[2023-03-18 08:36:16,001] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:36:16,001] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:36:16,001] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f1b76f6-56be-4af0-b828-9be857292e18/dqc_reference
[2023-03-18 08:36:17,826] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:36:17,826] [INFO] Task started: Prodigal
[2023-03-18 08:36:17,826] [INFO] Running command: cat /var/lib/cwl/stgf230b9ad-5e8a-43f1-bc76-96f4c7cc2e14/OceanDNA-b31709.fa | prodigal -d OceanDNA-b31709/cds.fna -a OceanDNA-b31709/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:36:25,406] [INFO] Task succeeded: Prodigal
[2023-03-18 08:36:25,407] [INFO] Task started: HMMsearch
[2023-03-18 08:36:25,407] [INFO] Running command: hmmsearch --tblout OceanDNA-b31709/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f1b76f6-56be-4af0-b828-9be857292e18/dqc_reference/reference_markers.hmm OceanDNA-b31709/protein.faa > /dev/null
[2023-03-18 08:36:25,582] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:36:25,582] [INFO] Found 6/6 markers.
[2023-03-18 08:36:25,600] [INFO] Query marker FASTA was written to OceanDNA-b31709/markers.fasta
[2023-03-18 08:36:25,600] [INFO] Task started: Blastn
[2023-03-18 08:36:25,600] [INFO] Running command: blastn -query OceanDNA-b31709/markers.fasta -db /var/lib/cwl/stg5f1b76f6-56be-4af0-b828-9be857292e18/dqc_reference/reference_markers.fasta -out OceanDNA-b31709/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:36:26,340] [INFO] Task succeeded: Blastn
[2023-03-18 08:36:26,341] [INFO] Selected 21 target genomes.
[2023-03-18 08:36:26,341] [INFO] Target genome list was writen to OceanDNA-b31709/target_genomes.txt
[2023-03-18 08:36:26,355] [INFO] Task started: fastANI
[2023-03-18 08:36:26,355] [INFO] Running command: fastANI --query /var/lib/cwl/stgf230b9ad-5e8a-43f1-bc76-96f4c7cc2e14/OceanDNA-b31709.fa --refList OceanDNA-b31709/target_genomes.txt --output OceanDNA-b31709/fastani_result.tsv --threads 1
[2023-03-18 08:36:36,937] [INFO] Task succeeded: fastANI
[2023-03-18 08:36:36,938] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f1b76f6-56be-4af0-b828-9be857292e18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:36:36,938] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f1b76f6-56be-4af0-b828-9be857292e18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:36:36,950] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:36:36,950] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:36:36,950] [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 pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	90.9907	314	348	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	80.0744	202	348	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	79.6847	196	348	95	below_threshold
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	79.5894	191	348	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	79.5807	189	348	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	79.4814	183	348	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	79.3547	170	348	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	79.3339	205	348	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	79.3152	176	348	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	79.2564	187	348	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	78.9944	176	348	95	below_threshold
Qipengyuania algicida	strain=KEMB 9005-328	GCA_009828025.1	1836209	1836209	type	True	78.9648	153	348	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	78.9398	171	348	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	78.8962	183	348	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_000714795.1	39960	39960	type	True	78.8366	177	348	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_001719165.1	39960	39960	type	True	78.7902	180	348	95	below_threshold
Qipengyuania pacifica	strain=NZ-96	GCA_019857205.1	2860199	2860199	type	True	78.5462	151	348	95	below_threshold
Aurantiacibacter luteus	strain=KA37	GCA_001010945.1	1581420	1581420	type	True	78.5132	153	348	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	78.0721	111	348	95	below_threshold
Novosphingobium olei	strain=TW-4	GCA_012927405.1	2728851	2728851	type	True	77.9869	116	348	95	below_threshold
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	77.8566	127	348	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:36:36,950] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31709/tc_result.tsv
[2023-03-18 08:36:36,950] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:36:36,951] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:36:36,951] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f1b76f6-56be-4af0-b828-9be857292e18/dqc_reference/checkm_data
[2023-03-18 08:36:36,951] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:36:36,955] [INFO] Task started: CheckM
[2023-03-18 08:36:36,955] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31709/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31709/checkm_input OceanDNA-b31709/checkm_result
[2023-03-18 08:37:01,000] [INFO] Task succeeded: CheckM
[2023-03-18 08:37:01,000] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.92%
Contamintation: 3.47%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 08:37:01,003] [INFO] ===== Completeness check finished =====
[2023-03-18 08:37:01,003] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:37:01,003] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31709/markers.fasta)
[2023-03-18 08:37:01,004] [INFO] Task started: Blastn
[2023-03-18 08:37:01,004] [INFO] Running command: blastn -query OceanDNA-b31709/markers.fasta -db /var/lib/cwl/stg5f1b76f6-56be-4af0-b828-9be857292e18/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31709/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:37:02,308] [INFO] Task succeeded: Blastn
[2023-03-18 08:37:02,313] [INFO] Selected 15 target genomes.
[2023-03-18 08:37:02,313] [INFO] Target genome list was writen to OceanDNA-b31709/target_genomes_gtdb.txt
[2023-03-18 08:37:02,375] [INFO] Task started: fastANI
[2023-03-18 08:37:02,375] [INFO] Running command: fastANI --query /var/lib/cwl/stgf230b9ad-5e8a-43f1-bc76-96f4c7cc2e14/OceanDNA-b31709.fa --refList OceanDNA-b31709/target_genomes_gtdb.txt --output OceanDNA-b31709/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:37:09,686] [INFO] Task succeeded: fastANI
[2023-03-18 08:37:09,695] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 08:37:09,696] [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_009993605.1	s__Qipengyuania sp009993605	95.5119	318	348	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009827295.1	s__Qipengyuania pelagi	90.9907	314	348	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	87.6305	301	348	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.58	97.35	0.92	0.89	12	-
GCA_018828205.1	s__Qipengyuania sp018828205	80.2269	187	348	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828015.1	s__Qipengyuania citrea	79.7597	202	348	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.91	97.49	0.87	0.80	20	-
GCA_003248395.1	s__Qipengyuania sp003248395	79.759	158	348	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016764075.1	s__Qipengyuania sp016764075	79.6212	165	348	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	79.4605	202	348	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.07	97.03	0.89	0.88	4	-
GCF_018636735.1	s__Alteriqipengyuania sp018636735	79.1497	170	348	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018819685.1	s__Qipengyuania sp018819685	79.1363	166	348	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.48	99.48	0.85	0.85	2	-
GCF_015529805.1	s__Qipengyuania soli	78.9398	171	348	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011765465.1	s__Erythrobacter sp011765465	78.8586	177	348	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002712945.1	s__Alteriqipengyuania sp002712945	78.8512	102	348	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001719165.1	s__Erythrobacter litoralis	78.8126	179	348	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006542605.1	s__Erythrobacter sp006542605	78.7905	189	348	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:37:09,698] [INFO] GTDB search result was written to OceanDNA-b31709/result_gtdb.tsv
[2023-03-18 08:37:09,702] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:37:09,706] [INFO] DFAST_QC result json was written to OceanDNA-b31709/dqc_result.json
[2023-03-18 08:37:09,706] [INFO] DFAST_QC completed!
[2023-03-18 08:37:09,706] [INFO] Total running time: 0h0m54s