[2023-03-15 07:58:33,368] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:58:33,371] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:58:33,371] [INFO] DQC Reference Directory: /var/lib/cwl/stg6ef76081-3ec5-49a1-a29c-18485d9cb52b/dqc_reference
[2023-03-15 07:58:35,135] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:58:35,136] [INFO] Task started: Prodigal
[2023-03-15 07:58:35,137] [INFO] Running command: cat /var/lib/cwl/stgbed1a997-b5ca-4557-a897-094e359e86bd/OceanDNA-b11530.fa | prodigal -d OceanDNA-b11530/cds.fna -a OceanDNA-b11530/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:58:42,269] [INFO] Task succeeded: Prodigal
[2023-03-15 07:58:42,270] [INFO] Task started: HMMsearch
[2023-03-15 07:58:42,270] [INFO] Running command: hmmsearch --tblout OceanDNA-b11530/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6ef76081-3ec5-49a1-a29c-18485d9cb52b/dqc_reference/reference_markers.hmm OceanDNA-b11530/protein.faa > /dev/null
[2023-03-15 07:58:42,445] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:58:42,446] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbed1a997-b5ca-4557-a897-094e359e86bd/OceanDNA-b11530.fa]
[2023-03-15 07:58:42,491] [INFO] Query marker FASTA was written to OceanDNA-b11530/markers.fasta
[2023-03-15 07:58:42,493] [INFO] Task started: Blastn
[2023-03-15 07:58:42,493] [INFO] Running command: blastn -query OceanDNA-b11530/markers.fasta -db /var/lib/cwl/stg6ef76081-3ec5-49a1-a29c-18485d9cb52b/dqc_reference/reference_markers.fasta -out OceanDNA-b11530/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:58:43,001] [INFO] Task succeeded: Blastn
[2023-03-15 07:58:43,015] [INFO] Selected 24 target genomes.
[2023-03-15 07:58:43,016] [INFO] Target genome list was writen to OceanDNA-b11530/target_genomes.txt
[2023-03-15 07:58:43,031] [INFO] Task started: fastANI
[2023-03-15 07:58:43,031] [INFO] Running command: fastANI --query /var/lib/cwl/stgbed1a997-b5ca-4557-a897-094e359e86bd/OceanDNA-b11530.fa --refList OceanDNA-b11530/target_genomes.txt --output OceanDNA-b11530/fastani_result.tsv --threads 1
[2023-03-15 07:58:56,335] [INFO] Task succeeded: fastANI
[2023-03-15 07:58:56,335] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6ef76081-3ec5-49a1-a29c-18485d9cb52b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:58:56,335] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6ef76081-3ec5-49a1-a29c-18485d9cb52b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:58:56,335] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:58:56,335] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 07:58:56,335] [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
--------------------------------------------------------------------------------
[2023-03-15 07:58:56,338] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11530/tc_result.tsv
[2023-03-15 07:58:56,342] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:58:56,342] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:58:56,343] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6ef76081-3ec5-49a1-a29c-18485d9cb52b/dqc_reference/checkm_data
[2023-03-15 07:58:56,346] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:58:56,358] [INFO] Task started: CheckM
[2023-03-15 07:58:56,358] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11530/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11530/checkm_input OceanDNA-b11530/checkm_result
[2023-03-15 07:59:20,508] [INFO] Task succeeded: CheckM
[2023-03-15 07:59:20,509] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.75%
Contamintation: 4.63%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:59:20,547] [INFO] ===== Completeness check finished =====
[2023-03-15 07:59:20,547] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:59:20,547] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11530/markers.fasta)
[2023-03-15 07:59:20,547] [INFO] Task started: Blastn
[2023-03-15 07:59:20,547] [INFO] Running command: blastn -query OceanDNA-b11530/markers.fasta -db /var/lib/cwl/stg6ef76081-3ec5-49a1-a29c-18485d9cb52b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11530/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:59:21,181] [INFO] Task succeeded: Blastn
[2023-03-15 07:59:21,185] [INFO] Selected 20 target genomes.
[2023-03-15 07:59:21,185] [INFO] Target genome list was writen to OceanDNA-b11530/target_genomes_gtdb.txt
[2023-03-15 07:59:21,267] [INFO] Task started: fastANI
[2023-03-15 07:59:21,267] [INFO] Running command: fastANI --query /var/lib/cwl/stgbed1a997-b5ca-4557-a897-094e359e86bd/OceanDNA-b11530.fa --refList OceanDNA-b11530/target_genomes_gtdb.txt --output OceanDNA-b11530/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:59:31,001] [INFO] Task succeeded: fastANI
[2023-03-15 07:59:31,004] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 07:59:31,004] [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_905480125.1	s__NORP312 sp905480125	99.0851	183	213	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__GCA-2746335;g__NORP312	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018669945.1	s__NORP312 sp018669945	89.9697	175	213	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__GCA-2746335;g__NORP312	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016763645.1	s__NORP312 sp016763645	76.4521	50	213	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__GCA-2746335;g__NORP312	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 07:59:31,019] [INFO] GTDB search result was written to OceanDNA-b11530/result_gtdb.tsv
[2023-03-15 07:59:31,040] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:59:31,052] [INFO] DFAST_QC result json was written to OceanDNA-b11530/dqc_result.json
[2023-03-15 07:59:31,052] [INFO] DFAST_QC completed!
[2023-03-15 07:59:31,053] [INFO] Total running time: 0h0m58s