[2023-03-16 10:35:15,178] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:35:15,178] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:35:15,178] [INFO] DQC Reference Directory: /var/lib/cwl/stg84684c6a-c47f-4313-802d-38ba5dd4e8be/dqc_reference
[2023-03-16 10:35:16,291] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:35:16,291] [INFO] Task started: Prodigal
[2023-03-16 10:35:16,291] [INFO] Running command: cat /var/lib/cwl/stg8fcdbd61-b517-4c22-8b08-d42802b78535/OceanDNA-b31693.fa | prodigal -d OceanDNA-b31693/cds.fna -a OceanDNA-b31693/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:35:33,586] [INFO] Task succeeded: Prodigal
[2023-03-16 10:35:33,586] [INFO] Task started: HMMsearch
[2023-03-16 10:35:33,587] [INFO] Running command: hmmsearch --tblout OceanDNA-b31693/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84684c6a-c47f-4313-802d-38ba5dd4e8be/dqc_reference/reference_markers.hmm OceanDNA-b31693/protein.faa > /dev/null
[2023-03-16 10:35:33,780] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:35:33,781] [INFO] Found 6/6 markers.
[2023-03-16 10:35:33,797] [INFO] Query marker FASTA was written to OceanDNA-b31693/markers.fasta
[2023-03-16 10:35:33,798] [INFO] Task started: Blastn
[2023-03-16 10:35:33,798] [INFO] Running command: blastn -query OceanDNA-b31693/markers.fasta -db /var/lib/cwl/stg84684c6a-c47f-4313-802d-38ba5dd4e8be/dqc_reference/reference_markers.fasta -out OceanDNA-b31693/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:35:34,762] [INFO] Task succeeded: Blastn
[2023-03-16 10:35:34,763] [INFO] Selected 22 target genomes.
[2023-03-16 10:35:34,764] [INFO] Target genome list was writen to OceanDNA-b31693/target_genomes.txt
[2023-03-16 10:35:34,771] [INFO] Task started: fastANI
[2023-03-16 10:35:34,771] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fcdbd61-b517-4c22-8b08-d42802b78535/OceanDNA-b31693.fa --refList OceanDNA-b31693/target_genomes.txt --output OceanDNA-b31693/fastani_result.tsv --threads 1
[2023-03-16 10:35:48,087] [INFO] Task succeeded: fastANI
[2023-03-16 10:35:48,087] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84684c6a-c47f-4313-802d-38ba5dd4e8be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:35:48,087] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84684c6a-c47f-4313-802d-38ba5dd4e8be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:35:48,100] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:35:48,100] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 10:35:48,100] [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
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	80.8498	540	937	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	80.8216	560	937	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	80.3453	530	937	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	80.2069	521	937	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	79.9829	506	937	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	79.8803	484	937	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	79.7852	472	937	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	79.7292	453	937	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	79.7277	495	937	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	79.6859	484	937	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	79.6283	470	937	95	below_threshold
Alteriqipengyuania lutimaris	strain=CECT 8624	GCA_014191645.1	1538146	1538146	type	True	79.5407	503	937	95	below_threshold
Alteriqipengyuania lutimaris	strain=S-5	GCA_003363135.1	1538146	1538146	type	True	79.5337	500	937	95	below_threshold
Tsuneonella rigui	strain=KCTC 42620	GCA_003958625.1	1708790	1708790	type	True	79.4985	438	937	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_001719165.1	39960	39960	type	True	79.4861	469	937	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_000714795.1	39960	39960	type	True	79.4416	474	937	95	below_threshold
Aurantiacibacter xanthus	strain=CCTCC AB 2015396	GCA_003584015.1	1784712	1784712	type	True	79.2543	383	937	95	below_threshold
Qipengyuania intermedia	strain=GH38	GCA_019711615.1	2867244	2867244	type	True	79.1486	426	937	95	below_threshold
Qipengyuania algicida	strain=KEMB 9005-328	GCA_009828025.1	1836209	1836209	type	True	79.1119	417	937	95	below_threshold
Pelagerythrobacter marensis	strain=DSM 21428	GCA_001461885.1	543877	543877	type	True	79.1076	418	937	95	below_threshold
Pelagerythrobacter marensis	strain=KCTC 22370	GCA_001028625.1	543877	543877	type	True	79.0238	420	937	95	below_threshold
Aurantiacibacter luteus	strain=KA37	GCA_001010945.1	1581420	1581420	type	True	78.9162	427	937	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 10:35:48,100] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31693/tc_result.tsv
