[2023-03-15 16:25:56,990] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:25:56,998] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:25:56,998] [INFO] DQC Reference Directory: /var/lib/cwl/stg8cfc30f4-7228-4de8-9b8d-395e9eee241d/dqc_reference
[2023-03-15 16:25:58,595] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:25:58,595] [INFO] Task started: Prodigal
[2023-03-15 16:25:58,595] [INFO] Running command: cat /var/lib/cwl/stg5e0daa74-2b3e-414c-9850-97873c3ad82d/OceanDNA-b45845.fa | prodigal -d OceanDNA-b45845/cds.fna -a OceanDNA-b45845/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:26:22,430] [INFO] Task succeeded: Prodigal
[2023-03-15 16:26:22,430] [INFO] Task started: HMMsearch
[2023-03-15 16:26:22,430] [INFO] Running command: hmmsearch --tblout OceanDNA-b45845/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8cfc30f4-7228-4de8-9b8d-395e9eee241d/dqc_reference/reference_markers.hmm OceanDNA-b45845/protein.faa > /dev/null
[2023-03-15 16:26:22,629] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:26:22,630] [INFO] Found 6/6 markers.
[2023-03-15 16:26:22,692] [INFO] Query marker FASTA was written to OceanDNA-b45845/markers.fasta
[2023-03-15 16:26:22,693] [INFO] Task started: Blastn
[2023-03-15 16:26:22,693] [INFO] Running command: blastn -query OceanDNA-b45845/markers.fasta -db /var/lib/cwl/stg8cfc30f4-7228-4de8-9b8d-395e9eee241d/dqc_reference/reference_markers.fasta -out OceanDNA-b45845/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:26:23,269] [INFO] Task succeeded: Blastn
[2023-03-15 16:26:23,280] [INFO] Selected 9 target genomes.
[2023-03-15 16:26:23,281] [INFO] Target genome list was writen to OceanDNA-b45845/target_genomes.txt
[2023-03-15 16:26:23,287] [INFO] Task started: fastANI
[2023-03-15 16:26:23,287] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e0daa74-2b3e-414c-9850-97873c3ad82d/OceanDNA-b45845.fa --refList OceanDNA-b45845/target_genomes.txt --output OceanDNA-b45845/fastani_result.tsv --threads 1
[2023-03-15 16:26:30,124] [INFO] Task succeeded: fastANI
[2023-03-15 16:26:30,124] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8cfc30f4-7228-4de8-9b8d-395e9eee241d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:26:30,125] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8cfc30f4-7228-4de8-9b8d-395e9eee241d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:26:30,125] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:26:30,125] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 16:26:30,125] [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 16:26:30,130] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45845/tc_result.tsv
[2023-03-15 16:26:30,136] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:26:30,136] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:26:30,137] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8cfc30f4-7228-4de8-9b8d-395e9eee241d/dqc_reference/checkm_data
[2023-03-15 16:26:30,139] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:26:30,147] [INFO] Task started: CheckM
[2023-03-15 16:26:30,148] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45845/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45845/checkm_input OceanDNA-b45845/checkm_result
[2023-03-15 16:27:30,464] [INFO] Task succeeded: CheckM
[2023-03-15 16:27:30,465] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 16:27:30,587] [INFO] ===== Completeness check finished =====
[2023-03-15 16:27:30,587] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:27:30,587] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45845/markers.fasta)
[2023-03-15 16:27:30,588] [INFO] Task started: Blastn
[2023-03-15 16:27:30,588] [INFO] Running command: blastn -query OceanDNA-b45845/markers.fasta -db /var/lib/cwl/stg8cfc30f4-7228-4de8-9b8d-395e9eee241d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45845/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:27:31,535] [INFO] Task succeeded: Blastn
[2023-03-15 16:27:31,564] [INFO] Selected 18 target genomes.
[2023-03-15 16:27:31,564] [INFO] Target genome list was writen to OceanDNA-b45845/target_genomes_gtdb.txt
[2023-03-15 16:27:31,583] [INFO] Task started: fastANI
[2023-03-15 16:27:31,583] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e0daa74-2b3e-414c-9850-97873c3ad82d/OceanDNA-b45845.fa --refList OceanDNA-b45845/target_genomes_gtdb.txt --output OceanDNA-b45845/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:27:42,701] [INFO] Task succeeded: fastANI
[2023-03-15 16:27:42,705] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 16:27:42,705] [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_002474325.1	s__UBA5691 sp002474325	98.9119	726	1001	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA5691	95.0	98.86	98.86	0.81	0.81	2	conclusive
GCA_002694885.1	s__UBA5691 sp002694885	82.2471	575	1001	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA5691	95.0	99.79	99.79	0.86	0.86	2	-
GCA_014529625.1	s__UBA5691 sp002420265	80.4721	127	1001	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA5691	95.0	96.17	95.09	0.91	0.87	4	-
GCA_002420185.1	s__UBA5691 sp002420185	77.5842	88	1001	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	77.144	67	1001	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA5691	95.0	99.68	99.65	0.95	0.94	5	-
--------------------------------------------------------------------------------
[2023-03-15 16:27:42,708] [INFO] GTDB search result was written to OceanDNA-b45845/result_gtdb.tsv
[2023-03-15 16:27:42,711] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:27:42,714] [INFO] DFAST_QC result json was written to OceanDNA-b45845/dqc_result.json
[2023-03-15 16:27:42,715] [INFO] DFAST_QC completed!
[2023-03-15 16:27:42,715] [INFO] Total running time: 0h1m46s