[2023-03-16 06:31:19,180] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:31:19,180] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:31:19,180] [INFO] DQC Reference Directory: /var/lib/cwl/stg1cc34e4e-1aab-47b9-9bdf-1ee0b4fa62f1/dqc_reference
[2023-03-16 06:31:20,350] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:31:20,350] [INFO] Task started: Prodigal
[2023-03-16 06:31:20,351] [INFO] Running command: cat /var/lib/cwl/stg3f4d917b-1dbe-4b9d-bafa-a105aab4e4c9/OceanDNA-b46970.fa | prodigal -d OceanDNA-b46970/cds.fna -a OceanDNA-b46970/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:31:44,025] [INFO] Task succeeded: Prodigal
[2023-03-16 06:31:44,025] [INFO] Task started: HMMsearch
[2023-03-16 06:31:44,025] [INFO] Running command: hmmsearch --tblout OceanDNA-b46970/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1cc34e4e-1aab-47b9-9bdf-1ee0b4fa62f1/dqc_reference/reference_markers.hmm OceanDNA-b46970/protein.faa > /dev/null
[2023-03-16 06:31:44,236] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:31:44,236] [INFO] Found 6/6 markers.
[2023-03-16 06:31:44,264] [INFO] Query marker FASTA was written to OceanDNA-b46970/markers.fasta
[2023-03-16 06:31:44,264] [INFO] Task started: Blastn
[2023-03-16 06:31:44,264] [INFO] Running command: blastn -query OceanDNA-b46970/markers.fasta -db /var/lib/cwl/stg1cc34e4e-1aab-47b9-9bdf-1ee0b4fa62f1/dqc_reference/reference_markers.fasta -out OceanDNA-b46970/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:31:44,780] [INFO] Task succeeded: Blastn
[2023-03-16 06:31:44,782] [INFO] Selected 5 target genomes.
[2023-03-16 06:31:44,783] [INFO] Target genome list was writen to OceanDNA-b46970/target_genomes.txt
[2023-03-16 06:31:44,786] [INFO] Task started: fastANI
[2023-03-16 06:31:44,786] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f4d917b-1dbe-4b9d-bafa-a105aab4e4c9/OceanDNA-b46970.fa --refList OceanDNA-b46970/target_genomes.txt --output OceanDNA-b46970/fastani_result.tsv --threads 1
[2023-03-16 06:31:47,458] [INFO] Task succeeded: fastANI
[2023-03-16 06:31:47,458] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1cc34e4e-1aab-47b9-9bdf-1ee0b4fa62f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:31:47,459] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1cc34e4e-1aab-47b9-9bdf-1ee0b4fa62f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:31:47,459] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:31:47,459] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 06:31:47,459] [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
--------------------------------------------------------------------------------
[2023-03-16 06:31:47,461] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46970/tc_result.tsv
[2023-03-16 06:31:47,461] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:31:47,461] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:31:47,461] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1cc34e4e-1aab-47b9-9bdf-1ee0b4fa62f1/dqc_reference/checkm_data
[2023-03-16 06:31:47,464] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:31:47,496] [INFO] Task started: CheckM
[2023-03-16 06:31:47,496] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46970/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46970/checkm_input OceanDNA-b46970/checkm_result
[2023-03-16 06:32:49,059] [INFO] Task succeeded: CheckM
[2023-03-16 06:32:49,059] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:32:49,098] [INFO] ===== Completeness check finished =====
[2023-03-16 06:32:49,098] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:32:49,098] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46970/markers.fasta)
[2023-03-16 06:32:49,099] [INFO] Task started: Blastn
[2023-03-16 06:32:49,099] [INFO] Running command: blastn -query OceanDNA-b46970/markers.fasta -db /var/lib/cwl/stg1cc34e4e-1aab-47b9-9bdf-1ee0b4fa62f1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46970/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:32:49,777] [INFO] Task succeeded: Blastn
[2023-03-16 06:32:49,819] [INFO] Selected 7 target genomes.
[2023-03-16 06:32:49,819] [INFO] Target genome list was writen to OceanDNA-b46970/target_genomes_gtdb.txt
[2023-03-16 06:32:49,836] [INFO] Task started: fastANI
[2023-03-16 06:32:49,837] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f4d917b-1dbe-4b9d-bafa-a105aab4e4c9/OceanDNA-b46970.fa --refList OceanDNA-b46970/target_genomes_gtdb.txt --output OceanDNA-b46970/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:32:54,684] [INFO] Task succeeded: fastANI
[2023-03-16 06:32:54,689] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 06:32:54,689] [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_012960505.1	s__EC70 sp012960505	96.309	1008	1087	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__EC70	95.0	99.96	99.96	0.97	0.97	2	conclusive
GCA_014239335.1	s__EC70 sp014239335	90.6143	642	1087	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__EC70	95.0	98.68	98.68	0.76	0.76	2	-
GCA_902591645.1	s__EC70 sp902591645	88.2595	504	1087	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__EC70	95.0	95.33	95.33	0.70	0.70	2	-
GCA_013213965.1	s__EC70 sp013213965	87.0674	669	1087	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__EC70	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004211885.1	s__EC70 sp004211885	86.9839	819	1087	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__EC70	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002708885.1	s__EC70 sp002708885	81.9825	718	1087	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__EC70	95.0	98.95	98.84	0.89	0.88	3	-
--------------------------------------------------------------------------------
[2023-03-16 06:32:54,704] [INFO] GTDB search result was written to OceanDNA-b46970/result_gtdb.tsv
[2023-03-16 06:32:54,724] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:32:54,736] [INFO] DFAST_QC result json was written to OceanDNA-b46970/dqc_result.json
[2023-03-16 06:32:54,737] [INFO] DFAST_QC completed!
[2023-03-16 06:32:54,737] [INFO] Total running time: 0h1m36s