[2023-03-17 11:08:00,270] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:08:00,271] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:08:00,271] [INFO] DQC Reference Directory: /var/lib/cwl/stg95d7f9dd-399b-4426-b009-2e77cab0b873/dqc_reference
[2023-03-17 11:08:01,418] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:08:01,419] [INFO] Task started: Prodigal
[2023-03-17 11:08:01,420] [INFO] Running command: cat /var/lib/cwl/stg4f68e801-ca9e-4343-a5cd-b8808d1ebd1e/OceanDNA-b15465.fa | prodigal -d OceanDNA-b15465/cds.fna -a OceanDNA-b15465/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:08:13,491] [INFO] Task succeeded: Prodigal
[2023-03-17 11:08:13,492] [INFO] Task started: HMMsearch
[2023-03-17 11:08:13,492] [INFO] Running command: hmmsearch --tblout OceanDNA-b15465/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95d7f9dd-399b-4426-b009-2e77cab0b873/dqc_reference/reference_markers.hmm OceanDNA-b15465/protein.faa > /dev/null
[2023-03-17 11:08:13,669] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:08:13,670] [INFO] Found 6/6 markers.
[2023-03-17 11:08:13,725] [INFO] Query marker FASTA was written to OceanDNA-b15465/markers.fasta
[2023-03-17 11:08:13,726] [INFO] Task started: Blastn
[2023-03-17 11:08:13,727] [INFO] Running command: blastn -query OceanDNA-b15465/markers.fasta -db /var/lib/cwl/stg95d7f9dd-399b-4426-b009-2e77cab0b873/dqc_reference/reference_markers.fasta -out OceanDNA-b15465/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:08:14,239] [INFO] Task succeeded: Blastn
[2023-03-17 11:08:14,254] [INFO] Selected 20 target genomes.
[2023-03-17 11:08:14,254] [INFO] Target genome list was writen to OceanDNA-b15465/target_genomes.txt
[2023-03-17 11:08:14,266] [INFO] Task started: fastANI
[2023-03-17 11:08:14,266] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f68e801-ca9e-4343-a5cd-b8808d1ebd1e/OceanDNA-b15465.fa --refList OceanDNA-b15465/target_genomes.txt --output OceanDNA-b15465/fastani_result.tsv --threads 1
[2023-03-17 11:08:30,598] [INFO] Task succeeded: fastANI
[2023-03-17 11:08:30,599] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95d7f9dd-399b-4426-b009-2e77cab0b873/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:08:30,599] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95d7f9dd-399b-4426-b009-2e77cab0b873/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:08:30,599] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:08:30,599] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 11:08:30,599] [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 11:08:30,603] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15465/tc_result.tsv
[2023-03-17 11:08:30,612] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:08:30,612] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:08:30,612] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95d7f9dd-399b-4426-b009-2e77cab0b873/dqc_reference/checkm_data
[2023-03-17 11:08:30,615] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:08:30,622] [INFO] Task started: CheckM
[2023-03-17 11:08:30,622] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15465/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15465/checkm_input OceanDNA-b15465/checkm_result
[2023-03-17 11:09:04,388] [INFO] Task succeeded: CheckM
[2023-03-17 11:09:04,388] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.77%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:09:04,414] [INFO] ===== Completeness check finished =====
[2023-03-17 11:09:04,414] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:09:04,415] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15465/markers.fasta)
[2023-03-17 11:09:04,415] [INFO] Task started: Blastn
[2023-03-17 11:09:04,415] [INFO] Running command: blastn -query OceanDNA-b15465/markers.fasta -db /var/lib/cwl/stg95d7f9dd-399b-4426-b009-2e77cab0b873/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15465/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:09:05,151] [INFO] Task succeeded: Blastn
[2023-03-17 11:09:05,159] [INFO] Selected 21 target genomes.
[2023-03-17 11:09:05,159] [INFO] Target genome list was writen to OceanDNA-b15465/target_genomes_gtdb.txt
[2023-03-17 11:09:05,404] [INFO] Task started: fastANI
[2023-03-17 11:09:05,404] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f68e801-ca9e-4343-a5cd-b8808d1ebd1e/OceanDNA-b15465.fa --refList OceanDNA-b15465/target_genomes_gtdb.txt --output OceanDNA-b15465/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:09:15,727] [INFO] Task succeeded: fastANI
[2023-03-17 11:09:15,730] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:09:15,730] [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_002816715.1	s__Casp-Chloro-G3 sp002816715	81.8004	252	661	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__Casp-Chloro-G3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009692925.1	s__SHYG01 sp009692925	76.0795	80	661	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__SHYG01	95.0	99.84	99.84	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-03-17 11:09:15,736] [INFO] GTDB search result was written to OceanDNA-b15465/result_gtdb.tsv
[2023-03-17 11:09:15,746] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:09:15,752] [INFO] DFAST_QC result json was written to OceanDNA-b15465/dqc_result.json
[2023-03-17 11:09:15,752] [INFO] DFAST_QC completed!
[2023-03-17 11:09:15,752] [INFO] Total running time: 0h1m15s