[2023-03-17 08:11:32,507] [INFO] DFAST_QC pipeline started.
[2023-03-17 08:11:32,507] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 08:11:32,507] [INFO] DQC Reference Directory: /var/lib/cwl/stga3741667-6f39-447f-bca1-866eff77e06e/dqc_reference
[2023-03-17 08:11:33,605] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 08:11:33,605] [INFO] Task started: Prodigal
[2023-03-17 08:11:33,605] [INFO] Running command: cat /var/lib/cwl/stg7cf0d799-d604-418e-8c90-b678528960be/OceanDNA-b35120.fa | prodigal -d OceanDNA-b35120/cds.fna -a OceanDNA-b35120/protein.faa -g 11 -q > /dev/null
[2023-03-17 08:11:53,054] [INFO] Task succeeded: Prodigal
[2023-03-17 08:11:53,054] [INFO] Task started: HMMsearch
[2023-03-17 08:11:53,054] [INFO] Running command: hmmsearch --tblout OceanDNA-b35120/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3741667-6f39-447f-bca1-866eff77e06e/dqc_reference/reference_markers.hmm OceanDNA-b35120/protein.faa > /dev/null
[2023-03-17 08:11:53,269] [INFO] Task succeeded: HMMsearch
[2023-03-17 08:11:53,269] [INFO] Found 6/6 markers.
[2023-03-17 08:11:53,292] [INFO] Query marker FASTA was written to OceanDNA-b35120/markers.fasta
[2023-03-17 08:11:53,293] [INFO] Task started: Blastn
[2023-03-17 08:11:53,293] [INFO] Running command: blastn -query OceanDNA-b35120/markers.fasta -db /var/lib/cwl/stga3741667-6f39-447f-bca1-866eff77e06e/dqc_reference/reference_markers.fasta -out OceanDNA-b35120/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:11:54,009] [INFO] Task succeeded: Blastn
[2023-03-17 08:11:54,010] [INFO] Selected 15 target genomes.
[2023-03-17 08:11:54,011] [INFO] Target genome list was writen to OceanDNA-b35120/target_genomes.txt
[2023-03-17 08:11:54,024] [INFO] Task started: fastANI
[2023-03-17 08:11:54,024] [INFO] Running command: fastANI --query /var/lib/cwl/stg7cf0d799-d604-418e-8c90-b678528960be/OceanDNA-b35120.fa --refList OceanDNA-b35120/target_genomes.txt --output OceanDNA-b35120/fastani_result.tsv --threads 1
[2023-03-17 08:12:04,883] [INFO] Task succeeded: fastANI
[2023-03-17 08:12:04,883] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3741667-6f39-447f-bca1-866eff77e06e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 08:12:04,883] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3741667-6f39-447f-bca1-866eff77e06e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 08:12:04,893] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 08:12:04,893] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 08:12:04,893] [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
Rheinheimera aquimaris	strain=KCTC 12840	GCA_020531985.1	412437	412437	type	True	80.8325	571	1135	95	below_threshold
Rheinheimera nanhaiensis	strain=E407-8	GCA_000296695.1	1163621	1163621	type	True	80.2073	593	1135	95	below_threshold
Rheinheimera pleomorphica	strain=PKS7	GCA_011634895.1	2703963	2703963	type	True	79.925	574	1135	95	below_threshold
Rheinheimera pacifica	strain=DSM 17616	GCA_900108485.1	173990	173990	type	True	79.7172	552	1135	95	below_threshold
Rheinheimera lutimaris	strain=YQF-2	GCA_013283795.1	2740584	2740584	type	True	79.6372	545	1135	95	below_threshold
Rheinheimera hassiensis	strain=LMG 27268	GCA_022436675.1	1193627	1193627	type	True	79.5886	541	1135	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_016918075.2	2793282	2793282	type	True	79.256	509	1135	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_017824735.1	2793282	2793282	type	True	79.2378	499	1135	95	below_threshold
Rheinheimera baltica	strain=DSM 14885	GCA_000425345.1	67576	67576	type	True	79.045	382	1135	95	below_threshold
Alishewanella aestuarii	strain=B11	GCA_000280055.1	453835	453835	type	True	78.4654	300	1135	95	below_threshold
Arsukibacterium tuosuense	strain=CGMCC 1.12461	GCA_900215315.1	1323745	1323745	type	True	78.2433	331	1135	95	below_threshold
Arsukibacterium indicum	strain=SM2107	GCA_019100565.1	2848612	2848612	type	True	78.136	343	1135	95	below_threshold
Rheinheimera salexigens	strain=KH87	GCA_001752395.1	1628148	1628148	type	True	77.7481	183	1135	95	below_threshold
