[2023-03-18 20:59:43,923] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:59:43,923] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:59:43,923] [INFO] DQC Reference Directory: /var/lib/cwl/stge0366730-266d-46f5-ace7-397bfa34b324/dqc_reference
[2023-03-18 20:59:45,683] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:59:45,683] [INFO] Task started: Prodigal
[2023-03-18 20:59:45,683] [INFO] Running command: cat /var/lib/cwl/stg5125472c-b848-4546-889b-9ba9d2c47f1c/OceanDNA-b31666.fa | prodigal -d OceanDNA-b31666/cds.fna -a OceanDNA-b31666/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:59:51,888] [INFO] Task succeeded: Prodigal
[2023-03-18 20:59:51,889] [INFO] Task started: HMMsearch
[2023-03-18 20:59:51,889] [INFO] Running command: hmmsearch --tblout OceanDNA-b31666/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0366730-266d-46f5-ace7-397bfa34b324/dqc_reference/reference_markers.hmm OceanDNA-b31666/protein.faa > /dev/null
[2023-03-18 20:59:52,052] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:59:52,053] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5125472c-b848-4546-889b-9ba9d2c47f1c/OceanDNA-b31666.fa]
[2023-03-18 20:59:52,065] [INFO] Query marker FASTA was written to OceanDNA-b31666/markers.fasta
[2023-03-18 20:59:52,066] [INFO] Task started: Blastn
[2023-03-18 20:59:52,066] [INFO] Running command: blastn -query OceanDNA-b31666/markers.fasta -db /var/lib/cwl/stge0366730-266d-46f5-ace7-397bfa34b324/dqc_reference/reference_markers.fasta -out OceanDNA-b31666/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:59:52,736] [INFO] Task succeeded: Blastn
[2023-03-18 20:59:52,737] [INFO] Selected 26 target genomes.
[2023-03-18 20:59:52,737] [INFO] Target genome list was writen to OceanDNA-b31666/target_genomes.txt
[2023-03-18 20:59:52,759] [INFO] Task started: fastANI
[2023-03-18 20:59:52,759] [INFO] Running command: fastANI --query /var/lib/cwl/stg5125472c-b848-4546-889b-9ba9d2c47f1c/OceanDNA-b31666.fa --refList OceanDNA-b31666/target_genomes.txt --output OceanDNA-b31666/fastani_result.tsv --threads 1
[2023-03-18 21:00:05,451] [INFO] Task succeeded: fastANI
[2023-03-18 21:00:05,452] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0366730-266d-46f5-ace7-397bfa34b324/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:00:05,452] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0366730-266d-46f5-ace7-397bfa34b324/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:00:05,456] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:00:05,456] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 21:00:05,456] [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
Erythrobacter longus	strain=DSM 6997	GCA_000715015.1	1044	1044	type	True	78.3535	52	133	95	below_threshold
Erythrobacter sanguineus	strain=JCM 20691	GCA_002155655.1	198312	198312	type	True	77.8671	60	133	95	below_threshold
Erythrobacter sanguineus	strain=DSM 11032	GCA_900143235.1	198312	198312	type	True	77.8671	60	133	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 21:00:05,456] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31666/tc_result.tsv
[2023-03-18 21:00:05,456] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:00:05,457] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:00:05,457] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0366730-266d-46f5-ace7-397bfa34b324/dqc_reference/checkm_data
[2023-03-18 21:00:05,457] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:00:05,471] [INFO] Task started: CheckM
[2023-03-18 21:00:05,471] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31666/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31666/checkm_input OceanDNA-b31666/checkm_result
[2023-03-18 21:00:26,755] [INFO] Task succeeded: CheckM
[2023-03-18 21:00:26,755] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.87%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:00:26,768] [INFO] ===== Completeness check finished =====
[2023-03-18 21:00:26,768] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:00:26,768] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31666/markers.fasta)
[2023-03-18 21:00:26,769] [INFO] Task started: Blastn
[2023-03-18 21:00:26,769] [INFO] Running command: blastn -query OceanDNA-b31666/markers.fasta -db /var/lib/cwl/stge0366730-266d-46f5-ace7-397bfa34b324/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31666/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:00:27,895] [INFO] Task succeeded: Blastn
[2023-03-18 21:00:27,896] [INFO] Selected 20 target genomes.
[2023-03-18 21:00:27,896] [INFO] Target genome list was writen to OceanDNA-b31666/target_genomes_gtdb.txt
[2023-03-18 21:00:27,912] [INFO] Task started: fastANI
[2023-03-18 21:00:27,913] [INFO] Running command: fastANI --query /var/lib/cwl/stg5125472c-b848-4546-889b-9ba9d2c47f1c/OceanDNA-b31666.fa --refList OceanDNA-b31666/target_genomes_gtdb.txt --output OceanDNA-b31666/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:00:36,881] [INFO] Task succeeded: fastANI
[2023-03-18 21:00:36,886] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 21:00:36,887] [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_013214365.1	s__Erythrobacter sp013214365	97.4628	120	133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000715015.1	s__Erythrobacter longus	78.3535	52	133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000714765.1	s__Erythrobacter sp000714765	78.2069	69	133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003264115.1	s__Erythrobacter sp003264115	77.9642	54	133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152865.1	s__Erythrobacter sp000152865	77.8646	52	133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744895.1	s__Erythrobacter sp000744895	77.5632	53	133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105095.1	s__Erythrobacter sp900105095	77.5249	51	133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001296025.1	s__Erythrobacter sp001296025	76.9667	52	133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 21:00:36,888] [INFO] GTDB search result was written to OceanDNA-b31666/result_gtdb.tsv
[2023-03-18 21:00:36,888] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:00:36,890] [INFO] DFAST_QC result json was written to OceanDNA-b31666/dqc_result.json
[2023-03-18 21:00:36,890] [INFO] DFAST_QC completed!
[2023-03-18 21:00:36,890] [INFO] Total running time: 0h0m53s