[2023-03-17 01:23:45,146] [INFO] DFAST_QC pipeline started.
[2023-03-17 01:23:45,146] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 01:23:45,146] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a3287f8-45fe-4603-bdbd-76fd9f60f11a/dqc_reference
[2023-03-17 01:23:46,318] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 01:23:46,318] [INFO] Task started: Prodigal
[2023-03-17 01:23:46,318] [INFO] Running command: cat /var/lib/cwl/stg0097e47f-a169-4699-b3d9-1ad0627a0d2d/OceanDNA-b4594.fa | prodigal -d OceanDNA-b4594/cds.fna -a OceanDNA-b4594/protein.faa -g 11 -q > /dev/null
[2023-03-17 01:24:05,624] [INFO] Task succeeded: Prodigal
[2023-03-17 01:24:05,625] [INFO] Task started: HMMsearch
[2023-03-17 01:24:05,625] [INFO] Running command: hmmsearch --tblout OceanDNA-b4594/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a3287f8-45fe-4603-bdbd-76fd9f60f11a/dqc_reference/reference_markers.hmm OceanDNA-b4594/protein.faa > /dev/null
[2023-03-17 01:24:05,807] [INFO] Task succeeded: HMMsearch
[2023-03-17 01:24:05,807] [INFO] Found 6/6 markers.
[2023-03-17 01:24:05,823] [INFO] Query marker FASTA was written to OceanDNA-b4594/markers.fasta
[2023-03-17 01:24:05,823] [INFO] Task started: Blastn
[2023-03-17 01:24:05,823] [INFO] Running command: blastn -query OceanDNA-b4594/markers.fasta -db /var/lib/cwl/stg2a3287f8-45fe-4603-bdbd-76fd9f60f11a/dqc_reference/reference_markers.fasta -out OceanDNA-b4594/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:24:06,348] [INFO] Task succeeded: Blastn
[2023-03-17 01:24:06,349] [INFO] Selected 28 target genomes.
[2023-03-17 01:24:06,349] [INFO] Target genome list was writen to OceanDNA-b4594/target_genomes.txt
[2023-03-17 01:24:06,364] [INFO] Task started: fastANI
[2023-03-17 01:24:06,365] [INFO] Running command: fastANI --query /var/lib/cwl/stg0097e47f-a169-4699-b3d9-1ad0627a0d2d/OceanDNA-b4594.fa --refList OceanDNA-b4594/target_genomes.txt --output OceanDNA-b4594/fastani_result.tsv --threads 1
[2023-03-17 01:24:23,442] [INFO] Task succeeded: fastANI
[2023-03-17 01:24:23,443] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a3287f8-45fe-4603-bdbd-76fd9f60f11a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 01:24:23,443] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a3287f8-45fe-4603-bdbd-76fd9f60f11a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 01:24:23,443] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 01:24:23,443] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 01:24:23,443] [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
--------------------------------------------------------------------------------
[2023-03-17 01:24:23,443] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4594/tc_result.tsv
[2023-03-17 01:24:23,444] [INFO] ===== Taxonomy check completed =====
[2023-03-17 01:24:23,444] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 01:24:23,444] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a3287f8-45fe-4603-bdbd-76fd9f60f11a/dqc_reference/checkm_data
[2023-03-17 01:24:23,446] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 01:24:23,450] [INFO] Task started: CheckM
[2023-03-17 01:24:23,450] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4594/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4594/checkm_input OceanDNA-b4594/checkm_result
[2023-03-17 01:25:16,068] [INFO] Task succeeded: CheckM
[2023-03-17 01:25:16,068] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 01:25:16,070] [INFO] ===== Completeness check finished =====
[2023-03-17 01:25:16,071] [INFO] ===== Start GTDB Search =====
[2023-03-17 01:25:16,071] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4594/markers.fasta)
[2023-03-17 01:25:16,071] [INFO] Task started: Blastn
[2023-03-17 01:25:16,071] [INFO] Running command: blastn -query OceanDNA-b4594/markers.fasta -db /var/lib/cwl/stg2a3287f8-45fe-4603-bdbd-76fd9f60f11a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4594/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:25:17,002] [INFO] Task succeeded: Blastn
[2023-03-17 01:25:17,003] [INFO] Selected 24 target genomes.
[2023-03-17 01:25:17,003] [INFO] Target genome list was writen to OceanDNA-b4594/target_genomes_gtdb.txt
[2023-03-17 01:25:17,551] [INFO] Task started: fastANI
[2023-03-17 01:25:17,551] [INFO] Running command: fastANI --query /var/lib/cwl/stg0097e47f-a169-4699-b3d9-1ad0627a0d2d/OceanDNA-b4594.fa --refList OceanDNA-b4594/target_genomes_gtdb.txt --output OceanDNA-b4594/fastani_result_gtdb.tsv --threads 1
[2023-03-17 01:25:32,721] [INFO] Task succeeded: fastANI
[2023-03-17 01:25:32,724] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 01:25:32,725] [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_002389645.1	s__SHAN690 sp002389645	99.9911	879	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Salibacteraceae;g__SHAN690	95.0	99.96	99.93	0.94	0.94	3	conclusive
GCA_905479105.1	s__SHAN690 sp002390775	79.9324	468	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Salibacteraceae;g__SHAN690	95.0	99.12	98.21	0.92	0.80	5	-
GCA_018401875.1	s__SHAN690 sp018401875	78.6416	317	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Salibacteraceae;g__SHAN690	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013204105.1	s__SHAN690 sp013204105	75.8589	72	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Salibacteraceae;g__SHAN690	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 01:25:32,725] [INFO] GTDB search result was written to OceanDNA-b4594/result_gtdb.tsv
[2023-03-17 01:25:32,725] [INFO] ===== GTDB Search completed =====
[2023-03-17 01:25:32,725] [INFO] DFAST_QC result json was written to OceanDNA-b4594/dqc_result.json
[2023-03-17 01:25:32,726] [INFO] DFAST_QC completed!
[2023-03-17 01:25:32,726] [INFO] Total running time: 0h1m48s