[2023-03-18 01:26:26,310] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:26:26,310] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:26:26,310] [INFO] DQC Reference Directory: /var/lib/cwl/stg47acbbc9-4444-4850-b567-90678886fb18/dqc_reference
[2023-03-18 01:26:27,508] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:26:27,509] [INFO] Task started: Prodigal
[2023-03-18 01:26:27,509] [INFO] Running command: cat /var/lib/cwl/stga1f52575-7993-4ebc-b1e4-1f57ef3bc89b/OceanDNA-b31685.fa | prodigal -d OceanDNA-b31685/cds.fna -a OceanDNA-b31685/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:26:46,028] [INFO] Task succeeded: Prodigal
[2023-03-18 01:26:46,028] [INFO] Task started: HMMsearch
[2023-03-18 01:26:46,028] [INFO] Running command: hmmsearch --tblout OceanDNA-b31685/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47acbbc9-4444-4850-b567-90678886fb18/dqc_reference/reference_markers.hmm OceanDNA-b31685/protein.faa > /dev/null
[2023-03-18 01:26:46,291] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:26:46,292] [INFO] Found 6/6 markers.
[2023-03-18 01:26:46,311] [INFO] Query marker FASTA was written to OceanDNA-b31685/markers.fasta
[2023-03-18 01:26:46,312] [INFO] Task started: Blastn
[2023-03-18 01:26:46,312] [INFO] Running command: blastn -query OceanDNA-b31685/markers.fasta -db /var/lib/cwl/stg47acbbc9-4444-4850-b567-90678886fb18/dqc_reference/reference_markers.fasta -out OceanDNA-b31685/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:26:47,058] [INFO] Task succeeded: Blastn
[2023-03-18 01:26:47,059] [INFO] Selected 19 target genomes.
[2023-03-18 01:26:47,059] [INFO] Target genome list was writen to OceanDNA-b31685/target_genomes.txt
[2023-03-18 01:26:47,148] [INFO] Task started: fastANI
[2023-03-18 01:26:47,149] [INFO] Running command: fastANI --query /var/lib/cwl/stga1f52575-7993-4ebc-b1e4-1f57ef3bc89b/OceanDNA-b31685.fa --refList OceanDNA-b31685/target_genomes.txt --output OceanDNA-b31685/fastani_result.tsv --threads 1
[2023-03-18 01:26:59,260] [INFO] Task succeeded: fastANI
[2023-03-18 01:26:59,261] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47acbbc9-4444-4850-b567-90678886fb18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:26:59,261] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47acbbc9-4444-4850-b567-90678886fb18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:26:59,273] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:26:59,273] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:26:59,274] [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 sanguineus	strain=JCM 20691	GCA_002155655.1	198312	198312	type	True	79.9845	541	974	95	below_threshold
Erythrobacter sanguineus	strain=DSM 11032	GCA_900143235.1	198312	198312	type	True	79.9767	536	974	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_001719165.1	39960	39960	type	True	79.9144	542	974	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	79.901	563	974	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_000714795.1	39960	39960	type	True	79.8846	566	974	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	79.7507	537	974	95	below_threshold
Erythrobacter dokdonensis	strain=DSM 17193	GCA_002155305.1	328225	328225	type	True	79.7226	544	974	95	below_threshold
Erythrobacter ramosus	strain=JCM 10282	GCA_009828055.1	35811	35811	type	True	79.4132	522	974	95	below_threshold
Erythrobacter rubeus	strain=KMU-140	GCA_014705715.1	2760803	2760803	type	True	79.4092	522	974	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	78.804	387	974	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	78.685	407	974	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	78.6533	399	974	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	78.6386	372	974	95	below_threshold
Alteriqipengyuania lutimaris	strain=S-5	GCA_003363135.1	1538146	1538146	type	True	78.633	373	974	95	below_threshold
Alteriqipengyuania lutimaris	strain=CECT 8624	GCA_014191645.1	1538146	1538146	type	True	78.5169	389	974	95	below_threshold
Pelagerythrobacter marensis	strain=KCTC 22370	GCA_001028625.1	543877	543877	type	True	78.458	349	974	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.3638	387	974	95	below_threshold
Pelagerythrobacter marensis	strain=DSM 21428	GCA_001461885.1	543877	543877	type	True	78.3323	360	974	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	78.0238	319	974	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:26:59,274] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31685/tc_result.tsv
