[2023-03-16 04:31:43,758] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:31:43,758] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:31:43,758] [INFO] DQC Reference Directory: /var/lib/cwl/stg06a1c02b-fee3-4fed-8f22-871358f2638f/dqc_reference
[2023-03-16 04:31:45,523] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:31:45,524] [INFO] Task started: Prodigal
[2023-03-16 04:31:45,524] [INFO] Running command: cat /var/lib/cwl/stgd06a0213-b09f-40e7-98ce-634c95a1df19/OceanDNA-b372.fa | prodigal -d OceanDNA-b372/cds.fna -a OceanDNA-b372/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:31:53,457] [INFO] Task succeeded: Prodigal
[2023-03-16 04:31:53,457] [INFO] Task started: HMMsearch
[2023-03-16 04:31:53,457] [INFO] Running command: hmmsearch --tblout OceanDNA-b372/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06a1c02b-fee3-4fed-8f22-871358f2638f/dqc_reference/reference_markers.hmm OceanDNA-b372/protein.faa > /dev/null
[2023-03-16 04:31:53,611] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:31:53,611] [INFO] Found 6/6 markers.
[2023-03-16 04:31:53,623] [INFO] Query marker FASTA was written to OceanDNA-b372/markers.fasta
[2023-03-16 04:31:53,624] [INFO] Task started: Blastn
[2023-03-16 04:31:53,624] [INFO] Running command: blastn -query OceanDNA-b372/markers.fasta -db /var/lib/cwl/stg06a1c02b-fee3-4fed-8f22-871358f2638f/dqc_reference/reference_markers.fasta -out OceanDNA-b372/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:31:54,153] [INFO] Task succeeded: Blastn
[2023-03-16 04:31:54,154] [INFO] Selected 8 target genomes.
[2023-03-16 04:31:54,154] [INFO] Target genome list was writen to OceanDNA-b372/target_genomes.txt
[2023-03-16 04:31:54,185] [INFO] Task started: fastANI
[2023-03-16 04:31:54,185] [INFO] Running command: fastANI --query /var/lib/cwl/stgd06a0213-b09f-40e7-98ce-634c95a1df19/OceanDNA-b372.fa --refList OceanDNA-b372/target_genomes.txt --output OceanDNA-b372/fastani_result.tsv --threads 1
[2023-03-16 04:31:57,891] [INFO] Task succeeded: fastANI
[2023-03-16 04:31:57,891] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06a1c02b-fee3-4fed-8f22-871358f2638f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:31:57,892] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06a1c02b-fee3-4fed-8f22-871358f2638f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:31:57,892] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:31:57,892] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:31:57,892] [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
--------------------------------------------------------------------------------
[2023-03-16 04:31:57,892] [INFO] DFAST Taxonomy check result was written to OceanDNA-b372/tc_result.tsv
[2023-03-16 04:31:57,892] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:31:57,892] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:31:57,892] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06a1c02b-fee3-4fed-8f22-871358f2638f/dqc_reference/checkm_data
[2023-03-16 04:31:57,895] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:31:58,100] [INFO] Task started: CheckM
[2023-03-16 04:31:58,100] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b372/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b372/checkm_input OceanDNA-b372/checkm_result
[2023-03-16 04:32:23,966] [INFO] Task succeeded: CheckM
[2023-03-16 04:32:23,966] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.70%
Contamintation: 6.86%
Strain heterogeneity: 57.14%
--------------------------------------------------------------------------------
[2023-03-16 04:32:23,968] [INFO] ===== Completeness check finished =====
[2023-03-16 04:32:23,968] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:32:23,968] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b372/markers.fasta)
[2023-03-16 04:32:23,969] [INFO] Task started: Blastn
[2023-03-16 04:32:23,970] [INFO] Running command: blastn -query OceanDNA-b372/markers.fasta -db /var/lib/cwl/stg06a1c02b-fee3-4fed-8f22-871358f2638f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b372/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:32:24,704] [INFO] Task succeeded: Blastn
[2023-03-16 04:32:24,705] [INFO] Selected 12 target genomes.
[2023-03-16 04:32:24,705] [INFO] Target genome list was writen to OceanDNA-b372/target_genomes_gtdb.txt
[2023-03-16 04:32:24,716] [INFO] Task started: fastANI
[2023-03-16 04:32:24,716] [INFO] Running command: fastANI --query /var/lib/cwl/stgd06a0213-b09f-40e7-98ce-634c95a1df19/OceanDNA-b372.fa --refList OceanDNA-b372/target_genomes_gtdb.txt --output OceanDNA-b372/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:32:27,947] [INFO] Task succeeded: fastANI
[2023-03-16 04:32:27,952] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:32:27,952] [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_009703975.1	s__BACL27 sp009703975	82.7966	242	402	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	97.18	96.93	0.73	0.69	4	-
GCA_003569125.1	s__BACL27 sp003569125	82.7915	316	402	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014190295.1	s__BACL27 sp014190295	79.1372	204	402	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016463105.1	s__BACL27 sp016463105	78.8986	166	402	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009927565.1	s__BACL27 sp009927565	78.0124	100	402	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016462185.1	s__BACL27 sp016462185	77.9299	117	402	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	98.92	98.92	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-03-16 04:32:27,952] [INFO] GTDB search result was written to OceanDNA-b372/result_gtdb.tsv
[2023-03-16 04:32:27,952] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:32:27,953] [INFO] DFAST_QC result json was written to OceanDNA-b372/dqc_result.json
[2023-03-16 04:32:27,953] [INFO] DFAST_QC completed!
[2023-03-16 04:32:27,953] [INFO] Total running time: 0h0m44s