[2023-03-18 09:42:02,218] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:42:02,218] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:42:02,218] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa21c329-962d-4124-9511-a2983e3109ae/dqc_reference
[2023-03-18 09:42:03,335] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:42:03,335] [INFO] Task started: Prodigal
[2023-03-18 09:42:03,335] [INFO] Running command: cat /var/lib/cwl/stg48ff2e59-d1f1-42ce-91ec-1c947710d3dd/OceanDNA-b41777.fa | prodigal -d OceanDNA-b41777/cds.fna -a OceanDNA-b41777/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:42:08,464] [INFO] Task succeeded: Prodigal
[2023-03-18 09:42:08,464] [INFO] Task started: HMMsearch
[2023-03-18 09:42:08,464] [INFO] Running command: hmmsearch --tblout OceanDNA-b41777/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa21c329-962d-4124-9511-a2983e3109ae/dqc_reference/reference_markers.hmm OceanDNA-b41777/protein.faa > /dev/null
[2023-03-18 09:42:08,610] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:42:08,611] [INFO] Found 6/6 markers.
[2023-03-18 09:42:08,619] [INFO] Query marker FASTA was written to OceanDNA-b41777/markers.fasta
[2023-03-18 09:42:08,619] [INFO] Task started: Blastn
[2023-03-18 09:42:08,619] [INFO] Running command: blastn -query OceanDNA-b41777/markers.fasta -db /var/lib/cwl/stgfa21c329-962d-4124-9511-a2983e3109ae/dqc_reference/reference_markers.fasta -out OceanDNA-b41777/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:42:09,154] [INFO] Task succeeded: Blastn
[2023-03-18 09:42:09,155] [INFO] Selected 19 target genomes.
[2023-03-18 09:42:09,155] [INFO] Target genome list was writen to OceanDNA-b41777/target_genomes.txt
[2023-03-18 09:42:09,166] [INFO] Task started: fastANI
[2023-03-18 09:42:09,166] [INFO] Running command: fastANI --query /var/lib/cwl/stg48ff2e59-d1f1-42ce-91ec-1c947710d3dd/OceanDNA-b41777.fa --refList OceanDNA-b41777/target_genomes.txt --output OceanDNA-b41777/fastani_result.tsv --threads 1
[2023-03-18 09:42:17,469] [INFO] Task succeeded: fastANI
[2023-03-18 09:42:17,469] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa21c329-962d-4124-9511-a2983e3109ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:42:17,469] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa21c329-962d-4124-9511-a2983e3109ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:42:17,469] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:42:17,469] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:42:17,469] [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
--------------------------------------------------------------------------------
[2023-03-18 09:42:17,470] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41777/tc_result.tsv
[2023-03-18 09:42:17,470] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:42:17,470] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:42:17,470] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa21c329-962d-4124-9511-a2983e3109ae/dqc_reference/checkm_data
[2023-03-18 09:42:17,472] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:42:17,489] [INFO] Task started: CheckM
[2023-03-18 09:42:17,490] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41777/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41777/checkm_input OceanDNA-b41777/checkm_result
[2023-03-18 09:42:35,988] [INFO] Task succeeded: CheckM
[2023-03-18 09:42:35,989] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:42:35,990] [INFO] ===== Completeness check finished =====
[2023-03-18 09:42:35,990] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:42:35,991] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41777/markers.fasta)
[2023-03-18 09:42:35,991] [INFO] Task started: Blastn
[2023-03-18 09:42:35,991] [INFO] Running command: blastn -query OceanDNA-b41777/markers.fasta -db /var/lib/cwl/stgfa21c329-962d-4124-9511-a2983e3109ae/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41777/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:42:36,874] [INFO] Task succeeded: Blastn
[2023-03-18 09:42:36,875] [INFO] Selected 27 target genomes.
[2023-03-18 09:42:36,875] [INFO] Target genome list was writen to OceanDNA-b41777/target_genomes_gtdb.txt
[2023-03-18 09:42:36,918] [INFO] Task started: fastANI
[2023-03-18 09:42:36,918] [INFO] Running command: fastANI --query /var/lib/cwl/stg48ff2e59-d1f1-42ce-91ec-1c947710d3dd/OceanDNA-b41777.fa --refList OceanDNA-b41777/target_genomes_gtdb.txt --output OceanDNA-b41777/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:42:42,858] [INFO] Task succeeded: fastANI
[2023-03-18 09:42:42,864] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 09:42:42,865] [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_902522825.1	s__AG-339-G14 sp902522825	77.5107	118	339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902523885.1	s__AG-339-G14 sp902523885	77.4179	104	339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902635045.1	s__AG-339-G14 sp902635045	77.3092	101	339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	98.24	96.50	0.87	0.84	4	-
GCA_902614235.1	s__AG-339-G14 sp902614235	77.3032	102	339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	98.30	98.01	0.83	0.80	7	-
GCA_902525735.1	s__AG-339-G14 sp902525735	77.2181	115	339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	98.66	98.66	0.90	0.90	2	-
GCA_902524805.1	s__AG-339-G14 sp902524805	77.145	97	339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902616715.1	s__AG-339-G14 sp902616715	76.8175	68	339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	98.52	98.27	0.93	0.90	8	-
GCA_004213955.1	s__AG-339-G14 sp004213955	76.4709	67	339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902613455.1	s__AG-339-G14 sp902613455	76.3626	59	339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	97.22	96.70	0.93	0.90	20	-
--------------------------------------------------------------------------------
[2023-03-18 09:42:42,865] [INFO] GTDB search result was written to OceanDNA-b41777/result_gtdb.tsv
[2023-03-18 09:42:42,865] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:42:42,866] [INFO] DFAST_QC result json was written to OceanDNA-b41777/dqc_result.json
[2023-03-18 09:42:42,866] [INFO] DFAST_QC completed!
[2023-03-18 09:42:42,866] [INFO] Total running time: 0h0m41s