[2023-03-17 03:28:37,101] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:28:37,101] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:28:37,101] [INFO] DQC Reference Directory: /var/lib/cwl/stgb50beb1f-fa48-45db-a17e-9c1be4bf43db/dqc_reference
[2023-03-17 03:28:38,235] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:28:38,236] [INFO] Task started: Prodigal
[2023-03-17 03:28:38,236] [INFO] Running command: cat /var/lib/cwl/stg48f0801a-5034-475c-94f5-9fd475d63465/OceanDNA-b44117.fa | prodigal -d OceanDNA-b44117/cds.fna -a OceanDNA-b44117/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:28:44,491] [INFO] Task succeeded: Prodigal
[2023-03-17 03:28:44,491] [INFO] Task started: HMMsearch
[2023-03-17 03:28:44,491] [INFO] Running command: hmmsearch --tblout OceanDNA-b44117/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb50beb1f-fa48-45db-a17e-9c1be4bf43db/dqc_reference/reference_markers.hmm OceanDNA-b44117/protein.faa > /dev/null
[2023-03-17 03:28:44,655] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:28:44,656] [INFO] Found 6/6 markers.
[2023-03-17 03:28:44,665] [INFO] Query marker FASTA was written to OceanDNA-b44117/markers.fasta
[2023-03-17 03:28:44,666] [INFO] Task started: Blastn
[2023-03-17 03:28:44,666] [INFO] Running command: blastn -query OceanDNA-b44117/markers.fasta -db /var/lib/cwl/stgb50beb1f-fa48-45db-a17e-9c1be4bf43db/dqc_reference/reference_markers.fasta -out OceanDNA-b44117/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:28:45,219] [INFO] Task succeeded: Blastn
[2023-03-17 03:28:45,220] [INFO] Selected 25 target genomes.
[2023-03-17 03:28:45,220] [INFO] Target genome list was writen to OceanDNA-b44117/target_genomes.txt
[2023-03-17 03:28:45,235] [INFO] Task started: fastANI
[2023-03-17 03:28:45,235] [INFO] Running command: fastANI --query /var/lib/cwl/stg48f0801a-5034-475c-94f5-9fd475d63465/OceanDNA-b44117.fa --refList OceanDNA-b44117/target_genomes.txt --output OceanDNA-b44117/fastani_result.tsv --threads 1
[2023-03-17 03:28:56,591] [INFO] Task succeeded: fastANI
[2023-03-17 03:28:56,591] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb50beb1f-fa48-45db-a17e-9c1be4bf43db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:28:56,592] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb50beb1f-fa48-45db-a17e-9c1be4bf43db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:28:56,592] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:28:56,592] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 03:28:56,592] [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 03:28:56,592] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44117/tc_result.tsv
[2023-03-17 03:28:56,592] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:28:56,592] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:28:56,593] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb50beb1f-fa48-45db-a17e-9c1be4bf43db/dqc_reference/checkm_data
[2023-03-17 03:28:56,595] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:28:56,617] [INFO] Task started: CheckM
[2023-03-17 03:28:56,617] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44117/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44117/checkm_input OceanDNA-b44117/checkm_result
[2023-03-17 03:29:17,673] [INFO] Task succeeded: CheckM
[2023-03-17 03:29:17,673] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:29:17,675] [INFO] ===== Completeness check finished =====
[2023-03-17 03:29:17,675] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:29:17,675] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44117/markers.fasta)
[2023-03-17 03:29:17,675] [INFO] Task started: Blastn
[2023-03-17 03:29:17,675] [INFO] Running command: blastn -query OceanDNA-b44117/markers.fasta -db /var/lib/cwl/stgb50beb1f-fa48-45db-a17e-9c1be4bf43db/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44117/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:29:18,567] [INFO] Task succeeded: Blastn
[2023-03-17 03:29:18,568] [INFO] Selected 25 target genomes.
[2023-03-17 03:29:18,568] [INFO] Target genome list was writen to OceanDNA-b44117/target_genomes_gtdb.txt
[2023-03-17 03:29:18,590] [INFO] Task started: fastANI
[2023-03-17 03:29:18,590] [INFO] Running command: fastANI --query /var/lib/cwl/stg48f0801a-5034-475c-94f5-9fd475d63465/OceanDNA-b44117.fa --refList OceanDNA-b44117/target_genomes_gtdb.txt --output OceanDNA-b44117/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:29:29,169] [INFO] Task succeeded: fastANI
[2023-03-17 03:29:29,172] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 03:29:29,172] [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_002698845.1	s__UBA11869 sp002698845	99.3109	327	403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA4486;f__UBA4486;g__UBA11869	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002692205.1	s__UBA11869 sp002692205	79.6993	233	403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA4486;f__UBA4486;g__UBA11869	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721165.1	s__UBA11869 sp002721165	77.976	150	403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA4486;f__UBA4486;g__UBA11869	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 03:29:29,172] [INFO] GTDB search result was written to OceanDNA-b44117/result_gtdb.tsv
[2023-03-17 03:29:29,172] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:29:29,173] [INFO] DFAST_QC result json was written to OceanDNA-b44117/dqc_result.json
[2023-03-17 03:29:29,173] [INFO] DFAST_QC completed!
[2023-03-17 03:29:29,173] [INFO] Total running time: 0h0m52s