[2023-03-18 03:45:10,275] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:45:10,275] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:45:10,275] [INFO] DQC Reference Directory: /var/lib/cwl/stgd57c05e2-af17-4b20-8964-5b4bbc21b5a3/dqc_reference
[2023-03-18 03:45:12,157] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:45:12,158] [INFO] Task started: Prodigal
[2023-03-18 03:45:12,158] [INFO] Running command: cat /var/lib/cwl/stg71f1de2f-95e5-41e4-84e6-68dd4e772425/OceanDNA-b17334.fa | prodigal -d OceanDNA-b17334/cds.fna -a OceanDNA-b17334/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:45:25,109] [INFO] Task succeeded: Prodigal
[2023-03-18 03:45:25,110] [INFO] Task started: HMMsearch
[2023-03-18 03:45:25,110] [INFO] Running command: hmmsearch --tblout OceanDNA-b17334/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd57c05e2-af17-4b20-8964-5b4bbc21b5a3/dqc_reference/reference_markers.hmm OceanDNA-b17334/protein.faa > /dev/null
[2023-03-18 03:45:25,326] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:45:25,326] [INFO] Found 6/6 markers.
[2023-03-18 03:45:25,342] [INFO] Query marker FASTA was written to OceanDNA-b17334/markers.fasta
[2023-03-18 03:45:25,342] [INFO] Task started: Blastn
[2023-03-18 03:45:25,342] [INFO] Running command: blastn -query OceanDNA-b17334/markers.fasta -db /var/lib/cwl/stgd57c05e2-af17-4b20-8964-5b4bbc21b5a3/dqc_reference/reference_markers.fasta -out OceanDNA-b17334/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:45:25,861] [INFO] Task succeeded: Blastn
[2023-03-18 03:45:25,862] [INFO] Selected 22 target genomes.
[2023-03-18 03:45:25,862] [INFO] Target genome list was writen to OceanDNA-b17334/target_genomes.txt
[2023-03-18 03:45:25,876] [INFO] Task started: fastANI
[2023-03-18 03:45:25,876] [INFO] Running command: fastANI --query /var/lib/cwl/stg71f1de2f-95e5-41e4-84e6-68dd4e772425/OceanDNA-b17334.fa --refList OceanDNA-b17334/target_genomes.txt --output OceanDNA-b17334/fastani_result.tsv --threads 1
[2023-03-18 03:45:42,433] [INFO] Task succeeded: fastANI
[2023-03-18 03:45:42,434] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd57c05e2-af17-4b20-8964-5b4bbc21b5a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:45:42,434] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd57c05e2-af17-4b20-8964-5b4bbc21b5a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:45:42,434] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:45:42,434] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 03:45:42,434] [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 03:45:42,434] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17334/tc_result.tsv
[2023-03-18 03:45:42,435] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:45:42,435] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:45:42,435] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd57c05e2-af17-4b20-8964-5b4bbc21b5a3/dqc_reference/checkm_data
[2023-03-18 03:45:42,437] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:45:42,442] [INFO] Task started: CheckM
[2023-03-18 03:45:42,442] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17334/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17334/checkm_input OceanDNA-b17334/checkm_result
[2023-03-18 03:46:18,303] [INFO] Task succeeded: CheckM
[2023-03-18 03:46:18,303] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 03:46:18,306] [INFO] ===== Completeness check finished =====
[2023-03-18 03:46:18,306] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:46:18,306] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17334/markers.fasta)
[2023-03-18 03:46:18,306] [INFO] Task started: Blastn
[2023-03-18 03:46:18,306] [INFO] Running command: blastn -query OceanDNA-b17334/markers.fasta -db /var/lib/cwl/stgd57c05e2-af17-4b20-8964-5b4bbc21b5a3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17334/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:46:18,995] [INFO] Task succeeded: Blastn
[2023-03-18 03:46:18,995] [INFO] Selected 14 target genomes.
[2023-03-18 03:46:18,996] [INFO] Target genome list was writen to OceanDNA-b17334/target_genomes_gtdb.txt
[2023-03-18 03:46:19,128] [INFO] Task started: fastANI
[2023-03-18 03:46:19,129] [INFO] Running command: fastANI --query /var/lib/cwl/stg71f1de2f-95e5-41e4-84e6-68dd4e772425/OceanDNA-b17334.fa --refList OceanDNA-b17334/target_genomes_gtdb.txt --output OceanDNA-b17334/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:46:26,269] [INFO] Task succeeded: fastANI
[2023-03-18 03:46:26,272] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 03:46:26,273] [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_002348265.1	s__UBA2589 sp002348265	99.6349	672	732	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2589	95.0	99.66	99.56	0.93	0.92	5	conclusive
GCA_002348465.1	s__UBA2589 sp002348465	94.0159	585	732	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2589	95.0	98.53	97.69	0.86	0.81	4	-
GCA_002500925.1	s__UBA2589 sp002500925	91.6737	601	732	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2589	95.0	99.15	98.29	0.89	0.88	10	-
--------------------------------------------------------------------------------
[2023-03-18 03:46:26,273] [INFO] GTDB search result was written to OceanDNA-b17334/result_gtdb.tsv
[2023-03-18 03:46:26,273] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:46:26,273] [INFO] DFAST_QC result json was written to OceanDNA-b17334/dqc_result.json
[2023-03-18 03:46:26,274] [INFO] DFAST_QC completed!
[2023-03-18 03:46:26,274] [INFO] Total running time: 0h1m16s