[2023-03-18 03:59:27,745] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:59:27,745] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:59:27,745] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e8092a8-8f91-4309-9a89-c72bb3d5dc6f/dqc_reference
[2023-03-18 03:59:29,369] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:59:29,369] [INFO] Task started: Prodigal
[2023-03-18 03:59:29,369] [INFO] Running command: cat /var/lib/cwl/stgadac98b9-f167-484a-93bc-b0d80c3a9ec6/OceanDNA-b45406.fa | prodigal -d OceanDNA-b45406/cds.fna -a OceanDNA-b45406/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:59:42,629] [INFO] Task succeeded: Prodigal
[2023-03-18 03:59:42,629] [INFO] Task started: HMMsearch
[2023-03-18 03:59:42,629] [INFO] Running command: hmmsearch --tblout OceanDNA-b45406/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e8092a8-8f91-4309-9a89-c72bb3d5dc6f/dqc_reference/reference_markers.hmm OceanDNA-b45406/protein.faa > /dev/null
[2023-03-18 03:59:42,786] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:59:42,787] [INFO] Found 6/6 markers.
[2023-03-18 03:59:42,800] [INFO] Query marker FASTA was written to OceanDNA-b45406/markers.fasta
[2023-03-18 03:59:42,801] [INFO] Task started: Blastn
[2023-03-18 03:59:42,801] [INFO] Running command: blastn -query OceanDNA-b45406/markers.fasta -db /var/lib/cwl/stg2e8092a8-8f91-4309-9a89-c72bb3d5dc6f/dqc_reference/reference_markers.fasta -out OceanDNA-b45406/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:59:43,353] [INFO] Task succeeded: Blastn
[2023-03-18 03:59:43,354] [INFO] Selected 19 target genomes.
[2023-03-18 03:59:43,354] [INFO] Target genome list was writen to OceanDNA-b45406/target_genomes.txt
[2023-03-18 03:59:43,367] [INFO] Task started: fastANI
[2023-03-18 03:59:43,367] [INFO] Running command: fastANI --query /var/lib/cwl/stgadac98b9-f167-484a-93bc-b0d80c3a9ec6/OceanDNA-b45406.fa --refList OceanDNA-b45406/target_genomes.txt --output OceanDNA-b45406/fastani_result.tsv --threads 1
[2023-03-18 03:59:58,363] [INFO] Task succeeded: fastANI
[2023-03-18 03:59:58,363] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e8092a8-8f91-4309-9a89-c72bb3d5dc6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:59:58,364] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e8092a8-8f91-4309-9a89-c72bb3d5dc6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:59:58,364] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:59:58,364] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 03:59:58,364] [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 03:59:58,364] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45406/tc_result.tsv
[2023-03-18 03:59:58,364] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:59:58,364] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:59:58,364] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e8092a8-8f91-4309-9a89-c72bb3d5dc6f/dqc_reference/checkm_data
[2023-03-18 03:59:58,367] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:59:58,370] [INFO] Task started: CheckM
[2023-03-18 03:59:58,370] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45406/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45406/checkm_input OceanDNA-b45406/checkm_result
[2023-03-18 04:00:34,669] [INFO] Task succeeded: CheckM
[2023-03-18 04:00:34,670] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 4.69%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:00:34,671] [INFO] ===== Completeness check finished =====
[2023-03-18 04:00:34,672] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:00:34,672] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45406/markers.fasta)
[2023-03-18 04:00:34,672] [INFO] Task started: Blastn
[2023-03-18 04:00:34,672] [INFO] Running command: blastn -query OceanDNA-b45406/markers.fasta -db /var/lib/cwl/stg2e8092a8-8f91-4309-9a89-c72bb3d5dc6f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45406/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:00:35,521] [INFO] Task succeeded: Blastn
[2023-03-18 04:00:35,521] [INFO] Selected 9 target genomes.
[2023-03-18 04:00:35,522] [INFO] Target genome list was writen to OceanDNA-b45406/target_genomes_gtdb.txt
[2023-03-18 04:00:35,546] [INFO] Task started: fastANI
[2023-03-18 04:00:35,546] [INFO] Running command: fastANI --query /var/lib/cwl/stgadac98b9-f167-484a-93bc-b0d80c3a9ec6/OceanDNA-b45406.fa --refList OceanDNA-b45406/target_genomes_gtdb.txt --output OceanDNA-b45406/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:00:40,751] [INFO] Task succeeded: fastANI
[2023-03-18 04:00:40,755] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 04:00:40,755] [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_903934135.1	s__JACTMZ01 sp903934135	97.2153	338	402	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__JACTMZ01;g__JACTMZ01	95.0	99.34	99.34	0.86	0.86	2	conclusive
GCA_018402585.1	s__JACTMZ01 sp018402585	86.9937	352	402	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__JACTMZ01;g__JACTMZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903953565.1	s__JACTMZ01 sp903953565	80.477	264	402	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__JACTMZ01;g__JACTMZ01	95.0	99.90	99.90	0.96	0.96	2	-
GCA_017853515.1	s__JACTMZ01 sp017853515	79.6782	188	402	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__JACTMZ01;g__JACTMZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883245.1	s__JACTMZ01 sp018883245	78.6273	172	402	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__JACTMZ01;g__JACTMZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879535.1	s__JACTMZ01 sp014879535	78.3346	172	402	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__JACTMZ01;g__JACTMZ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 04:00:40,756] [INFO] GTDB search result was written to OceanDNA-b45406/result_gtdb.tsv
[2023-03-18 04:00:40,756] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:00:40,756] [INFO] DFAST_QC result json was written to OceanDNA-b45406/dqc_result.json
[2023-03-18 04:00:40,757] [INFO] DFAST_QC completed!
[2023-03-18 04:00:40,757] [INFO] Total running time: 0h1m13s