[2023-03-16 00:33:46,150] [INFO] DFAST_QC pipeline started.
[2023-03-16 00:33:46,150] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 00:33:46,150] [INFO] DQC Reference Directory: /var/lib/cwl/stg18d4e6c2-8d37-4422-bbdc-05a4b555a24b/dqc_reference
[2023-03-16 00:33:47,243] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 00:33:47,243] [INFO] Task started: Prodigal
[2023-03-16 00:33:47,243] [INFO] Running command: cat /var/lib/cwl/stg7aea6d15-7671-4fbf-b385-bb6a369f471a/OceanDNA-b17579.fa | prodigal -d OceanDNA-b17579/cds.fna -a OceanDNA-b17579/protein.faa -g 11 -q > /dev/null
[2023-03-16 00:34:08,974] [INFO] Task succeeded: Prodigal
[2023-03-16 00:34:08,974] [INFO] Task started: HMMsearch
[2023-03-16 00:34:08,975] [INFO] Running command: hmmsearch --tblout OceanDNA-b17579/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18d4e6c2-8d37-4422-bbdc-05a4b555a24b/dqc_reference/reference_markers.hmm OceanDNA-b17579/protein.faa > /dev/null
[2023-03-16 00:34:09,195] [INFO] Task succeeded: HMMsearch
[2023-03-16 00:34:09,195] [INFO] Found 6/6 markers.
[2023-03-16 00:34:09,222] [INFO] Query marker FASTA was written to OceanDNA-b17579/markers.fasta
[2023-03-16 00:34:09,224] [INFO] Task started: Blastn
[2023-03-16 00:34:09,224] [INFO] Running command: blastn -query OceanDNA-b17579/markers.fasta -db /var/lib/cwl/stg18d4e6c2-8d37-4422-bbdc-05a4b555a24b/dqc_reference/reference_markers.fasta -out OceanDNA-b17579/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:34:09,754] [INFO] Task succeeded: Blastn
[2023-03-16 00:34:09,755] [INFO] Selected 27 target genomes.
[2023-03-16 00:34:09,755] [INFO] Target genome list was writen to OceanDNA-b17579/target_genomes.txt
[2023-03-16 00:34:09,941] [INFO] Task started: fastANI
[2023-03-16 00:34:09,941] [INFO] Running command: fastANI --query /var/lib/cwl/stg7aea6d15-7671-4fbf-b385-bb6a369f471a/OceanDNA-b17579.fa --refList OceanDNA-b17579/target_genomes.txt --output OceanDNA-b17579/fastani_result.tsv --threads 1
[2023-03-16 00:34:27,209] [INFO] Task succeeded: fastANI
[2023-03-16 00:34:27,209] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18d4e6c2-8d37-4422-bbdc-05a4b555a24b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 00:34:27,210] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18d4e6c2-8d37-4422-bbdc-05a4b555a24b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 00:34:27,210] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 00:34:27,210] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 00:34:27,210] [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
--------------------------------------------------------------------------------
[2023-03-16 00:34:27,210] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17579/tc_result.tsv
[2023-03-16 00:34:27,210] [INFO] ===== Taxonomy check completed =====
[2023-03-16 00:34:27,210] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 00:34:27,211] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18d4e6c2-8d37-4422-bbdc-05a4b555a24b/dqc_reference/checkm_data
[2023-03-16 00:34:27,214] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 00:34:27,313] [INFO] Task started: CheckM
[2023-03-16 00:34:27,313] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17579/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17579/checkm_input OceanDNA-b17579/checkm_result
[2023-03-16 00:35:21,698] [INFO] Task succeeded: CheckM
[2023-03-16 00:35:21,698] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.20%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 00:35:21,720] [INFO] ===== Completeness check finished =====
[2023-03-16 00:35:21,720] [INFO] ===== Start GTDB Search =====
[2023-03-16 00:35:21,720] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17579/markers.fasta)
[2023-03-16 00:35:21,721] [INFO] Task started: Blastn
[2023-03-16 00:35:21,721] [INFO] Running command: blastn -query OceanDNA-b17579/markers.fasta -db /var/lib/cwl/stg18d4e6c2-8d37-4422-bbdc-05a4b555a24b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17579/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:35:22,443] [INFO] Task succeeded: Blastn
[2023-03-16 00:35:22,444] [INFO] Selected 34 target genomes.
[2023-03-16 00:35:22,444] [INFO] Target genome list was writen to OceanDNA-b17579/target_genomes_gtdb.txt
[2023-03-16 00:35:22,473] [INFO] Task started: fastANI
[2023-03-16 00:35:22,473] [INFO] Running command: fastANI --query /var/lib/cwl/stg7aea6d15-7671-4fbf-b385-bb6a369f471a/OceanDNA-b17579.fa --refList OceanDNA-b17579/target_genomes_gtdb.txt --output OceanDNA-b17579/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:35:42,417] [INFO] Task succeeded: fastANI
[2023-03-16 00:35:42,419] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 00:35:42,419] [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_012270675.1	s__JAAXHW01 sp012270675	75.9571	52	1211	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA2968;f__GCA-2709665;g__JAAXHW01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 00:35:42,440] [INFO] GTDB search result was written to OceanDNA-b17579/result_gtdb.tsv
[2023-03-16 00:35:42,476] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:35:42,476] [INFO] DFAST_QC result json was written to OceanDNA-b17579/dqc_result.json
[2023-03-16 00:35:42,476] [INFO] DFAST_QC completed!
[2023-03-16 00:35:42,477] [INFO] Total running time: 0h1m56s