[2023-03-19 02:40:15,878] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:40:15,879] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:40:15,879] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d7ea026-f7ee-4548-bdb1-1a74c0c7e972/dqc_reference
[2023-03-19 02:40:17,008] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:40:17,008] [INFO] Task started: Prodigal
[2023-03-19 02:40:17,008] [INFO] Running command: cat /var/lib/cwl/stg1acb9846-4797-4294-8cbb-c7b532aefbf3/OceanDNA-b402.fa | prodigal -d OceanDNA-b402/cds.fna -a OceanDNA-b402/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:40:25,697] [INFO] Task succeeded: Prodigal
[2023-03-19 02:40:25,698] [INFO] Task started: HMMsearch
[2023-03-19 02:40:25,698] [INFO] Running command: hmmsearch --tblout OceanDNA-b402/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d7ea026-f7ee-4548-bdb1-1a74c0c7e972/dqc_reference/reference_markers.hmm OceanDNA-b402/protein.faa > /dev/null
[2023-03-19 02:40:25,849] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:40:25,850] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1acb9846-4797-4294-8cbb-c7b532aefbf3/OceanDNA-b402.fa]
[2023-03-19 02:40:25,867] [INFO] Query marker FASTA was written to OceanDNA-b402/markers.fasta
[2023-03-19 02:40:25,867] [INFO] Task started: Blastn
[2023-03-19 02:40:25,867] [INFO] Running command: blastn -query OceanDNA-b402/markers.fasta -db /var/lib/cwl/stg0d7ea026-f7ee-4548-bdb1-1a74c0c7e972/dqc_reference/reference_markers.fasta -out OceanDNA-b402/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:40:26,405] [INFO] Task succeeded: Blastn
[2023-03-19 02:40:26,407] [INFO] Selected 13 target genomes.
[2023-03-19 02:40:26,407] [INFO] Target genome list was writen to OceanDNA-b402/target_genomes.txt
[2023-03-19 02:40:26,414] [INFO] Task started: fastANI
[2023-03-19 02:40:26,414] [INFO] Running command: fastANI --query /var/lib/cwl/stg1acb9846-4797-4294-8cbb-c7b532aefbf3/OceanDNA-b402.fa --refList OceanDNA-b402/target_genomes.txt --output OceanDNA-b402/fastani_result.tsv --threads 1
[2023-03-19 02:40:33,368] [INFO] Task succeeded: fastANI
[2023-03-19 02:40:33,369] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d7ea026-f7ee-4548-bdb1-1a74c0c7e972/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:40:33,369] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d7ea026-f7ee-4548-bdb1-1a74c0c7e972/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:40:33,372] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:40:33,372] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 02:40:33,372] [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
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	75.9116	52	430	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 02:40:33,373] [INFO] DFAST Taxonomy check result was written to OceanDNA-b402/tc_result.tsv
[2023-03-19 02:40:33,374] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:40:33,375] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:40:33,375] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d7ea026-f7ee-4548-bdb1-1a74c0c7e972/dqc_reference/checkm_data
[2023-03-19 02:40:33,375] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:40:33,380] [INFO] Task started: CheckM
[2023-03-19 02:40:33,380] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b402/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b402/checkm_input OceanDNA-b402/checkm_result
[2023-03-19 02:41:00,273] [INFO] Task succeeded: CheckM
[2023-03-19 02:41:00,273] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:41:00,280] [INFO] ===== Completeness check finished =====
[2023-03-19 02:41:00,280] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:41:00,280] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b402/markers.fasta)
[2023-03-19 02:41:00,281] [INFO] Task started: Blastn
[2023-03-19 02:41:00,281] [INFO] Running command: blastn -query OceanDNA-b402/markers.fasta -db /var/lib/cwl/stg0d7ea026-f7ee-4548-bdb1-1a74c0c7e972/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b402/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:41:01,008] [INFO] Task succeeded: Blastn
[2023-03-19 02:41:01,012] [INFO] Selected 24 target genomes.
[2023-03-19 02:41:01,012] [INFO] Target genome list was writen to OceanDNA-b402/target_genomes_gtdb.txt
[2023-03-19 02:41:01,033] [INFO] Task started: fastANI
[2023-03-19 02:41:01,033] [INFO] Running command: fastANI --query /var/lib/cwl/stg1acb9846-4797-4294-8cbb-c7b532aefbf3/OceanDNA-b402.fa --refList OceanDNA-b402/target_genomes_gtdb.txt --output OceanDNA-b402/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:41:10,248] [INFO] Task succeeded: fastANI
[2023-03-19 02:41:10,253] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:41:10,253] [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_002501485.1	s__Casp-actino5 sp002501485	77.2544	68	430	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	99.77	99.74	0.92	0.90	3	-
GCA_001510385.1	s__Casp-actino5 sp001510385	77.1836	71	430	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	99.68	99.68	0.96	0.96	2	-
GCA_002727235.1	s__Casp-actino5 sp002727235	76.9939	68	430	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	97.22	95.99	0.84	0.77	5	-
GCA_012269985.1	s__Casp-actino5 sp012269985	76.6842	81	430	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	98.07	98.07	0.92	0.92	2	-
GCA_017859785.1	s__Casp-actino5 sp017859785	76.4982	56	430	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	99.23	98.27	0.91	0.86	15	-
GCA_017859395.1	s__Casp-actino5 sp017859395	76.4593	51	430	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	99.27	98.20	0.94	0.88	4	-
GCF_004364865.1	s__Ilumatobacter fluminis	75.9116	52	430	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:41:10,255] [INFO] GTDB search result was written to OceanDNA-b402/result_gtdb.tsv
[2023-03-19 02:41:10,255] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:41:10,257] [INFO] DFAST_QC result json was written to OceanDNA-b402/dqc_result.json
[2023-03-19 02:41:10,257] [INFO] DFAST_QC completed!
[2023-03-19 02:41:10,257] [INFO] Total running time: 0h0m54s