[2023-03-15 23:38:54,948] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:38:54,952] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:38:54,952] [INFO] DQC Reference Directory: /var/lib/cwl/stg577bfee9-16ea-4d0a-b922-9f41c101def9/dqc_reference
[2023-03-15 23:38:56,088] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:38:56,088] [INFO] Task started: Prodigal
[2023-03-15 23:38:56,088] [INFO] Running command: cat /var/lib/cwl/stgeed8a782-90d6-4a39-b56f-8d88fed28c70/OceanDNA-a1913.fa | prodigal -d OceanDNA-a1913/cds.fna -a OceanDNA-a1913/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:39:04,716] [INFO] Task succeeded: Prodigal
[2023-03-15 23:39:04,716] [INFO] Task started: HMMsearch
[2023-03-15 23:39:04,716] [INFO] Running command: hmmsearch --tblout OceanDNA-a1913/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg577bfee9-16ea-4d0a-b922-9f41c101def9/dqc_reference/reference_markers.hmm OceanDNA-a1913/protein.faa > /dev/null
[2023-03-15 23:39:04,879] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:39:04,879] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgeed8a782-90d6-4a39-b56f-8d88fed28c70/OceanDNA-a1913.fa]
[2023-03-15 23:39:04,962] [INFO] Query marker FASTA was written to OceanDNA-a1913/markers.fasta
[2023-03-15 23:39:04,962] [INFO] Task started: Blastn
[2023-03-15 23:39:04,962] [INFO] Running command: blastn -query OceanDNA-a1913/markers.fasta -db /var/lib/cwl/stg577bfee9-16ea-4d0a-b922-9f41c101def9/dqc_reference/reference_markers.fasta -out OceanDNA-a1913/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:39:05,407] [INFO] Task succeeded: Blastn
[2023-03-15 23:39:05,417] [INFO] Selected 5 target genomes.
[2023-03-15 23:39:05,417] [INFO] Target genome list was writen to OceanDNA-a1913/target_genomes.txt
[2023-03-15 23:39:05,421] [INFO] Task started: fastANI
[2023-03-15 23:39:05,421] [INFO] Running command: fastANI --query /var/lib/cwl/stgeed8a782-90d6-4a39-b56f-8d88fed28c70/OceanDNA-a1913.fa --refList OceanDNA-a1913/target_genomes.txt --output OceanDNA-a1913/fastani_result.tsv --threads 1
[2023-03-15 23:39:09,585] [INFO] Task succeeded: fastANI
[2023-03-15 23:39:09,586] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg577bfee9-16ea-4d0a-b922-9f41c101def9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:39:09,586] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg577bfee9-16ea-4d0a-b922-9f41c101def9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:39:09,586] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:39:09,586] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 23:39:09,586] [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
--------------------------------------------------------------------------------
[2023-03-15 23:39:09,590] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1913/tc_result.tsv
[2023-03-15 23:39:09,596] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:39:09,596] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:39:09,596] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg577bfee9-16ea-4d0a-b922-9f41c101def9/dqc_reference/checkm_data
[2023-03-15 23:39:09,600] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:39:09,621] [INFO] Task started: CheckM
[2023-03-15 23:39:09,621] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1913/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1913/checkm_input OceanDNA-a1913/checkm_result
[2023-03-15 23:39:36,556] [INFO] Task succeeded: CheckM
[2023-03-15 23:39:36,556] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.14%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:39:36,654] [INFO] ===== Completeness check finished =====
[2023-03-15 23:39:36,654] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:39:36,654] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1913/markers.fasta)
[2023-03-15 23:39:36,655] [INFO] Task started: Blastn
[2023-03-15 23:39:36,655] [INFO] Running command: blastn -query OceanDNA-a1913/markers.fasta -db /var/lib/cwl/stg577bfee9-16ea-4d0a-b922-9f41c101def9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1913/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:39:37,089] [INFO] Task succeeded: Blastn
[2023-03-15 23:39:37,094] [INFO] Selected 11 target genomes.
[2023-03-15 23:39:37,094] [INFO] Target genome list was writen to OceanDNA-a1913/target_genomes_gtdb.txt
[2023-03-15 23:39:37,108] [INFO] Task started: fastANI
[2023-03-15 23:39:37,108] [INFO] Running command: fastANI --query /var/lib/cwl/stgeed8a782-90d6-4a39-b56f-8d88fed28c70/OceanDNA-a1913.fa --refList OceanDNA-a1913/target_genomes_gtdb.txt --output OceanDNA-a1913/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:39:40,454] [INFO] Task succeeded: fastANI
[2023-03-15 23:39:40,460] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 23:39:40,460] [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_009936765.1	s__MGIIa-K1 sp009936765	98.3826	384	504	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	98.29	98.25	0.77	0.75	3	conclusive
GCA_018650165.1	s__MGIIa-K1 sp018650165	79.1041	193	504	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	99.75	99.69	0.90	0.90	3	-
GCA_002689345.1	s__MGIIa-K1 sp002689345	78.2455	213	504	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003602415.1	s__MGIIa-K1 sp003602415	78.1052	222	504	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	97.94	97.94	0.93	0.93	2	-
GCA_902563095.1	s__MGIIa-K1 sp902563095	77.9298	114	504	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	98.06	97.94	0.61	0.59	4	-
GCA_002498185.1	s__MGIIa-K1 sp002498185	77.5059	163	504	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	99.51	99.39	0.80	0.77	3	-
GCA_002694245.1	s__MGIIa-K1 sp002694245	76.8266	91	504	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002710015.1	s__MGIIa-K1 sp002710015	76.6873	61	504	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	99.68	99.68	0.80	0.80	2	-
GCA_002707335.2	s__MGIIa-K1 sp002707335	76.6055	59	504	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 23:39:40,464] [INFO] GTDB search result was written to OceanDNA-a1913/result_gtdb.tsv
[2023-03-15 23:39:40,467] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:39:40,468] [INFO] DFAST_QC result json was written to OceanDNA-a1913/dqc_result.json
[2023-03-15 23:39:40,468] [INFO] DFAST_QC completed!
[2023-03-15 23:39:40,468] [INFO] Total running time: 0h0m46s