[2023-03-18 10:03:47,667] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:03:47,667] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:03:47,668] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c14e42d-001b-40ec-a007-6ec7bbbe39e4/dqc_reference
[2023-03-18 10:03:48,822] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:03:48,823] [INFO] Task started: Prodigal
[2023-03-18 10:03:48,823] [INFO] Running command: cat /var/lib/cwl/stgbc0e9035-60f2-45c8-9f7c-b05904a131f6/OceanDNA-b37856.fa | prodigal -d OceanDNA-b37856/cds.fna -a OceanDNA-b37856/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:03:59,107] [INFO] Task succeeded: Prodigal
[2023-03-18 10:03:59,108] [INFO] Task started: HMMsearch
[2023-03-18 10:03:59,108] [INFO] Running command: hmmsearch --tblout OceanDNA-b37856/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c14e42d-001b-40ec-a007-6ec7bbbe39e4/dqc_reference/reference_markers.hmm OceanDNA-b37856/protein.faa > /dev/null
[2023-03-18 10:03:59,267] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:03:59,267] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgbc0e9035-60f2-45c8-9f7c-b05904a131f6/OceanDNA-b37856.fa]
[2023-03-18 10:03:59,288] [INFO] Query marker FASTA was written to OceanDNA-b37856/markers.fasta
[2023-03-18 10:03:59,290] [INFO] Task started: Blastn
[2023-03-18 10:03:59,290] [INFO] Running command: blastn -query OceanDNA-b37856/markers.fasta -db /var/lib/cwl/stg5c14e42d-001b-40ec-a007-6ec7bbbe39e4/dqc_reference/reference_markers.fasta -out OceanDNA-b37856/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:03:59,861] [INFO] Task succeeded: Blastn
[2023-03-18 10:03:59,862] [INFO] Selected 25 target genomes.
[2023-03-18 10:03:59,863] [INFO] Target genome list was writen to OceanDNA-b37856/target_genomes.txt
[2023-03-18 10:03:59,877] [INFO] Task started: fastANI
[2023-03-18 10:03:59,877] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc0e9035-60f2-45c8-9f7c-b05904a131f6/OceanDNA-b37856.fa --refList OceanDNA-b37856/target_genomes.txt --output OceanDNA-b37856/fastani_result.tsv --threads 1
[2023-03-18 10:04:17,792] [INFO] Task succeeded: fastANI
[2023-03-18 10:04:17,792] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c14e42d-001b-40ec-a007-6ec7bbbe39e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:04:17,792] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c14e42d-001b-40ec-a007-6ec7bbbe39e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:04:17,792] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:04:17,792] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 10:04:17,792] [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 10:04:17,793] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37856/tc_result.tsv
[2023-03-18 10:04:17,793] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:04:17,793] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:04:17,793] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c14e42d-001b-40ec-a007-6ec7bbbe39e4/dqc_reference/checkm_data
[2023-03-18 10:04:17,843] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:04:18,147] [INFO] Task started: CheckM
[2023-03-18 10:04:18,147] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37856/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37856/checkm_input OceanDNA-b37856/checkm_result
[2023-03-18 10:04:50,299] [INFO] Task succeeded: CheckM
[2023-03-18 10:04:50,299] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 43.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 10:04:50,301] [INFO] ===== Completeness check finished =====
[2023-03-18 10:04:50,301] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:04:50,302] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37856/markers.fasta)
[2023-03-18 10:04:50,303] [INFO] Task started: Blastn
[2023-03-18 10:04:50,303] [INFO] Running command: blastn -query OceanDNA-b37856/markers.fasta -db /var/lib/cwl/stg5c14e42d-001b-40ec-a007-6ec7bbbe39e4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37856/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:04:51,201] [INFO] Task succeeded: Blastn
[2023-03-18 10:04:51,202] [INFO] Selected 23 target genomes.
[2023-03-18 10:04:51,202] [INFO] Target genome list was writen to OceanDNA-b37856/target_genomes_gtdb.txt
[2023-03-18 10:04:51,248] [INFO] Task started: fastANI
[2023-03-18 10:04:51,248] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc0e9035-60f2-45c8-9f7c-b05904a131f6/OceanDNA-b37856.fa --refList OceanDNA-b37856/target_genomes_gtdb.txt --output OceanDNA-b37856/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:05:03,532] [INFO] Task succeeded: fastANI
[2023-03-18 10:05:03,535] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 10:05:03,535] [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_002456975.1	s__Luminiphilus sp002456975	84.064	333	560	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	99.72	99.71	0.90	0.87	3	-
GCA_000227505.4	s__Luminiphilus sp000227505	76.6939	51	560	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 10:05:03,535] [INFO] GTDB search result was written to OceanDNA-b37856/result_gtdb.tsv
[2023-03-18 10:05:03,535] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:05:03,536] [INFO] DFAST_QC result json was written to OceanDNA-b37856/dqc_result.json
[2023-03-18 10:05:03,536] [INFO] DFAST_QC completed!
[2023-03-18 10:05:03,536] [INFO] Total running time: 0h1m16s