Pararheinheimera mesophila	strain=IITR-13	GCA_000986865.1	1547515	1547515	type	True	77.5922	189	1135	95	below_threshold
Pararheinheimera texasensis	strain=DSM 17496	GCA_000711985.1	306205	306205	type	True	77.1588	203	1135	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 08:12:04,893] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35120/tc_result.tsv
[2023-03-17 08:12:04,893] [INFO] ===== Taxonomy check completed =====
[2023-03-17 08:12:04,893] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 08:12:04,894] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3741667-6f39-447f-bca1-866eff77e06e/dqc_reference/checkm_data
[2023-03-17 08:12:04,894] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 08:12:04,946] [INFO] Task started: CheckM
[2023-03-17 08:12:04,946] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35120/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35120/checkm_input OceanDNA-b35120/checkm_result
[2023-03-17 08:12:54,700] [INFO] Task succeeded: CheckM
[2023-03-17 08:12:54,701] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 08:12:54,704] [INFO] ===== Completeness check finished =====
[2023-03-17 08:12:54,704] [INFO] ===== Start GTDB Search =====
[2023-03-17 08:12:54,704] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35120/markers.fasta)
[2023-03-17 08:12:54,704] [INFO] Task started: Blastn
[2023-03-17 08:12:54,704] [INFO] Running command: blastn -query OceanDNA-b35120/markers.fasta -db /var/lib/cwl/stga3741667-6f39-447f-bca1-866eff77e06e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35120/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:12:55,826] [INFO] Task succeeded: Blastn
[2023-03-17 08:12:55,826] [INFO] Selected 13 target genomes.
[2023-03-17 08:12:55,827] [INFO] Target genome list was writen to OceanDNA-b35120/target_genomes_gtdb.txt
[2023-03-17 08:12:55,846] [INFO] Task started: fastANI
[2023-03-17 08:12:55,846] [INFO] Running command: fastANI --query /var/lib/cwl/stg7cf0d799-d604-418e-8c90-b678528960be/OceanDNA-b35120.fa --refList OceanDNA-b35120/target_genomes_gtdb.txt --output OceanDNA-b35120/fastani_result_gtdb.tsv --threads 1
[2023-03-17 08:13:06,060] [INFO] Task succeeded: fastANI
[2023-03-17 08:13:06,068] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 08:13:06,069] [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
GCF_004369005.1	s__Rheinheimera aquimaris	80.5297	573	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	98.51	97.48	0.94	0.92	4	-
GCF_000296695.1	s__Rheinheimera nanhaiensis	80.2104	594	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018826295.1	s__Rheinheimera sp018826295	80.0031	633	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	99.95	99.91	0.97	0.92	5	-
GCF_011634895.1	s__Rheinheimera pleomorphica	79.9155	575	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108485.1	s__Rheinheimera pacifica	79.7029	554	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840125.1	s__Rheinheimera sp002840125	79.6995	561	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013283795.1	s__Rheinheimera sp013283795	79.6279	546	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001513785.1	s__Rheinheimera sp001513785	79.5209	558	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018831085.1	s__Rheinheimera sp018831085	79.4479	550	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	100.00	100.00	1.00	1.00	3	-
GCF_017824735.1	s__Rheinheimera sp017824735	79.2318	500	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000425345.1	s__Rheinheimera baltica	79.0399	382	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215315.1	s__Arsukibacterium tuosuense	78.2317	332	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001752395.1	s__Rheinheimera salexigens	77.7298	184	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 08:13:06,069] [INFO] GTDB search result was written to OceanDNA-b35120/result_gtdb.tsv
[2023-03-17 08:13:06,069] [INFO] ===== GTDB Search completed =====
[2023-03-17 08:13:06,071] [INFO] DFAST_QC result json was written to OceanDNA-b35120/dqc_result.json
[2023-03-17 08:13:06,072] [INFO] DFAST_QC completed!
[2023-03-17 08:13:06,072] [INFO] Total running time: 0h1m34s