[2023-03-15 03:30:24,298] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:30:24,298] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:30:24,299] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3047298-3607-4ae7-a083-607dba0a22bd/dqc_reference
[2023-03-15 03:30:25,393] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:30:25,394] [INFO] Task started: Prodigal
[2023-03-15 03:30:25,394] [INFO] Running command: cat /var/lib/cwl/stg2774fd27-ee18-43c4-bd43-02bf79c6a4fa/OceanDNA-b29542.fa | prodigal -d OceanDNA-b29542/cds.fna -a OceanDNA-b29542/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:30:45,214] [INFO] Task succeeded: Prodigal
[2023-03-15 03:30:45,215] [INFO] Task started: HMMsearch
[2023-03-15 03:30:45,215] [INFO] Running command: hmmsearch --tblout OceanDNA-b29542/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3047298-3607-4ae7-a083-607dba0a22bd/dqc_reference/reference_markers.hmm OceanDNA-b29542/protein.faa > /dev/null
[2023-03-15 03:30:45,399] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:30:45,399] [INFO] Found 6/6 markers.
[2023-03-15 03:30:45,421] [INFO] Query marker FASTA was written to OceanDNA-b29542/markers.fasta
[2023-03-15 03:30:45,422] [INFO] Task started: Blastn
[2023-03-15 03:30:45,422] [INFO] Running command: blastn -query OceanDNA-b29542/markers.fasta -db /var/lib/cwl/stgb3047298-3607-4ae7-a083-607dba0a22bd/dqc_reference/reference_markers.fasta -out OceanDNA-b29542/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:30:46,034] [INFO] Task succeeded: Blastn
[2023-03-15 03:30:46,035] [INFO] Selected 14 target genomes.
[2023-03-15 03:30:46,035] [INFO] Target genome list was writen to OceanDNA-b29542/target_genomes.txt
[2023-03-15 03:30:46,045] [INFO] Task started: fastANI
[2023-03-15 03:30:46,046] [INFO] Running command: fastANI --query /var/lib/cwl/stg2774fd27-ee18-43c4-bd43-02bf79c6a4fa/OceanDNA-b29542.fa --refList OceanDNA-b29542/target_genomes.txt --output OceanDNA-b29542/fastani_result.tsv --threads 1
[2023-03-15 03:30:57,275] [INFO] Task succeeded: fastANI
[2023-03-15 03:30:57,276] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3047298-3607-4ae7-a083-607dba0a22bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:30:57,276] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3047298-3607-4ae7-a083-607dba0a22bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:30:57,284] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:30:57,284] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 03:30:57,284] [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
Marivita geojedonensis	strain=DPG-138	GCA_002115805.1	1123756	1123756	type	True	82.377	661	1030	95	below_threshold
Marivita geojedonensis	strain=DSM 29432	GCA_003002975.1	1123756	1123756	type	True	82.3428	666	1030	95	below_threshold
Marivita cryptomonadis	strain=CL-SK44	GCA_002115725.1	505252	505252	type	True	81.7549	727	1030	95	below_threshold
Marivita lacus	strain=CGMCC 1.12478	GCA_014637725.1	1323742	1323742	type	True	81.0636	660	1030	95	below_threshold
Marivita hallyeonensis	strain=DSM 29431	GCA_900129875.1	996342	996342	type	True	78.8618	472	1030	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	77.043	220	1030	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	77.0025	224	1030	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	76.8508	209	1030	95	below_threshold
Thalassococcus halodurans	strain=DSM 26915	GCA_900108225.1	373675	373675	type	True	76.773	177	1030	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.5475	120	1030	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	76.1507	133	1030	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 03:30:57,284] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29542/tc_result.tsv
[2023-03-15 03:30:57,284] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:30:57,284] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:30:57,284] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3047298-3607-4ae7-a083-607dba0a22bd/dqc_reference/checkm_data
[2023-03-15 03:30:57,285] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:30:57,290] [INFO] Task started: CheckM
[2023-03-15 03:30:57,290] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29542/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29542/checkm_input OceanDNA-b29542/checkm_result
[2023-03-15 03:31:48,639] [INFO] Task succeeded: CheckM
[2023-03-15 03:31:48,639] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.35%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:31:48,656] [INFO] ===== Completeness check finished =====
[2023-03-15 03:31:48,656] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:31:48,656] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29542/markers.fasta)
[2023-03-15 03:31:48,657] [INFO] Task started: Blastn
[2023-03-15 03:31:48,657] [INFO] Running command: blastn -query OceanDNA-b29542/markers.fasta -db /var/lib/cwl/stgb3047298-3607-4ae7-a083-607dba0a22bd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29542/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:31:49,753] [INFO] Task succeeded: Blastn
[2023-03-15 03:31:49,755] [INFO] Selected 10 target genomes.
[2023-03-15 03:31:49,755] [INFO] Target genome list was writen to OceanDNA-b29542/target_genomes_gtdb.txt
[2023-03-15 03:31:49,762] [INFO] Task started: fastANI
[2023-03-15 03:31:49,763] [INFO] Running command: fastANI --query /var/lib/cwl/stg2774fd27-ee18-43c4-bd43-02bf79c6a4fa/OceanDNA-b29542.fa --refList OceanDNA-b29542/target_genomes_gtdb.txt --output OceanDNA-b29542/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:31:58,570] [INFO] Task succeeded: fastANI
[2023-03-15 03:31:58,577] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 03:31:58,577] [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_003149565.1	s__Marivita sp003149565	87.5997	901	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643905.1	s__Marivita sp017643905	82.6247	672	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002115805.1	s__Marivita geojedonensis	82.3889	660	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002115725.1	s__Marivita cryptomonadis	81.7549	727	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	99.81	99.78	0.91	0.91	31	-
GCF_014637725.1	s__Marivita lacus	81.0595	660	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018224955.1	s__Aestuariicoccus sp018224955	77.3555	273	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001969385.1	s__Salipiger profundus	76.9911	225	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.85	99.64	0.97	0.94	5	-
GCF_002210105.1	s__Pseudooceanicola sp002210105	76.8176	207	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108225.1	s__Thalassococcus halodurans	76.773	177	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassococcus	95.0	96.13	96.13	0.95	0.95	2	-
GCA_013042605.1	s__IMCC34051 sp013042605	76.2486	155	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__IMCC34051	95.0	99.10	98.86	0.88	0.86	4	-
--------------------------------------------------------------------------------
[2023-03-15 03:31:58,577] [INFO] GTDB search result was written to OceanDNA-b29542/result_gtdb.tsv
[2023-03-15 03:31:58,577] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:31:58,578] [INFO] DFAST_QC result json was written to OceanDNA-b29542/dqc_result.json
[2023-03-15 03:31:58,578] [INFO] DFAST_QC completed!
[2023-03-15 03:31:58,579] [INFO] Total running time: 0h1m34s