[2023-03-17 13:01:51,485] [INFO] DFAST_QC pipeline started.
[2023-03-17 13:01:51,485] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 13:01:51,485] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f8f334c-3187-42ab-8667-3d9193271583/dqc_reference
[2023-03-17 13:01:52,724] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 13:01:52,724] [INFO] Task started: Prodigal
[2023-03-17 13:01:52,724] [INFO] Running command: cat /var/lib/cwl/stg905187c5-d0c1-4530-8b30-f08b13973197/OceanDNA-b22348.fa | prodigal -d OceanDNA-b22348/cds.fna -a OceanDNA-b22348/protein.faa -g 11 -q > /dev/null
[2023-03-17 13:02:14,217] [INFO] Task succeeded: Prodigal
[2023-03-17 13:02:14,217] [INFO] Task started: HMMsearch
[2023-03-17 13:02:14,217] [INFO] Running command: hmmsearch --tblout OceanDNA-b22348/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f8f334c-3187-42ab-8667-3d9193271583/dqc_reference/reference_markers.hmm OceanDNA-b22348/protein.faa > /dev/null
[2023-03-17 13:02:14,476] [INFO] Task succeeded: HMMsearch
[2023-03-17 13:02:14,477] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg905187c5-d0c1-4530-8b30-f08b13973197/OceanDNA-b22348.fa]
[2023-03-17 13:02:14,514] [INFO] Query marker FASTA was written to OceanDNA-b22348/markers.fasta
[2023-03-17 13:02:14,514] [INFO] Task started: Blastn
[2023-03-17 13:02:14,514] [INFO] Running command: blastn -query OceanDNA-b22348/markers.fasta -db /var/lib/cwl/stg7f8f334c-3187-42ab-8667-3d9193271583/dqc_reference/reference_markers.fasta -out OceanDNA-b22348/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:02:15,029] [INFO] Task succeeded: Blastn
[2023-03-17 13:02:15,030] [INFO] Selected 16 target genomes.
[2023-03-17 13:02:15,030] [INFO] Target genome list was writen to OceanDNA-b22348/target_genomes.txt
[2023-03-17 13:02:15,039] [INFO] Task started: fastANI
[2023-03-17 13:02:15,039] [INFO] Running command: fastANI --query /var/lib/cwl/stg905187c5-d0c1-4530-8b30-f08b13973197/OceanDNA-b22348.fa --refList OceanDNA-b22348/target_genomes.txt --output OceanDNA-b22348/fastani_result.tsv --threads 1
[2023-03-17 13:02:24,275] [INFO] Task succeeded: fastANI
[2023-03-17 13:02:24,276] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f8f334c-3187-42ab-8667-3d9193271583/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 13:02:24,276] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f8f334c-3187-42ab-8667-3d9193271583/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 13:02:24,276] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 13:02:24,276] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 13:02:24,276] [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 13:02:24,276] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22348/tc_result.tsv
[2023-03-17 13:02:24,276] [INFO] ===== Taxonomy check completed =====
[2023-03-17 13:02:24,277] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 13:02:24,277] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f8f334c-3187-42ab-8667-3d9193271583/dqc_reference/checkm_data
[2023-03-17 13:02:24,279] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 13:02:24,285] [INFO] Task started: CheckM
[2023-03-17 13:02:24,286] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22348/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22348/checkm_input OceanDNA-b22348/checkm_result
[2023-03-17 13:03:19,096] [INFO] Task succeeded: CheckM
[2023-03-17 13:03:19,097] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 13:03:19,100] [INFO] ===== Completeness check finished =====
[2023-03-17 13:03:19,100] [INFO] ===== Start GTDB Search =====
[2023-03-17 13:03:19,100] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22348/markers.fasta)
[2023-03-17 13:03:19,100] [INFO] Task started: Blastn
[2023-03-17 13:03:19,100] [INFO] Running command: blastn -query OceanDNA-b22348/markers.fasta -db /var/lib/cwl/stg7f8f334c-3187-42ab-8667-3d9193271583/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22348/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:03:19,816] [INFO] Task succeeded: Blastn
[2023-03-17 13:03:19,817] [INFO] Selected 14 target genomes.
[2023-03-17 13:03:19,817] [INFO] Target genome list was writen to OceanDNA-b22348/target_genomes_gtdb.txt
[2023-03-17 13:03:20,139] [INFO] Task started: fastANI
[2023-03-17 13:03:20,139] [INFO] Running command: fastANI --query /var/lib/cwl/stg905187c5-d0c1-4530-8b30-f08b13973197/OceanDNA-b22348.fa --refList OceanDNA-b22348/target_genomes_gtdb.txt --output OceanDNA-b22348/fastani_result_gtdb.tsv --threads 1
[2023-03-17 13:03:31,295] [INFO] Task succeeded: fastANI
[2023-03-17 13:03:31,298] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 13:03:31,298] [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	88.1564	760	1202	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA721	95.0	99.43	99.43	0.81	0.81	2	-
GCA_018658605.1	s__UBA721 sp018658605	86.709	891	1202	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA721	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018660825.1	s__UBA721 sp018660825	86.2126	1000	1202	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA721	95.0	99.75	99.55	0.94	0.93	7	-
--------------------------------------------------------------------------------
[2023-03-17 13:03:31,298] [INFO] GTDB search result was written to OceanDNA-b22348/result_gtdb.tsv
[2023-03-17 13:03:31,298] [INFO] ===== GTDB Search completed =====
[2023-03-17 13:03:31,299] [INFO] DFAST_QC result json was written to OceanDNA-b22348/dqc_result.json
[2023-03-17 13:03:31,299] [INFO] DFAST_QC completed!
[2023-03-17 13:03:31,299] [INFO] Total running time: 0h1m40s