16 00:43:47,840] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg31f80b5e-3212-4d5e-9232-2596cac286d4/OceanDNA-b16198.fa]
[2023-03-16 00:43:47,871] [INFO] Query marker FASTA was written to OceanDNA-b16198/markers.fasta
[2023-03-16 00:43:47,873] [INFO] Task started: Blastn
[2023-03-16 00:43:47,873] [INFO] Running command: blastn -query OceanDNA-b16198/markers.fasta -db /var/lib/cwl/stg149ab1e6-7c9f-4e45-9aa8-b487dfc98ac4/dqc_reference/reference_markers.fasta -out OceanDNA-b16198/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:43:48,469] [INFO] Task succeeded: Blastn
[2023-03-16 00:43:48,472] [INFO] Selected 21 target genomes.
[2023-03-16 00:43:48,472] [INFO] Target genome list was writen to OceanDNA-b16198/target_genomes.txt
[2023-03-16 00:43:48,484] [INFO] Task started: fastANI
[2023-03-16 00:43:48,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg31f80b5e-3212-4d5e-9232-2596cac286d4/OceanDNA-b16198.fa --refList OceanDNA-b16198/target_genomes.txt --output OceanDNA-b16198/fastani_result.tsv --threads 1
[2023-03-16 00:44:02,750] [INFO] Task succeeded: fastANI
[2023-03-16 00:44:02,751] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg149ab1e6-7c9f-4e45-9aa8-b487dfc98ac4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 00:44:02,751] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg149ab1e6-7c9f-4e45-9aa8-b487dfc98ac4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 00:44:02,751] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 00:44:02,751] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 00:44:02,751] [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
--------------------------------------------------------------------------------
[2023-03-16 00:44:02,752] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16198/tc_result.tsv
[2023-03-16 00:44:02,753] [INFO] ===== Taxonomy check completed =====
[2023-03-16 00:44:02,753] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 00:44:02,753] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg149ab1e6-7c9f-4e45-9aa8-b487dfc98ac4/dqc_reference/checkm_data
[2023-03-16 00:44:02,757] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 00:44:02,834] [INFO] Task started: CheckM
[2023-03-16 00:44:02,834] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16198/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16198/checkm_input OceanDNA-b16198/checkm_result
[2023-03-16 00:44:58,031] [INFO] Task succeeded: CheckM
[2023-03-16 00:44:58,031] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 00:44:58,082] [INFO] ===== Completeness check finished =====
[2023-03-16 00:44:58,082] [INFO] ===== Start GTDB Search =====
[2023-03-16 00:44:58,082] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16198/markers.fasta)
[2023-03-16 00:44:58,083] [INFO] Task started: Blastn
[2023-03-16 00:44:58,083] [INFO] Running command: blastn -query OceanDNA-b16198/markers.fasta -db /var/lib/cwl/stg149ab1e6-7c9f-4e45-9aa8-b487dfc98ac4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16198/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:44:59,083] [INFO] Task succeeded: Blastn
[2023-03-16 00:44:59,087] [INFO] Selected 26 target genomes.
[2023-03-16 00:44:59,087] [INFO] Target genome list was writen to OceanDNA-b16198/target_genomes_gtdb.txt
[2023-03-16 00:44:59,125] [INFO] Task started: fastANI
[2023-03-16 00:44:59,125] [INFO] Running command: fastANI --query /var/lib/cwl/stg31f80b5e-3212-4d5e-9232-2596cac286d4/OceanDNA-b16198.fa --refList OceanDNA-b16198/target_genomes_gtdb.txt --output OceanDNA-b16198/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:45:16,031] [INFO] Task succeeded: fastANI
[2023-03-16 00:45:16,038] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 00:45:16,039] [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_000309385.1	s__Nodosilinea nodulosa	76.2917	137	1276	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241845.1	s__Nodosilinea antarctica	76.2377	131	1276	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	98.34	98.34	0.86	0.86	2	-
GCA_003017855.1	s__Nodosilinea sp003017855	76.2307	127	1276	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	99.92	99.92	0.94	0.94	2	-
GCF_014697375.1	s__Nodosilinea sp014697375	76.1711	82	1276	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003017785.1	s__CCP5 sp003017785	76.0925	81	1276	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__CCP5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007694115.1	s__Nodosilinea sp007694115	76.0671	98	1276	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003249105.1	s__Nodosilinea sp003249105	75.9625	115	1276	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015207265.1	s__Nodosilinea sp015207265	75.9192	109	1276	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014534385.1	s__JACVSF01 sp014534385	75.7585	56	1276	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__JACVSF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010671975.1	s__SIO4C1 sp010671975	75.695	54	1276	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__SIO4C1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016888135.1	s__RECH01 sp016888135	75.5743	74	1276	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__RECH01	95.0	96.61	96.61	0.91	0.91	3	-
--------------------------------------------------------------------------------
[2023-03-16 00:45:16,040] [INFO] GTDB search result was written to OceanDNA-b16198/result_gtdb.tsv
[2023-03-16 00:45:16,043] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:45:16,046] [INFO] DFAST_QC result json was written to OceanDNA-b16198/dqc_result.json
[2023-03-16 00:45:16,046] [INFO] DFAST_QC completed!
[2023-03-16 00:45:16,046] [INFO] Total running time: 0h1m52s