[2023-03-17 09:59:00,992] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:59:00,999] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:59:00,999] [INFO] DQC Reference Directory: /var/lib/cwl/stg493a90ec-c284-4859-9c81-9e3009363243/dqc_reference
[2023-03-17 09:59:02,093] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:59:02,093] [INFO] Task started: Prodigal
[2023-03-17 09:59:02,094] [INFO] Running command: cat /var/lib/cwl/stg257288a3-0a55-401d-9579-d05ca5333935/OceanDNA-b22372.fa | prodigal -d OceanDNA-b22372/cds.fna -a OceanDNA-b22372/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:59:11,712] [INFO] Task succeeded: Prodigal
[2023-03-17 09:59:11,712] [INFO] Task started: HMMsearch
[2023-03-17 09:59:11,712] [INFO] Running command: hmmsearch --tblout OceanDNA-b22372/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg493a90ec-c284-4859-9c81-9e3009363243/dqc_reference/reference_markers.hmm OceanDNA-b22372/protein.faa > /dev/null
[2023-03-17 09:59:11,875] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:59:11,876] [INFO] Found 6/6 markers.
[2023-03-17 09:59:11,963] [INFO] Query marker FASTA was written to OceanDNA-b22372/markers.fasta
[2023-03-17 09:59:11,964] [INFO] Task started: Blastn
[2023-03-17 09:59:11,964] [INFO] Running command: blastn -query OceanDNA-b22372/markers.fasta -db /var/lib/cwl/stg493a90ec-c284-4859-9c81-9e3009363243/dqc_reference/reference_markers.fasta -out OceanDNA-b22372/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:59:12,504] [INFO] Task succeeded: Blastn
[2023-03-17 09:59:12,506] [INFO] Selected 13 target genomes.
[2023-03-17 09:59:12,507] [INFO] Target genome list was writen to OceanDNA-b22372/target_genomes.txt
[2023-03-17 09:59:12,618] [INFO] Task started: fastANI
[2023-03-17 09:59:12,619] [INFO] Running command: fastANI --query /var/lib/cwl/stg257288a3-0a55-401d-9579-d05ca5333935/OceanDNA-b22372.fa --refList OceanDNA-b22372/target_genomes.txt --output OceanDNA-b22372/fastani_result.tsv --threads 1
[2023-03-17 09:59:20,371] [INFO] Task succeeded: fastANI
[2023-03-17 09:59:20,371] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg493a90ec-c284-4859-9c81-9e3009363243/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:59:20,371] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg493a90ec-c284-4859-9c81-9e3009363243/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:59:20,372] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:59:20,372] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 09:59:20,372] [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 09:59:20,381] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22372/tc_result.tsv
[2023-03-17 09:59:20,395] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:59:20,395] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:59:20,395] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg493a90ec-c284-4859-9c81-9e3009363243/dqc_reference/checkm_data
[2023-03-17 09:59:20,398] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:59:20,509] [INFO] Task started: CheckM
[2023-03-17 09:59:20,509] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22372/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22372/checkm_input OceanDNA-b22372/checkm_result
[2023-03-17 09:59:49,741] [INFO] Task succeeded: CheckM
[2023-03-17 09:59:49,741] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.72%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 09:59:49,858] [INFO] ===== Completeness check finished =====
[2023-03-17 09:59:49,858] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:59:49,858] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22372/markers.fasta)
[2023-03-17 09:59:49,859] [INFO] Task started: Blastn
[2023-03-17 09:59:49,859] [INFO] Running command: blastn -query OceanDNA-b22372/markers.fasta -db /var/lib/cwl/stg493a90ec-c284-4859-9c81-9e3009363243/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22372/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:59:50,650] [INFO] Task succeeded: Blastn
[2023-03-17 09:59:50,679] [INFO] Selected 13 target genomes.
[2023-03-17 09:59:50,679] [INFO] Target genome list was writen to OceanDNA-b22372/target_genomes_gtdb.txt
[2023-03-17 09:59:51,080] [INFO] Task started: fastANI
[2023-03-17 09:59:51,080] [INFO] Running command: fastANI --query /var/lib/cwl/stg257288a3-0a55-401d-9579-d05ca5333935/OceanDNA-b22372.fa --refList OceanDNA-b22372/target_genomes_gtdb.txt --output OceanDNA-b22372/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:59:59,145] [INFO] Task succeeded: fastANI
[2023-03-17 09:59:59,149] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 09:59:59,149] [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_012965455.1	s__UBA721 sp012965455	89.1311	407	521	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA721	95.0	99.43	99.43	0.81	0.81	2	-
GCA_018660825.1	s__UBA721 sp018660825	88.441	494	521	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA721	95.0	99.75	99.55	0.94	0.93	7	-
GCA_018658605.1	s__UBA721 sp018658605	87.1618	450	521	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA721	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 09:59:59,157] [INFO] GTDB search result was written to OceanDNA-b22372/result_gtdb.tsv
[2023-03-17 09:59:59,173] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:59:59,183] [INFO] DFAST_QC result json was written to OceanDNA-b22372/dqc_result.json
[2023-03-17 09:59:59,183] [INFO] DFAST_QC completed!
[2023-03-17 09:59:59,183] [INFO] Total running time: 0h0m58s