[2023-03-15 05:55:10,895] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:55:10,895] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:55:10,895] [INFO] DQC Reference Directory: /var/lib/cwl/stgc4724968-ad49-442d-95a1-8791cfcbe82e/dqc_reference
[2023-03-15 05:55:11,994] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:55:11,995] [INFO] Task started: Prodigal
[2023-03-15 05:55:11,995] [INFO] Running command: cat /var/lib/cwl/stg9aa6d582-f999-419c-a26a-bd036f0993e5/OceanDNA-b23825.fa | prodigal -d OceanDNA-b23825/cds.fna -a OceanDNA-b23825/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:55:27,613] [INFO] Task succeeded: Prodigal
[2023-03-15 05:55:27,613] [INFO] Task started: HMMsearch
[2023-03-15 05:55:27,613] [INFO] Running command: hmmsearch --tblout OceanDNA-b23825/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc4724968-ad49-442d-95a1-8791cfcbe82e/dqc_reference/reference_markers.hmm OceanDNA-b23825/protein.faa > /dev/null
[2023-03-15 05:55:27,808] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:55:27,809] [INFO] Found 6/6 markers.
[2023-03-15 05:55:27,849] [INFO] Query marker FASTA was written to OceanDNA-b23825/markers.fasta
[2023-03-15 05:55:27,852] [INFO] Task started: Blastn
[2023-03-15 05:55:27,853] [INFO] Running command: blastn -query OceanDNA-b23825/markers.fasta -db /var/lib/cwl/stgc4724968-ad49-442d-95a1-8791cfcbe82e/dqc_reference/reference_markers.fasta -out OceanDNA-b23825/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:55:28,469] [INFO] Task succeeded: Blastn
[2023-03-15 05:55:28,474] [INFO] Selected 30 target genomes.
[2023-03-15 05:55:28,474] [INFO] Target genome list was writen to OceanDNA-b23825/target_genomes.txt
[2023-03-15 05:55:28,489] [INFO] Task started: fastANI
[2023-03-15 05:55:28,489] [INFO] Running command: fastANI --query /var/lib/cwl/stg9aa6d582-f999-419c-a26a-bd036f0993e5/OceanDNA-b23825.fa --refList OceanDNA-b23825/target_genomes.txt --output OceanDNA-b23825/fastani_result.tsv --threads 1
[2023-03-15 05:55:51,004] [INFO] Task succeeded: fastANI
[2023-03-15 05:55:51,004] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc4724968-ad49-442d-95a1-8791cfcbe82e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:55:51,004] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc4724968-ad49-442d-95a1-8791cfcbe82e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:55:51,009] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:55:51,009] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 05:55:51,009] [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
Ponticaulis koreensis	strain=DSM 19734	GCA_000420665.1	1123045	1123045	type	True	92.1506	801	881	95	below_threshold
Henriciella mobilis	strain=M65	GCA_003576315.1	2305467	2305467	type	True	75.937	54	881	95	below_threshold
Henriciella litoralis	strain=DSM 22014	GCA_002088935.1	568102	568102	type	True	75.8917	51	881	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 05:55:51,012] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23825/tc_result.tsv
[2023-03-15 05:55:51,018] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:55:51,018] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:55:51,018] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc4724968-ad49-442d-95a1-8791cfcbe82e/dqc_reference/checkm_data
[2023-03-15 05:55:51,019] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:55:51,126] [INFO] Task started: CheckM
[2023-03-15 05:55:51,126] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23825/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23825/checkm_input OceanDNA-b23825/checkm_result
[2023-03-15 05:56:34,547] [INFO] Task succeeded: CheckM
[2023-03-15 05:56:34,547] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.06%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:56:34,673] [INFO] ===== Completeness check finished =====
[2023-03-15 05:56:34,673] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:56:34,673] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23825/markers.fasta)
[2023-03-15 05:56:34,674] [INFO] Task started: Blastn
[2023-03-15 05:56:34,674] [INFO] Running command: blastn -query OceanDNA-b23825/markers.fasta -db /var/lib/cwl/stgc4724968-ad49-442d-95a1-8791cfcbe82e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23825/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:56:35,706] [INFO] Task succeeded: Blastn
[2023-03-15 05:56:35,715] [INFO] Selected 12 target genomes.
[2023-03-15 05:56:35,715] [INFO] Target genome list was writen to OceanDNA-b23825/target_genomes_gtdb.txt
[2023-03-15 05:56:35,725] [INFO] Task started: fastANI
[2023-03-15 05:56:35,725] [INFO] Running command: fastANI --query /var/lib/cwl/stg9aa6d582-f999-419c-a26a-bd036f0993e5/OceanDNA-b23825.fa --refList OceanDNA-b23825/target_genomes_gtdb.txt --output OceanDNA-b23825/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:56:43,890] [INFO] Task succeeded: fastANI
[2023-03-15 05:56:43,896] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 05:56:43,896] [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_002723155.1	s__Ponticaulis sp002723155	99.9875	881	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Ponticaulis	95.0	99.28	99.28	0.86	0.86	2	conclusive
GCA_002338565.1	s__Ponticaulis sp002338565	92.812	804	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Ponticaulis	95.0	99.94	99.86	0.98	0.96	4	-
GCF_000420665.1	s__Ponticaulis koreensis	92.1506	801	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Ponticaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002173095.1	s__Ponticaulis sp002173095	78.8773	386	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Ponticaulis	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002692725.1	s__Ponticaulis sp002692725	77.2814	187	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Ponticaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701295.1	s__Ponticaulis sp002701295	77.2812	199	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Ponticaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699325.1	s__Ponticaulis sp002699325	77.0591	160	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Ponticaulis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:56:43,902] [INFO] GTDB search result was written to OceanDNA-b23825/result_gtdb.tsv
[2023-03-15 05:56:43,908] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:56:43,915] [INFO] DFAST_QC result json was written to OceanDNA-b23825/dqc_result.json
[2023-03-15 05:56:43,915] [INFO] DFAST_QC completed!
[2023-03-15 05:56:43,915] [INFO] Total running time: 0h1m33s