[2023-03-18 01:08:39,213] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:08:39,214] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:08:39,214] [INFO] DQC Reference Directory: /var/lib/cwl/stg47549312-0c07-485f-a53a-edfba4ebab8d/dqc_reference
[2023-03-18 01:08:40,335] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:08:40,336] [INFO] Task started: Prodigal
[2023-03-18 01:08:40,336] [INFO] Running command: cat /var/lib/cwl/stg0fa0319c-f07b-4c2c-af7e-53188d7f509b/OceanDNA-b22828.fa | prodigal -d OceanDNA-b22828/cds.fna -a OceanDNA-b22828/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:09:04,184] [INFO] Task succeeded: Prodigal
[2023-03-18 01:09:04,185] [INFO] Task started: HMMsearch
[2023-03-18 01:09:04,185] [INFO] Running command: hmmsearch --tblout OceanDNA-b22828/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47549312-0c07-485f-a53a-edfba4ebab8d/dqc_reference/reference_markers.hmm OceanDNA-b22828/protein.faa > /dev/null
[2023-03-18 01:09:04,430] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:09:04,430] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0fa0319c-f07b-4c2c-af7e-53188d7f509b/OceanDNA-b22828.fa]
[2023-03-18 01:09:04,480] [INFO] Query marker FASTA was written to OceanDNA-b22828/markers.fasta
[2023-03-18 01:09:04,481] [INFO] Task started: Blastn
[2023-03-18 01:09:04,481] [INFO] Running command: blastn -query OceanDNA-b22828/markers.fasta -db /var/lib/cwl/stg47549312-0c07-485f-a53a-edfba4ebab8d/dqc_reference/reference_markers.fasta -out OceanDNA-b22828/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:09:05,060] [INFO] Task succeeded: Blastn
[2023-03-18 01:09:05,063] [INFO] Selected 20 target genomes.
[2023-03-18 01:09:05,063] [INFO] Target genome list was writen to OceanDNA-b22828/target_genomes.txt
[2023-03-18 01:09:05,076] [INFO] Task started: fastANI
[2023-03-18 01:09:05,076] [INFO] Running command: fastANI --query /var/lib/cwl/stg0fa0319c-f07b-4c2c-af7e-53188d7f509b/OceanDNA-b22828.fa --refList OceanDNA-b22828/target_genomes.txt --output OceanDNA-b22828/fastani_result.tsv --threads 1
[2023-03-18 01:09:20,880] [INFO] Task succeeded: fastANI
[2023-03-18 01:09:20,880] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47549312-0c07-485f-a53a-edfba4ebab8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:09:20,880] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47549312-0c07-485f-a53a-edfba4ebab8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:09:20,883] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:09:20,884] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:09:20,884] [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
Maioricimonas rarisocia	strain=Mal4	GCA_007747795.1	2528026	2528026	type	True	75.2064	63	1022	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:09:20,885] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22828/tc_result.tsv
[2023-03-18 01:09:20,885] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:09:20,885] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:09:20,885] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47549312-0c07-485f-a53a-edfba4ebab8d/dqc_reference/checkm_data
[2023-03-18 01:09:20,886] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:09:20,892] [INFO] Task started: CheckM
[2023-03-18 01:09:20,892] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22828/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22828/checkm_input OceanDNA-b22828/checkm_result
[2023-03-18 01:10:21,365] [INFO] Task succeeded: CheckM
[2023-03-18 01:10:21,366] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.32%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:10:21,370] [INFO] ===== Completeness check finished =====
[2023-03-18 01:10:21,370] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:10:21,371] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22828/markers.fasta)
[2023-03-18 01:10:21,372] [INFO] Task started: Blastn
[2023-03-18 01:10:21,372] [INFO] Running command: blastn -query OceanDNA-b22828/markers.fasta -db /var/lib/cwl/stg47549312-0c07-485f-a53a-edfba4ebab8d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22828/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:10:22,287] [INFO] Task succeeded: Blastn
[2023-03-18 01:10:22,288] [INFO] Selected 23 target genomes.
[2023-03-18 01:10:22,288] [INFO] Target genome list was writen to OceanDNA-b22828/target_genomes_gtdb.txt
[2023-03-18 01:10:22,304] [INFO] Task started: fastANI
[2023-03-18 01:10:22,304] [INFO] Running command: fastANI --query /var/lib/cwl/stg0fa0319c-f07b-4c2c-af7e-53188d7f509b/OceanDNA-b22828.fa --refList OceanDNA-b22828/target_genomes_gtdb.txt --output OceanDNA-b22828/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:10:43,272] [INFO] Task succeeded: fastANI
[2023-03-18 01:10:43,274] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:10:43,275] [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_018699955.1	s__JABISG01 sp018699955	99.9749	998	1022	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABISG01	95.0	99.95	99.95	0.96	0.96	3	conclusive
GCF_007747795.1	s__Maioricimonas rarisocia	75.2064	63	1022	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Maioricimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:10:43,275] [INFO] GTDB search result was written to OceanDNA-b22828/result_gtdb.tsv
[2023-03-18 01:10:43,275] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:10:43,276] [INFO] DFAST_QC result json was written to OceanDNA-b22828/dqc_result.json
[2023-03-18 01:10:43,276] [INFO] DFAST_QC completed!
[2023-03-18 01:10:43,276] [INFO] Total running time: 0h2m4s