[2023-03-17 00:45:47,179] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:45:47,179] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:45:47,179] [INFO] DQC Reference Directory: /var/lib/cwl/stg0938c9b8-1289-4f29-bfdf-7be6d41bf0a4/dqc_reference
[2023-03-17 00:45:48,352] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:45:48,352] [INFO] Task started: Prodigal
[2023-03-17 00:45:48,353] [INFO] Running command: cat /var/lib/cwl/stg93f183b8-3acc-4e33-8a01-a3728b07ae85/OceanDNA-a2158.fa | prodigal -d OceanDNA-a2158/cds.fna -a OceanDNA-a2158/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:45:57,477] [INFO] Task succeeded: Prodigal
[2023-03-17 00:45:57,477] [INFO] Task started: HMMsearch
[2023-03-17 00:45:57,477] [INFO] Running command: hmmsearch --tblout OceanDNA-a2158/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0938c9b8-1289-4f29-bfdf-7be6d41bf0a4/dqc_reference/reference_markers.hmm OceanDNA-a2158/protein.faa > /dev/null
[2023-03-17 00:45:57,650] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:45:57,650] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg93f183b8-3acc-4e33-8a01-a3728b07ae85/OceanDNA-a2158.fa]
[2023-03-17 00:45:57,662] [INFO] Query marker FASTA was written to OceanDNA-a2158/markers.fasta
[2023-03-17 00:45:57,663] [INFO] Task started: Blastn
[2023-03-17 00:45:57,663] [INFO] Running command: blastn -query OceanDNA-a2158/markers.fasta -db /var/lib/cwl/stg0938c9b8-1289-4f29-bfdf-7be6d41bf0a4/dqc_reference/reference_markers.fasta -out OceanDNA-a2158/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:45:58,087] [INFO] Task succeeded: Blastn
[2023-03-17 00:45:58,088] [INFO] Selected 6 target genomes.
[2023-03-17 00:45:58,088] [INFO] Target genome list was writen to OceanDNA-a2158/target_genomes.txt
[2023-03-17 00:45:58,137] [INFO] Task started: fastANI
[2023-03-17 00:45:58,137] [INFO] Running command: fastANI --query /var/lib/cwl/stg93f183b8-3acc-4e33-8a01-a3728b07ae85/OceanDNA-a2158.fa --refList OceanDNA-a2158/target_genomes.txt --output OceanDNA-a2158/fastani_result.tsv --threads 1
[2023-03-17 00:46:01,083] [INFO] Task succeeded: fastANI
[2023-03-17 00:46:01,083] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0938c9b8-1289-4f29-bfdf-7be6d41bf0a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:46:01,083] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0938c9b8-1289-4f29-bfdf-7be6d41bf0a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:46:01,084] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:46:01,084] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 00:46:01,084] [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
--------------------------------------------------------------------------------
[2023-03-17 00:46:01,084] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2158/tc_result.tsv
[2023-03-17 00:46:01,084] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:46:01,084] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:46:01,084] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0938c9b8-1289-4f29-bfdf-7be6d41bf0a4/dqc_reference/checkm_data
[2023-03-17 00:46:01,087] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:46:01,090] [INFO] Task started: CheckM
[2023-03-17 00:46:01,090] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2158/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2158/checkm_input OceanDNA-a2158/checkm_result
[2023-03-17 00:46:28,907] [INFO] Task succeeded: CheckM
[2023-03-17 00:46:28,907] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 00:46:28,909] [INFO] ===== Completeness check finished =====
[2023-03-17 00:46:28,909] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:46:28,909] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2158/markers.fasta)
[2023-03-17 00:46:28,909] [INFO] Task started: Blastn
[2023-03-17 00:46:28,910] [INFO] Running command: blastn -query OceanDNA-a2158/markers.fasta -db /var/lib/cwl/stg0938c9b8-1289-4f29-bfdf-7be6d41bf0a4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2158/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:46:29,324] [INFO] Task succeeded: Blastn
[2023-03-17 00:46:29,324] [INFO] Selected 9 target genomes.
[2023-03-17 00:46:29,325] [INFO] Target genome list was writen to OceanDNA-a2158/target_genomes_gtdb.txt
[2023-03-17 00:46:29,518] [INFO] Task started: fastANI
[2023-03-17 00:46:29,518] [INFO] Running command: fastANI --query /var/lib/cwl/stg93f183b8-3acc-4e33-8a01-a3728b07ae85/OceanDNA-a2158.fa --refList OceanDNA-a2158/target_genomes_gtdb.txt --output OceanDNA-a2158/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:46:32,203] [INFO] Task succeeded: fastANI
[2023-03-17 00:46:32,208] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 00:46:32,208] [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_013329295.1	s__MGIIa-L1 sp9596u	91.9122	339	544	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.51	99.26	0.88	0.84	4	-
GCA_002688825.1	s__MGIIa-L1 sp002688825	77.8447	125	544	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018659375.1	s__MGIIa-L1 sp018659375	77.7491	180	544	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.68	99.68	0.93	0.93	2	-
GCA_009887195.1	s__MGIIa-L1 sp009887195	77.7463	178	544	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	98.91	98.88	0.90	0.86	3	-
GCA_013329865.1	s__MGIIa-L1 sp8725u	77.4419	132	544	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	100.00	100.00	0.97	0.97	2	-
GCA_002505355.1	s__MGIIa-L1 sp002505355	77.2649	159	544	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003602575.1	s__MGIIa-L1 sp003602575	77.1155	110	544	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 00:46:32,208] [INFO] GTDB search result was written to OceanDNA-a2158/result_gtdb.tsv
[2023-03-17 00:46:32,209] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:46:32,209] [INFO] DFAST_QC result json was written to OceanDNA-a2158/dqc_result.json
[2023-03-17 00:46:32,209] [INFO] DFAST_QC completed!
[2023-03-17 00:46:32,209] [INFO] Total running time: 0h0m45s