[2023-03-17 05:16:58,087] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:16:58,087] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:16:58,087] [INFO] DQC Reference Directory: /var/lib/cwl/stgf781412b-7c60-4d59-bcf5-7318f810aec8/dqc_reference
[2023-03-17 05:16:59,895] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:16:59,895] [INFO] Task started: Prodigal
[2023-03-17 05:16:59,896] [INFO] Running command: cat /var/lib/cwl/stg1e24d8db-30d4-446f-91aa-a1f6eb8c9213/OceanDNA-b45838.fa | prodigal -d OceanDNA-b45838/cds.fna -a OceanDNA-b45838/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:17:26,591] [INFO] Task succeeded: Prodigal
[2023-03-17 05:17:26,591] [INFO] Task started: HMMsearch
[2023-03-17 05:17:26,591] [INFO] Running command: hmmsearch --tblout OceanDNA-b45838/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf781412b-7c60-4d59-bcf5-7318f810aec8/dqc_reference/reference_markers.hmm OceanDNA-b45838/protein.faa > /dev/null
[2023-03-17 05:17:26,791] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:17:26,791] [INFO] Found 6/6 markers.
[2023-03-17 05:17:26,813] [INFO] Query marker FASTA was written to OceanDNA-b45838/markers.fasta
[2023-03-17 05:17:26,814] [INFO] Task started: Blastn
[2023-03-17 05:17:26,814] [INFO] Running command: blastn -query OceanDNA-b45838/markers.fasta -db /var/lib/cwl/stgf781412b-7c60-4d59-bcf5-7318f810aec8/dqc_reference/reference_markers.fasta -out OceanDNA-b45838/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:17:27,371] [INFO] Task succeeded: Blastn
[2023-03-17 05:17:27,371] [INFO] Selected 15 target genomes.
[2023-03-17 05:17:27,372] [INFO] Target genome list was writen to OceanDNA-b45838/target_genomes.txt
[2023-03-17 05:17:27,454] [INFO] Task started: fastANI
[2023-03-17 05:17:27,454] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e24d8db-30d4-446f-91aa-a1f6eb8c9213/OceanDNA-b45838.fa --refList OceanDNA-b45838/target_genomes.txt --output OceanDNA-b45838/fastani_result.tsv --threads 1
[2023-03-17 05:17:36,287] [INFO] Task succeeded: fastANI
[2023-03-17 05:17:36,287] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf781412b-7c60-4d59-bcf5-7318f810aec8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:17:36,287] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf781412b-7c60-4d59-bcf5-7318f810aec8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:17:36,288] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:17:36,288] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 05:17:36,288] [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 05:17:36,288] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45838/tc_result.tsv
[2023-03-17 05:17:36,288] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:17:36,288] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:17:36,288] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf781412b-7c60-4d59-bcf5-7318f810aec8/dqc_reference/checkm_data
[2023-03-17 05:17:36,291] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:17:36,295] [INFO] Task started: CheckM
[2023-03-17 05:17:36,296] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45838/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45838/checkm_input OceanDNA-b45838/checkm_result
[2023-03-17 05:18:43,158] [INFO] Task succeeded: CheckM
[2023-03-17 05:18:43,159] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 05:18:43,161] [INFO] ===== Completeness check finished =====
[2023-03-17 05:18:43,162] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:18:43,162] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45838/markers.fasta)
[2023-03-17 05:18:43,163] [INFO] Task started: Blastn
[2023-03-17 05:18:43,163] [INFO] Running command: blastn -query OceanDNA-b45838/markers.fasta -db /var/lib/cwl/stgf781412b-7c60-4d59-bcf5-7318f810aec8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45838/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:18:44,058] [INFO] Task succeeded: Blastn
[2023-03-17 05:18:44,059] [INFO] Selected 15 target genomes.
[2023-03-17 05:18:44,059] [INFO] Target genome list was writen to OceanDNA-b45838/target_genomes_gtdb.txt
[2023-03-17 05:18:44,224] [INFO] Task started: fastANI
[2023-03-17 05:18:44,224] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e24d8db-30d4-446f-91aa-a1f6eb8c9213/OceanDNA-b45838.fa --refList OceanDNA-b45838/target_genomes_gtdb.txt --output OceanDNA-b45838/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:18:53,563] [INFO] Task succeeded: fastANI
[2023-03-17 05:18:53,567] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 05:18:53,567] [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_014529625.1	s__UBA5691 sp002420265	95.232	1009	1132	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA5691	95.0	96.17	95.09	0.91	0.87	4	conclusive
GCA_002420185.1	s__UBA5691 sp002420185	92.3945	883	1132	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA5691	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018700525.1	s__UBA5691 sp018700525	78.8164	144	1132	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA5691	95.0	99.68	99.65	0.95	0.94	5	-
GCA_002474325.1	s__UBA5691 sp002474325	77.9804	85	1132	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA5691	95.0	98.86	98.86	0.81	0.81	2	-
GCA_002694885.1	s__UBA5691 sp002694885	77.2614	103	1132	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA5691	95.0	99.79	99.79	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-03-17 05:18:53,567] [INFO] GTDB search result was written to OceanDNA-b45838/result_gtdb.tsv
[2023-03-17 05:18:53,568] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:18:53,569] [INFO] DFAST_QC result json was written to OceanDNA-b45838/dqc_result.json
[2023-03-17 05:18:53,570] [INFO] DFAST_QC completed!
[2023-03-17 05:18:53,570] [INFO] Total running time: 0h1m55s