[2023-03-16 10:35:48,101] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:35:48,101] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:35:48,101] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84684c6a-c47f-4313-802d-38ba5dd4e8be/dqc_reference/checkm_data
[2023-03-16 10:35:48,102] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:35:48,106] [INFO] Task started: CheckM
[2023-03-16 10:35:48,106] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31693/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31693/checkm_input OceanDNA-b31693/checkm_result
[2023-03-16 10:36:50,443] [INFO] Task succeeded: CheckM
[2023-03-16 10:36:50,444] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:36:50,446] [INFO] ===== Completeness check finished =====
[2023-03-16 10:36:50,447] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:36:50,447] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31693/markers.fasta)
[2023-03-16 10:36:50,448] [INFO] Task started: Blastn
[2023-03-16 10:36:50,448] [INFO] Running command: blastn -query OceanDNA-b31693/markers.fasta -db /var/lib/cwl/stg84684c6a-c47f-4313-802d-38ba5dd4e8be/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31693/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:36:55,248] [INFO] Task succeeded: Blastn
[2023-03-16 10:36:55,250] [INFO] Selected 20 target genomes.
[2023-03-16 10:36:55,250] [INFO] Target genome list was writen to OceanDNA-b31693/target_genomes_gtdb.txt
[2023-03-16 10:36:55,269] [INFO] Task started: fastANI
[2023-03-16 10:36:55,269] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fcdbd61-b517-4c22-8b08-d42802b78535/OceanDNA-b31693.fa --refList OceanDNA-b31693/target_genomes_gtdb.txt --output OceanDNA-b31693/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:37:09,908] [INFO] Task succeeded: fastANI
[2023-03-16 10:37:09,920] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:37:09,920] [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_018828205.1	s__Qipengyuania sp018828205	89.7047	542	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001678665.1	s__Qipengyuania sp001678665	88.068	712	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018819685.1	s__Qipengyuania sp018819685	87.9265	459	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.48	99.48	0.85	0.85	2	-
GCA_016764075.1	s__Qipengyuania sp016764075	81.0171	420	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827295.1	s__Qipengyuania pelagi	80.8329	559	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001542855.1	s__Qipengyuania sp001542855	80.5942	536	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.07	97.03	0.89	0.88	4	-
GCA_009993605.1	s__Qipengyuania sp009993605	80.4752	539	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001635685.1	s__Qipengyuania sp001635685	80.3591	516	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.58	97.35	0.92	0.89	12	-
GCF_018636735.1	s__Alteriqipengyuania sp018636735	80.0705	441	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827515.1	s__Pelagerythrobacter marinus	79.9771	508	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001557325.1	s__Erythrobacter donghaensis_B	79.9053	452	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.70	99.64	0.86	0.85	7	-
GCF_016803135.1	s__Pelagerythrobacter sp016803135	79.8861	491	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135625.1	s__Pelagerythrobacter rhizovicinus	79.8082	470	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006542605.1	s__Erythrobacter sp006542605	79.6977	506	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001557115.1	s__Erythrobacter sp001557115	79.5332	436	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.84	99.84	0.90	0.90	2	-
GCF_009827535.1	s__Altererythrobacter_F oceanensis	79.4966	451	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Altererythrobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002377695.1	s__Alteriqipengyuania sp002377695	79.3826	435	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	99.97	99.97	1.00	1.00	2	-
GCF_005884405.1	s__Qipengyuania marisflavi	79.1876	419	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001028625.1	s__Pelagerythrobacter marensis	79.0226	420	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001010945.1	s__Alteraurantiacibacter luteus	78.9202	427	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:37:09,921] [INFO] GTDB search result was written to OceanDNA-b31693/result_gtdb.tsv
[2023-03-16 10:37:09,921] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:37:09,924] [INFO] DFAST_QC result json was written to OceanDNA-b31693/dqc_result.json
[2023-03-16 10:37:09,924] [INFO] DFAST_QC completed!
[2023-03-16 10:37:09,924] [INFO] Total running time: 0h1m55s