[2023-03-15 22:23:01,926] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:23:01,926] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:23:01,926] [INFO] DQC Reference Directory: /var/lib/cwl/stg93cb3fa6-7cc0-4d29-8b19-39851cade33e/dqc_reference
[2023-03-15 22:23:03,674] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:23:03,675] [INFO] Task started: Prodigal
[2023-03-15 22:23:03,675] [INFO] Running command: cat /var/lib/cwl/stg98c3ebaa-096d-4442-9520-694c30739442/OceanDNA-b1333.fa | prodigal -d OceanDNA-b1333/cds.fna -a OceanDNA-b1333/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:23:16,887] [INFO] Task succeeded: Prodigal
[2023-03-15 22:23:16,888] [INFO] Task started: HMMsearch
[2023-03-15 22:23:16,888] [INFO] Running command: hmmsearch --tblout OceanDNA-b1333/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93cb3fa6-7cc0-4d29-8b19-39851cade33e/dqc_reference/reference_markers.hmm OceanDNA-b1333/protein.faa > /dev/null
[2023-03-15 22:23:17,052] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:23:17,052] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg98c3ebaa-096d-4442-9520-694c30739442/OceanDNA-b1333.fa]
[2023-03-15 22:23:17,067] [INFO] Query marker FASTA was written to OceanDNA-b1333/markers.fasta
[2023-03-15 22:23:17,068] [INFO] Task started: Blastn
[2023-03-15 22:23:17,068] [INFO] Running command: blastn -query OceanDNA-b1333/markers.fasta -db /var/lib/cwl/stg93cb3fa6-7cc0-4d29-8b19-39851cade33e/dqc_reference/reference_markers.fasta -out OceanDNA-b1333/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:23:17,708] [INFO] Task succeeded: Blastn
[2023-03-15 22:23:17,709] [INFO] Selected 26 target genomes.
[2023-03-15 22:23:17,709] [INFO] Target genome list was writen to OceanDNA-b1333/target_genomes.txt
[2023-03-15 22:23:17,726] [INFO] Task started: fastANI
[2023-03-15 22:23:17,726] [INFO] Running command: fastANI --query /var/lib/cwl/stg98c3ebaa-096d-4442-9520-694c30739442/OceanDNA-b1333.fa --refList OceanDNA-b1333/target_genomes.txt --output OceanDNA-b1333/fastani_result.tsv --threads 1
[2023-03-15 22:23:35,839] [INFO] Task succeeded: fastANI
[2023-03-15 22:23:35,840] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg93cb3fa6-7cc0-4d29-8b19-39851cade33e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:23:35,840] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg93cb3fa6-7cc0-4d29-8b19-39851cade33e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:23:35,843] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:23:35,843] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 22:23:35,843] [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
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.0086	66	710	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 22:23:35,844] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1333/tc_result.tsv
[2023-03-15 22:23:35,844] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:23:35,844] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:23:35,844] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93cb3fa6-7cc0-4d29-8b19-39851cade33e/dqc_reference/checkm_data
[2023-03-15 22:23:35,845] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:23:36,159] [INFO] Task started: CheckM
[2023-03-15 22:23:36,159] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1333/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1333/checkm_input OceanDNA-b1333/checkm_result
[2023-03-15 22:24:11,736] [INFO] Task succeeded: CheckM
[2023-03-15 22:24:11,736] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 22:24:11,738] [INFO] ===== Completeness check finished =====
[2023-03-15 22:24:11,738] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:24:11,739] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1333/markers.fasta)
[2023-03-15 22:24:11,740] [INFO] Task started: Blastn
[2023-03-15 22:24:11,740] [INFO] Running command: blastn -query OceanDNA-b1333/markers.fasta -db /var/lib/cwl/stg93cb3fa6-7cc0-4d29-8b19-39851cade33e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1333/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:24:12,789] [INFO] Task succeeded: Blastn
[2023-03-15 22:24:12,790] [INFO] Selected 13 target genomes.
[2023-03-15 22:24:12,790] [INFO] Target genome list was writen to OceanDNA-b1333/target_genomes_gtdb.txt
[2023-03-15 22:24:12,798] [INFO] Task started: fastANI
[2023-03-15 22:24:12,798] [INFO] Running command: fastANI --query /var/lib/cwl/stg98c3ebaa-096d-4442-9520-694c30739442/OceanDNA-b1333.fa --refList OceanDNA-b1333/target_genomes_gtdb.txt --output OceanDNA-b1333/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:24:17,946] [INFO] Task succeeded: fastANI
[2023-03-15 22:24:17,953] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 22:24:17,953] [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_002717365.1	s__UBA9410 sp002717365	99.4779	532	710	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016845305.1	s__UBA9410 sp016845305	79.726	404	710	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002727895.1	s__UBA9410 sp002727895	79.4555	275	710	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	97.12	97.12	0.93	0.93	2	-
GCA_014239855.1	s__UBA9410 sp014239855	79.245	330	710	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014237715.1	s__UBA9410 sp014237715	78.9954	328	710	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	98.52	98.52	0.97	0.97	2	-
GCA_003541675.1	s__UBA9410 sp003541675	78.9029	193	710	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002714485.1	s__UBA9410 sp002714485	78.8884	231	710	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012961035.1	s__UBA9410 sp012961035	78.8135	317	710	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	99.67	99.67	0.93	0.93	2	-
GCA_014240365.1	s__UBA9410 sp014240365	78.6205	282	710	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	98.11	98.07	0.86	0.84	5	-
GCA_002348705.1	s__UBA9410 sp002348705	77.9666	178	710	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	99.53	98.86	0.93	0.89	6	-
GCA_002501135.1	s__UBA3125 sp002501135	76.879	123	710	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA3125	95.0	99.79	99.79	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-03-15 22:24:17,953] [INFO] GTDB search result was written to OceanDNA-b1333/result_gtdb.tsv
[2023-03-15 22:24:17,953] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:24:17,954] [INFO] DFAST_QC result json was written to OceanDNA-b1333/dqc_result.json
[2023-03-15 22:24:17,955] [INFO] DFAST_QC completed!
[2023-03-15 22:24:17,955] [INFO] Total running time: 0h1m16s