[2023-03-18 20:40:39,434] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:40:39,434] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:40:39,435] [INFO] DQC Reference Directory: /var/lib/cwl/stg828f1517-e0e6-4b3d-9e7f-bc081e61988b/dqc_reference
[2023-03-18 20:40:41,213] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:40:41,213] [INFO] Task started: Prodigal
[2023-03-18 20:40:41,213] [INFO] Running command: cat /var/lib/cwl/stgb1a18b39-a32b-4d3b-b3f7-75705afe671c/OceanDNA-b13586.fa | prodigal -d OceanDNA-b13586/cds.fna -a OceanDNA-b13586/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:40:59,424] [INFO] Task succeeded: Prodigal
[2023-03-18 20:40:59,424] [INFO] Task started: HMMsearch
[2023-03-18 20:40:59,424] [INFO] Running command: hmmsearch --tblout OceanDNA-b13586/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg828f1517-e0e6-4b3d-9e7f-bc081e61988b/dqc_reference/reference_markers.hmm OceanDNA-b13586/protein.faa > /dev/null
[2023-03-18 20:40:59,664] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:40:59,665] [INFO] Found 6/6 markers.
[2023-03-18 20:40:59,686] [INFO] Query marker FASTA was written to OceanDNA-b13586/markers.fasta
[2023-03-18 20:40:59,686] [INFO] Task started: Blastn
[2023-03-18 20:40:59,686] [INFO] Running command: blastn -query OceanDNA-b13586/markers.fasta -db /var/lib/cwl/stg828f1517-e0e6-4b3d-9e7f-bc081e61988b/dqc_reference/reference_markers.fasta -out OceanDNA-b13586/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:41:00,210] [INFO] Task succeeded: Blastn
[2023-03-18 20:41:00,211] [INFO] Selected 12 target genomes.
[2023-03-18 20:41:00,211] [INFO] Target genome list was writen to OceanDNA-b13586/target_genomes.txt
[2023-03-18 20:41:00,216] [INFO] Task started: fastANI
[2023-03-18 20:41:00,216] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1a18b39-a32b-4d3b-b3f7-75705afe671c/OceanDNA-b13586.fa --refList OceanDNA-b13586/target_genomes.txt --output OceanDNA-b13586/fastani_result.tsv --threads 1
[2023-03-18 20:41:09,331] [INFO] Task succeeded: fastANI
[2023-03-18 20:41:09,332] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg828f1517-e0e6-4b3d-9e7f-bc081e61988b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:41:09,332] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg828f1517-e0e6-4b3d-9e7f-bc081e61988b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:41:09,332] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:41:09,332] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 20:41:09,332] [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 20:41:09,332] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13586/tc_result.tsv
[2023-03-18 20:41:09,333] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:41:09,333] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:41:09,333] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg828f1517-e0e6-4b3d-9e7f-bc081e61988b/dqc_reference/checkm_data
[2023-03-18 20:41:09,335] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:41:09,340] [INFO] Task started: CheckM
[2023-03-18 20:41:09,340] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13586/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13586/checkm_input OceanDNA-b13586/checkm_result
[2023-03-18 20:41:57,857] [INFO] Task succeeded: CheckM
[2023-03-18 20:41:57,857] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.72%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:41:57,860] [INFO] ===== Completeness check finished =====
[2023-03-18 20:41:57,860] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:41:57,860] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13586/markers.fasta)
[2023-03-18 20:41:57,861] [INFO] Task started: Blastn
[2023-03-18 20:41:57,861] [INFO] Running command: blastn -query OceanDNA-b13586/markers.fasta -db /var/lib/cwl/stg828f1517-e0e6-4b3d-9e7f-bc081e61988b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13586/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:41:58,613] [INFO] Task succeeded: Blastn
[2023-03-18 20:41:58,614] [INFO] Selected 20 target genomes.
[2023-03-18 20:41:58,614] [INFO] Target genome list was writen to OceanDNA-b13586/target_genomes_gtdb.txt
[2023-03-18 20:41:58,678] [INFO] Task started: fastANI
[2023-03-18 20:41:58,678] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1a18b39-a32b-4d3b-b3f7-75705afe671c/OceanDNA-b13586.fa --refList OceanDNA-b13586/target_genomes_gtdb.txt --output OceanDNA-b13586/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:42:09,633] [INFO] Task succeeded: fastANI
[2023-03-18 20:42:09,638] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 20:42:09,638] [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_016875555.1	s__UBA965 sp016875555	77.6582	119	843	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Roseiflexaceae;g__UBA965	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903932805.1	s__UBA965 sp903932805	77.4808	76	843	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Roseiflexaceae;g__UBA965	95.0	98.41	98.37	0.82	0.80	4	-
GCA_903889425.1	s__UBA965 sp903889425	77.445	196	843	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Roseiflexaceae;g__UBA965	95.0	98.96	98.84	0.87	0.85	6	-
GCA_002292925.1	s__UBA965 sp002292925	77.3158	213	843	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Roseiflexaceae;g__UBA965	95.0	99.56	99.56	0.89	0.89	2	-
GCA_003670675.1	s__UBA965 sp003670675	77.188	84	843	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Roseiflexaceae;g__UBA965	95.0	99.45	99.45	0.71	0.71	2	-
GCA_903868295.1	s__UBA965 sp903868295	76.9734	90	843	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Roseiflexaceae;g__UBA965	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 20:42:09,638] [INFO] GTDB search result was written to OceanDNA-b13586/result_gtdb.tsv
[2023-03-18 20:42:09,638] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:42:09,639] [INFO] DFAST_QC result json was written to OceanDNA-b13586/dqc_result.json
[2023-03-18 20:42:09,639] [INFO] DFAST_QC completed!
[2023-03-18 20:42:09,639] [INFO] Total running time: 0h1m30s