[2023-03-18 01:26:59,274] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:26:59,274] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:26:59,274] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47acbbc9-4444-4850-b567-90678886fb18/dqc_reference/checkm_data
[2023-03-18 01:26:59,282] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:26:59,292] [INFO] Task started: CheckM
[2023-03-18 01:26:59,293] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31685/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31685/checkm_input OceanDNA-b31685/checkm_result
[2023-03-18 01:27:46,557] [INFO] Task succeeded: CheckM
[2023-03-18 01:27:46,557] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.89%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:27:46,560] [INFO] ===== Completeness check finished =====
[2023-03-18 01:27:46,560] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:27:46,561] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31685/markers.fasta)
[2023-03-18 01:27:46,562] [INFO] Task started: Blastn
[2023-03-18 01:27:46,562] [INFO] Running command: blastn -query OceanDNA-b31685/markers.fasta -db /var/lib/cwl/stg47acbbc9-4444-4850-b567-90678886fb18/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31685/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:27:47,924] [INFO] Task succeeded: Blastn
[2023-03-18 01:27:47,925] [INFO] Selected 17 target genomes.
[2023-03-18 01:27:47,925] [INFO] Target genome list was writen to OceanDNA-b31685/target_genomes_gtdb.txt
[2023-03-18 01:27:48,023] [INFO] Task started: fastANI
[2023-03-18 01:27:48,023] [INFO] Running command: fastANI --query /var/lib/cwl/stga1f52575-7993-4ebc-b1e4-1f57ef3bc89b/OceanDNA-b31685.fa --refList OceanDNA-b31685/target_genomes_gtdb.txt --output OceanDNA-b31685/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:27:58,337] [INFO] Task succeeded: fastANI
[2023-03-18 01:27:58,347] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:27:58,347] [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_018205975.1	s__Erythrobacter sp018205975	80.8685	661	974	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363635.1	s__Erythrobacter sp009363635	80.3112	606	974	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	80.2839	598	974	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125555.1	s__Erythrobacter sp016125555	80.2645	535	974	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822695.1	s__Erythrobacter sp013822695	80.0288	502	974	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.78	99.78	0.82	0.82	2	-
GCF_900143235.1	s__Erythrobacter sanguineus	79.972	536	974	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_011054555.1	s__Erythrobacter sp011054555	79.8848	443	974	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331285.1	s__Erythrobacter sp000331285	79.8636	524	974	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001557325.1	s__Erythrobacter donghaensis_B	79.751	492	974	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.70	99.64	0.86	0.85	7	-
GCA_013911835.1	s__Erythrobacter sp013911835	79.6487	348	974	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014705715.1	s__Erythrobacter sp014705715	79.4092	522	974	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	79.1864	491	974	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	79.1093	485	974	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763545.1	s__JACXVD01 sp014763545	78.8712	395	974	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__JACXVD01	95.0	99.92	99.92	0.96	0.96	2	-
GCA_019204025.1	s__Erythrobacter sp019204025	78.8027	494	974	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827515.1	s__Pelagerythrobacter marinus	78.7934	387	974	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013005.1	s__Altererythrobacter_D litoralis_A	78.7851	439	974	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Altererythrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:27:58,348] [INFO] GTDB search result was written to OceanDNA-b31685/result_gtdb.tsv
[2023-03-18 01:27:58,348] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:27:58,350] [INFO] DFAST_QC result json was written to OceanDNA-b31685/dqc_result.json
[2023-03-18 01:27:58,350] [INFO] DFAST_QC completed!
[2023-03-18 01:27:58,350] [INFO] Total running time: 0h1m32s