[2023-03-14 10:55:58,922] [INFO] DFAST_QC pipeline started.
[2023-03-14 10:55:58,932] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 10:55:58,932] [INFO] DQC Reference Directory: /var/lib/cwl/stg27a3b202-1cf4-45d0-beec-06ae2b86cd1d/dqc_reference
[2023-03-14 10:56:00,754] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 10:56:00,754] [INFO] Task started: Prodigal
[2023-03-14 10:56:00,754] [INFO] Running command: cat /var/lib/cwl/stgee67e86b-4bd9-4b97-b035-b657c0bdf803/OceanDNA-b31592.fa | prodigal -d OceanDNA-b31592/cds.fna -a OceanDNA-b31592/protein.faa -g 11 -q > /dev/null
[2023-03-14 10:56:20,511] [INFO] Task succeeded: Prodigal
[2023-03-14 10:56:20,512] [INFO] Task started: HMMsearch
[2023-03-14 10:56:20,512] [INFO] Running command: hmmsearch --tblout OceanDNA-b31592/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg27a3b202-1cf4-45d0-beec-06ae2b86cd1d/dqc_reference/reference_markers.hmm OceanDNA-b31592/protein.faa > /dev/null
[2023-03-14 10:56:20,765] [INFO] Task succeeded: HMMsearch
[2023-03-14 10:56:20,765] [INFO] Found 6/6 markers.
[2023-03-14 10:56:20,786] [INFO] Query marker FASTA was written to OceanDNA-b31592/markers.fasta
[2023-03-14 10:56:20,786] [INFO] Task started: Blastn
[2023-03-14 10:56:20,786] [INFO] Running command: blastn -query OceanDNA-b31592/markers.fasta -db /var/lib/cwl/stg27a3b202-1cf4-45d0-beec-06ae2b86cd1d/dqc_reference/reference_markers.fasta -out OceanDNA-b31592/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:21,681] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:21,682] [INFO] Selected 15 target genomes.
[2023-03-14 10:56:21,682] [INFO] Target genome list was writen to OceanDNA-b31592/target_genomes.txt
[2023-03-14 10:56:21,695] [INFO] Task started: fastANI
[2023-03-14 10:56:21,695] [INFO] Running command: fastANI --query /var/lib/cwl/stgee67e86b-4bd9-4b97-b035-b657c0bdf803/OceanDNA-b31592.fa --refList OceanDNA-b31592/target_genomes.txt --output OceanDNA-b31592/fastani_result.tsv --threads 1
[2023-03-14 10:56:31,557] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:31,557] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg27a3b202-1cf4-45d0-beec-06ae2b86cd1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 10:56:31,557] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg27a3b202-1cf4-45d0-beec-06ae2b86cd1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 10:56:31,567] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 10:56:31,567] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 10:56:31,567] [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
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	94.5984	902	1059	95	below_threshold
Alteriqipengyuania lutimaris	strain=S-5	GCA_003363135.1	1538146	1538146	type	True	85.292	736	1059	95	below_threshold
Alteriqipengyuania lutimaris	strain=CECT 8624	GCA_014191645.1	1538146	1538146	type	True	85.2712	727	1059	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	79.8512	487	1059	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	79.7881	478	1059	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	79.7691	491	1059	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	79.3313	466	1059	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	79.1594	437	1059	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	79.0775	476	1059	95	below_threshold
Aurantiacibacter xanthus	strain=CCTCC AB 2015396	GCA_003584015.1	1784712	1784712	type	True	78.9997	415	1059	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	78.8452	387	1059	95	below_threshold
Qipengyuania algicida	strain=KEMB 9005-328	GCA_009828025.1	1836209	1836209	type	True	78.8028	364	1059	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	78.7749	440	1059	95	below_threshold
Aurantiacibacter odishensis	strain=KCTC 23981	GCA_003605195.1	1155476	1155476	type	True	78.6655	387	1059	95	below_threshold
Erythrobacter tepidarius	strain=DSM 10594	GCA_002155695.1	60454	60454	type	True	78.6281	428	1059	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 10:56:31,567] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31592/tc_result.tsv
[2023-03-14 10:56:31,567] [INFO] ===== Taxonomy check completed =====
[2023-03-14 10:56:31,567] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 10:56:31,567] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg27a3b202-1cf4-45d0-beec-06ae2b86cd1d/dqc_reference/checkm_data
[2023-03-14 10:56:31,568] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 10:56:31,572] [INFO] Task started: CheckM
[2023-03-14 10:56:31,572] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31592/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31592/checkm_input OceanDNA-b31592/checkm_result
[2023-03-14 10:57:21,000] [INFO] Task succeeded: CheckM
[2023-03-14 10:57:21,000] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.06%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 10:57:21,003] [INFO] ===== Completeness check finished =====
[2023-03-14 10:57:21,003] [INFO] ===== Start GTDB Search =====
[2023-03-14 10:57:21,003] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31592/markers.fasta)
[2023-03-14 10:57:21,003] [INFO] Task started: Blastn
[2023-03-14 10:57:21,003] [INFO] Running command: blastn -query OceanDNA-b31592/markers.fasta -db /var/lib/cwl/stg27a3b202-1cf4-45d0-beec-06ae2b86cd1d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31592/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:57:22,702] [INFO] Task succeeded: Blastn
[2023-03-14 10:57:22,702] [INFO] Selected 8 target genomes.
[2023-03-14 10:57:22,703] [INFO] Target genome list was writen to OceanDNA-b31592/target_genomes_gtdb.txt
[2023-03-14 10:57:22,711] [INFO] Task started: fastANI
[2023-03-14 10:57:22,711] [INFO] Running command: fastANI --query /var/lib/cwl/stgee67e86b-4bd9-4b97-b035-b657c0bdf803/OceanDNA-b31592.fa --refList OceanDNA-b31592/target_genomes_gtdb.txt --output OceanDNA-b31592/fastani_result_gtdb.tsv --threads 1
[2023-03-14 10:57:28,088] [INFO] Task succeeded: fastANI
[2023-03-14 10:57:28,094] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 10:57:28,094] [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_000176355.1	s__Alteriqipengyuania bathyomarina	96.9051	941	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	98.10	96.53	0.93	0.90	11	conclusive
GCF_015999305.1	s__Alteriqipengyuania sp015999305	93.7585	871	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729695.1	s__Alteriqipengyuania sp002729695	85.3968	703	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	99.53	99.11	0.93	0.90	4	-
GCF_003363135.1	s__Alteriqipengyuania lutimaris	85.2776	737	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000186705.1	s__Alteriqipengyuania sp000186705	84.6959	757	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009993635.1	s__Alteriqipengyuania sp009993635	84.5139	735	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	99.91	99.91	0.97	0.97	2	-
GCA_002377695.1	s__Alteriqipengyuania sp002377695	84.3788	721	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	99.97	99.97	1.00	1.00	2	-
GCA_002712945.1	s__Alteriqipengyuania sp002712945	84.2082	389	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 10:57:28,094] [INFO] GTDB search result was written to OceanDNA-b31592/result_gtdb.tsv
[2023-03-14 10:57:28,094] [INFO] ===== GTDB Search completed =====
[2023-03-14 10:57:28,096] [INFO] DFAST_QC result json was written to OceanDNA-b31592/dqc_result.json
[2023-03-14 10:57:28,096] [INFO] DFAST_QC completed!
[2023-03-14 10:57:28,096] [INFO] Total running time: 0h1m29s