[2023-03-15 03:14:16,302] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:14:16,302] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:14:16,302] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c9d1159-5706-4db6-8b8a-ff30cc8f57d3/dqc_reference
[2023-03-15 03:14:17,568] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:14:17,568] [INFO] Task started: Prodigal
[2023-03-15 03:14:17,568] [INFO] Running command: cat /var/lib/cwl/stgdf6ab89b-606f-4d4f-88e6-6a9caf0184ab/OceanDNA-b5226.fa | prodigal -d OceanDNA-b5226/cds.fna -a OceanDNA-b5226/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:14:22,300] [INFO] Task succeeded: Prodigal
[2023-03-15 03:14:22,301] [INFO] Task started: HMMsearch
[2023-03-15 03:14:22,301] [INFO] Running command: hmmsearch --tblout OceanDNA-b5226/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c9d1159-5706-4db6-8b8a-ff30cc8f57d3/dqc_reference/reference_markers.hmm OceanDNA-b5226/protein.faa > /dev/null
[2023-03-15 03:14:22,486] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:14:22,487] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdf6ab89b-606f-4d4f-88e6-6a9caf0184ab/OceanDNA-b5226.fa]
[2023-03-15 03:14:22,495] [INFO] Query marker FASTA was written to OceanDNA-b5226/markers.fasta
[2023-03-15 03:14:22,495] [INFO] Task started: Blastn
[2023-03-15 03:14:22,495] [INFO] Running command: blastn -query OceanDNA-b5226/markers.fasta -db /var/lib/cwl/stg1c9d1159-5706-4db6-8b8a-ff30cc8f57d3/dqc_reference/reference_markers.fasta -out OceanDNA-b5226/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:14:23,019] [INFO] Task succeeded: Blastn
[2023-03-15 03:14:23,020] [INFO] Selected 30 target genomes.
[2023-03-15 03:14:23,020] [INFO] Target genome list was writen to OceanDNA-b5226/target_genomes.txt
[2023-03-15 03:14:23,034] [INFO] Task started: fastANI
[2023-03-15 03:14:23,034] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf6ab89b-606f-4d4f-88e6-6a9caf0184ab/OceanDNA-b5226.fa --refList OceanDNA-b5226/target_genomes.txt --output OceanDNA-b5226/fastani_result.tsv --threads 1
[2023-03-15 03:14:38,079] [INFO] Task succeeded: fastANI
[2023-03-15 03:14:38,080] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c9d1159-5706-4db6-8b8a-ff30cc8f57d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:14:38,080] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c9d1159-5706-4db6-8b8a-ff30cc8f57d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:14:38,080] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:14:38,080] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 03:14:38,080] [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 03:14:38,080] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5226/tc_result.tsv
[2023-03-15 03:14:38,081] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:14:38,081] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:14:38,081] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c9d1159-5706-4db6-8b8a-ff30cc8f57d3/dqc_reference/checkm_data
[2023-03-15 03:14:38,084] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:14:38,086] [INFO] Task started: CheckM
[2023-03-15 03:14:38,086] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5226/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5226/checkm_input OceanDNA-b5226/checkm_result
[2023-03-15 03:14:56,929] [INFO] Task succeeded: CheckM
[2023-03-15 03:14:56,930] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:14:56,931] [INFO] ===== Completeness check finished =====
[2023-03-15 03:14:56,932] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:14:56,932] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5226/markers.fasta)
[2023-03-15 03:14:56,932] [INFO] Task started: Blastn
[2023-03-15 03:14:56,932] [INFO] Running command: blastn -query OceanDNA-b5226/markers.fasta -db /var/lib/cwl/stg1c9d1159-5706-4db6-8b8a-ff30cc8f57d3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5226/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:14:57,689] [INFO] Task succeeded: Blastn
[2023-03-15 03:14:57,690] [INFO] Selected 17 target genomes.
[2023-03-15 03:14:57,690] [INFO] Target genome list was writen to OceanDNA-b5226/target_genomes_gtdb.txt
[2023-03-15 03:14:57,731] [INFO] Task started: fastANI
[2023-03-15 03:14:57,731] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf6ab89b-606f-4d4f-88e6-6a9caf0184ab/OceanDNA-b5226.fa --refList OceanDNA-b5226/target_genomes_gtdb.txt --output OceanDNA-b5226/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:15:05,252] [INFO] Task succeeded: fastANI
[2023-03-15 03:15:05,256] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 03:15:05,256] [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_003454845.1	s__UBA8444 sp003454845	91.5966	110	208	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA7312;g__UBA8444	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779995.1	s__UBA8444 sp016779995	91.2074	192	208	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA7312;g__UBA8444	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002714805.1	s__UBA8444 sp002714805	85.7764	159	208	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA7312;g__UBA8444	95.0	95.59	95.59	0.86	0.86	2	-
GCA_016779935.1	s__GCA-2862585 sp016779935	77.0205	73	208	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA7312;g__GCA-2862585	95.0	99.89	99.89	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-03-15 03:15:05,256] [INFO] GTDB search result was written to OceanDNA-b5226/result_gtdb.tsv
[2023-03-15 03:15:05,257] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:15:05,257] [INFO] DFAST_QC result json was written to OceanDNA-b5226/dqc_result.json
[2023-03-15 03:15:05,257] [INFO] DFAST_QC completed!
[2023-03-15 03:15:05,257] [INFO] Total running time: 0h0m49s