[2023-03-17 08:39:27,226] [INFO] DFAST_QC pipeline started.
[2023-03-17 08:39:27,226] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 08:39:27,226] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1613395-05ef-4342-8a85-4758653ee365/dqc_reference
[2023-03-17 08:39:28,404] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 08:39:28,404] [INFO] Task started: Prodigal
[2023-03-17 08:39:28,404] [INFO] Running command: cat /var/lib/cwl/stgd3db1816-d4ef-403c-9705-ca031ded4ede/OceanDNA-b15285.fa | prodigal -d OceanDNA-b15285/cds.fna -a OceanDNA-b15285/protein.faa -g 11 -q > /dev/null
[2023-03-17 08:39:33,937] [INFO] Task succeeded: Prodigal
[2023-03-17 08:39:33,937] [INFO] Task started: HMMsearch
[2023-03-17 08:39:33,937] [INFO] Running command: hmmsearch --tblout OceanDNA-b15285/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1613395-05ef-4342-8a85-4758653ee365/dqc_reference/reference_markers.hmm OceanDNA-b15285/protein.faa > /dev/null
[2023-03-17 08:39:34,076] [INFO] Task succeeded: HMMsearch
[2023-03-17 08:39:34,076] [INFO] Found 6/6 markers.
[2023-03-17 08:39:34,087] [INFO] Query marker FASTA was written to OceanDNA-b15285/markers.fasta
[2023-03-17 08:39:34,088] [INFO] Task started: Blastn
[2023-03-17 08:39:34,088] [INFO] Running command: blastn -query OceanDNA-b15285/markers.fasta -db /var/lib/cwl/stgf1613395-05ef-4342-8a85-4758653ee365/dqc_reference/reference_markers.fasta -out OceanDNA-b15285/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:39:34,569] [INFO] Task succeeded: Blastn
[2023-03-17 08:39:34,571] [INFO] Selected 9 target genomes.
[2023-03-17 08:39:34,571] [INFO] Target genome list was writen to OceanDNA-b15285/target_genomes.txt
[2023-03-17 08:39:34,680] [INFO] Task started: fastANI
[2023-03-17 08:39:34,680] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3db1816-d4ef-403c-9705-ca031ded4ede/OceanDNA-b15285.fa --refList OceanDNA-b15285/target_genomes.txt --output OceanDNA-b15285/fastani_result.tsv --threads 1
[2023-03-17 08:39:39,897] [INFO] Task succeeded: fastANI
[2023-03-17 08:39:39,897] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1613395-05ef-4342-8a85-4758653ee365/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 08:39:39,897] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1613395-05ef-4342-8a85-4758653ee365/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 08:39:39,898] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 08:39:39,898] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 08:39:39,898] [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 08:39:39,899] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15285/tc_result.tsv
[2023-03-17 08:39:39,899] [INFO] ===== Taxonomy check completed =====
[2023-03-17 08:39:39,899] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 08:39:39,900] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1613395-05ef-4342-8a85-4758653ee365/dqc_reference/checkm_data
[2023-03-17 08:39:39,902] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 08:39:39,906] [INFO] Task started: CheckM
[2023-03-17 08:39:39,906] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15285/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15285/checkm_input OceanDNA-b15285/checkm_result
[2023-03-17 08:39:59,540] [INFO] Task succeeded: CheckM
[2023-03-17 08:39:59,541] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.40%
Strain heterogeneity: 80.00%
--------------------------------------------------------------------------------
[2023-03-17 08:39:59,546] [INFO] ===== Completeness check finished =====
[2023-03-17 08:39:59,546] [INFO] ===== Start GTDB Search =====
[2023-03-17 08:39:59,546] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15285/markers.fasta)
[2023-03-17 08:39:59,547] [INFO] Task started: Blastn
[2023-03-17 08:39:59,548] [INFO] Running command: blastn -query OceanDNA-b15285/markers.fasta -db /var/lib/cwl/stgf1613395-05ef-4342-8a85-4758653ee365/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15285/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:40:00,171] [INFO] Task succeeded: Blastn
[2023-03-17 08:40:00,173] [INFO] Selected 16 target genomes.
[2023-03-17 08:40:00,173] [INFO] Target genome list was writen to OceanDNA-b15285/target_genomes_gtdb.txt
[2023-03-17 08:40:01,033] [INFO] Task started: fastANI
[2023-03-17 08:40:01,033] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3db1816-d4ef-403c-9705-ca031ded4ede/OceanDNA-b15285.fa --refList OceanDNA-b15285/target_genomes_gtdb.txt --output OceanDNA-b15285/fastani_result_gtdb.tsv --threads 1
[2023-03-17 08:40:05,952] [INFO] Task succeeded: fastANI
[2023-03-17 08:40:05,954] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 08:40:05,955] [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_002717805.1	s__UBA2985 sp002717805	81.9945	255	338	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2985;f__UBA2985;g__UBA2985	95.0	99.39	99.38	0.91	0.86	3	-
--------------------------------------------------------------------------------
[2023-03-17 08:40:05,955] [INFO] GTDB search result was written to OceanDNA-b15285/result_gtdb.tsv
[2023-03-17 08:40:05,955] [INFO] ===== GTDB Search completed =====
[2023-03-17 08:40:05,956] [INFO] DFAST_QC result json was written to OceanDNA-b15285/dqc_result.json
[2023-03-17 08:40:05,956] [INFO] DFAST_QC completed!
[2023-03-17 08:40:05,956] [INFO] Total running time: 0h0m39s