[2023-03-15 12:06:59,542] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:06:59,542] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:06:59,542] [INFO] DQC Reference Directory: /var/lib/cwl/stgeba35667-ff99-4bca-a851-bed091ceafa1/dqc_reference
[2023-03-15 12:07:00,618] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:07:00,618] [INFO] Task started: Prodigal
[2023-03-15 12:07:00,618] [INFO] Running command: cat /var/lib/cwl/stgff8aa336-ba70-412b-8afa-b42aaf8992c5/OceanDNA-b78.fa | prodigal -d OceanDNA-b78/cds.fna -a OceanDNA-b78/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:07:14,248] [INFO] Task succeeded: Prodigal
[2023-03-15 12:07:14,248] [INFO] Task started: HMMsearch
[2023-03-15 12:07:14,249] [INFO] Running command: hmmsearch --tblout OceanDNA-b78/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeba35667-ff99-4bca-a851-bed091ceafa1/dqc_reference/reference_markers.hmm OceanDNA-b78/protein.faa > /dev/null
[2023-03-15 12:07:14,399] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:07:14,400] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgff8aa336-ba70-412b-8afa-b42aaf8992c5/OceanDNA-b78.fa]
[2023-03-15 12:07:14,414] [INFO] Query marker FASTA was written to OceanDNA-b78/markers.fasta
[2023-03-15 12:07:14,415] [INFO] Task started: Blastn
[2023-03-15 12:07:14,415] [INFO] Running command: blastn -query OceanDNA-b78/markers.fasta -db /var/lib/cwl/stgeba35667-ff99-4bca-a851-bed091ceafa1/dqc_reference/reference_markers.fasta -out OceanDNA-b78/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:07:14,858] [INFO] Task succeeded: Blastn
[2023-03-15 12:07:14,859] [INFO] Selected 12 target genomes.
[2023-03-15 12:07:14,859] [INFO] Target genome list was writen to OceanDNA-b78/target_genomes.txt
[2023-03-15 12:07:14,865] [INFO] Task started: fastANI
[2023-03-15 12:07:14,865] [INFO] Running command: fastANI --query /var/lib/cwl/stgff8aa336-ba70-412b-8afa-b42aaf8992c5/OceanDNA-b78.fa --refList OceanDNA-b78/target_genomes.txt --output OceanDNA-b78/fastani_result.tsv --threads 1
[2023-03-15 12:07:22,059] [INFO] Task succeeded: fastANI
[2023-03-15 12:07:22,059] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeba35667-ff99-4bca-a851-bed091ceafa1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:07:22,060] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeba35667-ff99-4bca-a851-bed091ceafa1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:07:22,060] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 12:07:22,060] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 12:07:22,060] [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
--------------------------------------------------------------------------------
[2023-03-15 12:07:22,060] [INFO] DFAST Taxonomy check result was written to OceanDNA-b78/tc_result.tsv
[2023-03-15 12:07:22,060] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:07:22,061] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:07:22,061] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeba35667-ff99-4bca-a851-bed091ceafa1/dqc_reference/checkm_data
[2023-03-15 12:07:22,063] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:07:22,082] [INFO] Task started: CheckM
[2023-03-15 12:07:22,083] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b78/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b78/checkm_input OceanDNA-b78/checkm_result
[2023-03-15 12:07:58,692] [INFO] Task succeeded: CheckM
[2023-03-15 12:07:58,693] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 12:07:58,805] [INFO] ===== Completeness check finished =====
[2023-03-15 12:07:58,805] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:07:58,805] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b78/markers.fasta)
[2023-03-15 12:07:58,806] [INFO] Task started: Blastn
[2023-03-15 12:07:58,806] [INFO] Running command: blastn -query OceanDNA-b78/markers.fasta -db /var/lib/cwl/stgeba35667-ff99-4bca-a851-bed091ceafa1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b78/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:07:59,263] [INFO] Task succeeded: Blastn
[2023-03-15 12:07:59,264] [INFO] Selected 14 target genomes.
[2023-03-15 12:07:59,264] [INFO] Target genome list was writen to OceanDNA-b78/target_genomes_gtdb.txt
[2023-03-15 12:07:59,299] [INFO] Task started: fastANI
[2023-03-15 12:07:59,299] [INFO] Running command: fastANI --query /var/lib/cwl/stgff8aa336-ba70-412b-8afa-b42aaf8992c5/OceanDNA-b78.fa --refList OceanDNA-b78/target_genomes_gtdb.txt --output OceanDNA-b78/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:08:06,232] [INFO] Task succeeded: fastANI
[2023-03-15 12:08:06,234] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 12:08:06,234] [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_002722645.1	s__UBA890 sp002722645	83.4225	471	735	d__Bacteria;p__Acidobacteriota;c__UBA890;o__UBA890;f__UBA890;g__UBA890	95.0	97.90	97.61	0.78	0.75	3	-
GCA_002731215.1	s__UBA890 sp002731215	80.4793	189	735	d__Bacteria;p__Acidobacteriota;c__UBA890;o__UBA890;f__UBA890;g__UBA890	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 12:08:06,235] [INFO] GTDB search result was written to OceanDNA-b78/result_gtdb.tsv
[2023-03-15 12:08:06,235] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:08:06,236] [INFO] DFAST_QC result json was written to OceanDNA-b78/dqc_result.json
[2023-03-15 12:08:06,237] [INFO] DFAST_QC completed!
[2023-03-15 12:08:06,237] [INFO] Total running time: 0h1m7s