[2023-03-17 05:39:41,585] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:39:41,600] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:39:41,600] [INFO] DQC Reference Directory: /var/lib/cwl/stg80f5130f-c472-447a-8640-c5c018d417d5/dqc_reference
[2023-03-17 05:39:42,707] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:39:42,708] [INFO] Task started: Prodigal
[2023-03-17 05:39:42,708] [INFO] Running command: cat /var/lib/cwl/stgc89968e0-b725-4ada-ac45-6410da32d3a3/OceanDNA-b20703.fa | prodigal -d OceanDNA-b20703/cds.fna -a OceanDNA-b20703/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:39:48,309] [INFO] Task succeeded: Prodigal
[2023-03-17 05:39:48,309] [INFO] Task started: HMMsearch
[2023-03-17 05:39:48,309] [INFO] Running command: hmmsearch --tblout OceanDNA-b20703/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80f5130f-c472-447a-8640-c5c018d417d5/dqc_reference/reference_markers.hmm OceanDNA-b20703/protein.faa > /dev/null
[2023-03-17 05:39:48,482] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:39:48,483] [INFO] Found 6/6 markers.
[2023-03-17 05:39:48,634] [INFO] Query marker FASTA was written to OceanDNA-b20703/markers.fasta
[2023-03-17 05:39:48,636] [INFO] Task started: Blastn
[2023-03-17 05:39:48,636] [INFO] Running command: blastn -query OceanDNA-b20703/markers.fasta -db /var/lib/cwl/stg80f5130f-c472-447a-8640-c5c018d417d5/dqc_reference/reference_markers.fasta -out OceanDNA-b20703/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:39:49,236] [INFO] Task succeeded: Blastn
[2023-03-17 05:39:49,286] [INFO] Selected 18 target genomes.
[2023-03-17 05:39:49,286] [INFO] Target genome list was writen to OceanDNA-b20703/target_genomes.txt
[2023-03-17 05:39:49,294] [INFO] Task started: fastANI
[2023-03-17 05:39:49,295] [INFO] Running command: fastANI --query /var/lib/cwl/stgc89968e0-b725-4ada-ac45-6410da32d3a3/OceanDNA-b20703.fa --refList OceanDNA-b20703/target_genomes.txt --output OceanDNA-b20703/fastani_result.tsv --threads 1
[2023-03-17 05:39:56,884] [INFO] Task succeeded: fastANI
[2023-03-17 05:39:56,884] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80f5130f-c472-447a-8640-c5c018d417d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:39:56,884] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80f5130f-c472-447a-8640-c5c018d417d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:39:56,884] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:39:56,885] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 05:39:56,885] [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 05:39:56,885] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20703/tc_result.tsv
[2023-03-17 05:39:56,885] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:39:56,885] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:39:56,885] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80f5130f-c472-447a-8640-c5c018d417d5/dqc_reference/checkm_data
[2023-03-17 05:39:56,895] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:39:56,950] [INFO] Task started: CheckM
[2023-03-17 05:39:56,950] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20703/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20703/checkm_input OceanDNA-b20703/checkm_result
[2023-03-17 05:40:17,712] [INFO] Task succeeded: CheckM
[2023-03-17 05:40:17,712] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.12%
Contamintation: 6.31%
Strain heterogeneity: 83.33%
--------------------------------------------------------------------------------
[2023-03-17 05:40:17,748] [INFO] ===== Completeness check finished =====
[2023-03-17 05:40:17,748] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:40:17,748] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20703/markers.fasta)
[2023-03-17 05:40:17,750] [INFO] Task started: Blastn
[2023-03-17 05:40:17,750] [INFO] Running command: blastn -query OceanDNA-b20703/markers.fasta -db /var/lib/cwl/stg80f5130f-c472-447a-8640-c5c018d417d5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20703/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:40:18,771] [INFO] Task succeeded: Blastn
[2023-03-17 05:40:18,772] [INFO] Selected 27 target genomes.
[2023-03-17 05:40:18,772] [INFO] Target genome list was writen to OceanDNA-b20703/target_genomes_gtdb.txt
[2023-03-17 05:40:18,923] [INFO] Task started: fastANI
[2023-03-17 05:40:18,923] [INFO] Running command: fastANI --query /var/lib/cwl/stgc89968e0-b725-4ada-ac45-6410da32d3a3/OceanDNA-b20703.fa --refList OceanDNA-b20703/target_genomes_gtdb.txt --output OceanDNA-b20703/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:40:27,611] [INFO] Task succeeded: fastANI
[2023-03-17 05:40:27,613] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 05:40:27,613] [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_002170735.1	s__TMED198 sp002170735	99.3624	220	326	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__TMED198;g__TMED198	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-17 05:40:27,614] [INFO] GTDB search result was written to OceanDNA-b20703/result_gtdb.tsv
[2023-03-17 05:40:27,615] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:40:27,615] [INFO] DFAST_QC result json was written to OceanDNA-b20703/dqc_result.json
[2023-03-17 05:40:27,615] [INFO] DFAST_QC completed!
[2023-03-17 05:40:27,615] [INFO] Total running time: 0h0m46s