[2023-03-16 17:26:52,007] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:26:52,008] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:26:52,008] [INFO] DQC Reference Directory: /var/lib/cwl/stg76611fea-12b2-4604-a7c9-d6768e3747ff/dqc_reference
[2023-03-16 17:26:53,265] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:26:53,265] [INFO] Task started: Prodigal
[2023-03-16 17:26:53,266] [INFO] Running command: cat /var/lib/cwl/stg58fd54cc-381b-4e72-85ae-1b93f010ceb4/OceanDNA-b2772.fa | prodigal -d OceanDNA-b2772/cds.fna -a OceanDNA-b2772/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:27:00,444] [INFO] Task succeeded: Prodigal
[2023-03-16 17:27:00,444] [INFO] Task started: HMMsearch
[2023-03-16 17:27:00,444] [INFO] Running command: hmmsearch --tblout OceanDNA-b2772/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg76611fea-12b2-4604-a7c9-d6768e3747ff/dqc_reference/reference_markers.hmm OceanDNA-b2772/protein.faa > /dev/null
[2023-03-16 17:27:00,694] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:27:00,695] [INFO] Found 6/6 markers.
[2023-03-16 17:27:00,704] [INFO] Query marker FASTA was written to OceanDNA-b2772/markers.fasta
[2023-03-16 17:27:00,705] [INFO] Task started: Blastn
[2023-03-16 17:27:00,705] [INFO] Running command: blastn -query OceanDNA-b2772/markers.fasta -db /var/lib/cwl/stg76611fea-12b2-4604-a7c9-d6768e3747ff/dqc_reference/reference_markers.fasta -out OceanDNA-b2772/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:27:01,274] [INFO] Task succeeded: Blastn
[2023-03-16 17:27:01,275] [INFO] Selected 22 target genomes.
[2023-03-16 17:27:01,275] [INFO] Target genome list was writen to OceanDNA-b2772/target_genomes.txt
[2023-03-16 17:27:01,303] [INFO] Task started: fastANI
[2023-03-16 17:27:01,303] [INFO] Running command: fastANI --query /var/lib/cwl/stg58fd54cc-381b-4e72-85ae-1b93f010ceb4/OceanDNA-b2772.fa --refList OceanDNA-b2772/target_genomes.txt --output OceanDNA-b2772/fastani_result.tsv --threads 1
[2023-03-16 17:27:13,812] [INFO] Task succeeded: fastANI
[2023-03-16 17:27:13,812] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg76611fea-12b2-4604-a7c9-d6768e3747ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:27:13,813] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg76611fea-12b2-4604-a7c9-d6768e3747ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:27:13,817] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:27:13,817] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 17:27:13,817] [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
Rhodoluna limnophila	strain=27D-LEPI	GCA_005845365.1	232537	232537	type	True	78.1883	50	404	95	below_threshold
Rhodoluna lacicola	strain=MWH-Ta8	GCA_000699505.1	529884	529884	type	True	78.1233	60	404	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 17:27:13,817] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2772/tc_result.tsv
[2023-03-16 17:27:13,818] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:27:13,818] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:27:13,819] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg76611fea-12b2-4604-a7c9-d6768e3747ff/dqc_reference/checkm_data
[2023-03-16 17:27:13,820] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:27:13,823] [INFO] Task started: CheckM
[2023-03-16 17:27:13,823] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2772/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2772/checkm_input OceanDNA-b2772/checkm_result
[2023-03-16 17:27:44,524] [INFO] Task succeeded: CheckM
[2023-03-16 17:27:44,524] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 17:27:44,527] [INFO] ===== Completeness check finished =====
[2023-03-16 17:27:44,527] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:27:44,527] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2772/markers.fasta)
[2023-03-16 17:27:44,528] [INFO] Task started: Blastn
[2023-03-16 17:27:44,528] [INFO] Running command: blastn -query OceanDNA-b2772/markers.fasta -db /var/lib/cwl/stg76611fea-12b2-4604-a7c9-d6768e3747ff/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2772/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:27:45,392] [INFO] Task succeeded: Blastn
[2023-03-16 17:27:45,394] [INFO] Selected 23 target genomes.
[2023-03-16 17:27:45,394] [INFO] Target genome list was writen to OceanDNA-b2772/target_genomes_gtdb.txt
[2023-03-16 17:27:45,421] [INFO] Task started: fastANI
[2023-03-16 17:27:45,421] [INFO] Running command: fastANI --query /var/lib/cwl/stg58fd54cc-381b-4e72-85ae-1b93f010ceb4/OceanDNA-b2772.fa --refList OceanDNA-b2772/target_genomes_gtdb.txt --output OceanDNA-b2772/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:27:51,458] [INFO] Task succeeded: fastANI
[2023-03-16 17:27:51,465] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 17:27:51,466] [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_009704605.1	s__Rhodoluna sp009704605	92.2405	229	404	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	98.13	98.01	0.83	0.83	3	-
GCF_005845365.1	s__Rhodoluna limnophila	78.1883	50	404	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	98.04	97.94	0.96	0.95	3	-
GCA_009703455.1	s__Rhodoluna sp009703455	78.1341	112	404	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000699505.1	s__Rhodoluna lacicola	78.1233	60	404	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009702645.1	s__Rhodoluna sp009702645	77.4536	73	404	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009702455.1	s__Rhodoluna sp009702455	76.8436	51	404	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	95.81	95.81	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-03-16 17:27:51,466] [INFO] GTDB search result was written to OceanDNA-b2772/result_gtdb.tsv
[2023-03-16 17:27:51,467] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:27:51,469] [INFO] DFAST_QC result json was written to OceanDNA-b2772/dqc_result.json
[2023-03-16 17:27:51,469] [INFO] DFAST_QC completed!
[2023-03-16 17:27:51,469] [INFO] Total running time: 0h0m59s