[2023-03-14 14:39:19,283] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:39:19,283] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:39:19,283] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa193647-7fad-4b18-b2f8-a66752d85469/dqc_reference
[2023-03-14 14:39:20,343] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:39:20,344] [INFO] Task started: Prodigal
[2023-03-14 14:39:20,344] [INFO] Running command: cat /var/lib/cwl/stg602e3c85-a745-4fb6-bf85-bd7fc4107e0f/OceanDNA-b31705.fa | prodigal -d OceanDNA-b31705/cds.fna -a OceanDNA-b31705/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:39:37,900] [INFO] Task succeeded: Prodigal
[2023-03-14 14:39:37,900] [INFO] Task started: HMMsearch
[2023-03-14 14:39:37,900] [INFO] Running command: hmmsearch --tblout OceanDNA-b31705/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa193647-7fad-4b18-b2f8-a66752d85469/dqc_reference/reference_markers.hmm OceanDNA-b31705/protein.faa > /dev/null
[2023-03-14 14:39:38,080] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:39:38,080] [INFO] Found 6/6 markers.
[2023-03-14 14:39:38,097] [INFO] Query marker FASTA was written to OceanDNA-b31705/markers.fasta
[2023-03-14 14:39:38,098] [INFO] Task started: Blastn
[2023-03-14 14:39:38,098] [INFO] Running command: blastn -query OceanDNA-b31705/markers.fasta -db /var/lib/cwl/stgaa193647-7fad-4b18-b2f8-a66752d85469/dqc_reference/reference_markers.fasta -out OceanDNA-b31705/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:39:38,837] [INFO] Task succeeded: Blastn
[2023-03-14 14:39:38,838] [INFO] Selected 20 target genomes.
[2023-03-14 14:39:38,838] [INFO] Target genome list was writen to OceanDNA-b31705/target_genomes.txt
[2023-03-14 14:39:38,896] [INFO] Task started: fastANI
[2023-03-14 14:39:38,897] [INFO] Running command: fastANI --query /var/lib/cwl/stg602e3c85-a745-4fb6-bf85-bd7fc4107e0f/OceanDNA-b31705.fa --refList OceanDNA-b31705/target_genomes.txt --output OceanDNA-b31705/fastani_result.tsv --threads 1
[2023-03-14 14:40:00,329] [INFO] Task succeeded: fastANI
[2023-03-14 14:40:00,329] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa193647-7fad-4b18-b2f8-a66752d85469/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:40:00,329] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa193647-7fad-4b18-b2f8-a66752d85469/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:40:00,342] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2023-03-14 14:40:00,342] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-14 14:40:00,342] [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	96.9922	706	749	95	conclusive
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	80.0894	466	749	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	79.8217	426	749	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	79.8137	472	749	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	79.8054	440	749	95	below_threshold
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	79.7033	421	749	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	79.6433	384	749	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	79.4335	430	749	95	below_threshold
Qipengyuania nanhaisediminis	strain=CGMCC 1.7715	GCA_900115585.1	604088	604088	type	True	79.3724	398	749	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	79.3308	430	749	95	below_threshold
Qipengyuania intermedia	strain=GH38	GCA_019711615.1	2867244	2867244	type	True	79.2858	413	749	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	79.2552	417	749	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_000714795.1	39960	39960	type	True	79.2544	379	749	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_001719165.1	39960	39960	type	True	79.191	380	749	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	79.0752	389	749	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	79.0396	390	749	95	below_threshold
Qipengyuania algicida	strain=KEMB 9005-328	GCA_009828025.1	1836209	1836209	type	True	79.0106	350	749	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	78.9621	406	749	95	below_threshold
Qipengyuania pacifica	strain=NZ-96	GCA_019857205.1	2860199	2860199	type	True	78.6986	362	749	95	below_threshold
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	78.5273	353	749	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 14:40:00,343] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31705/tc_result.tsv
[2023-03-14 14:40:00,343] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:40:00,343] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:40:00,343] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa193647-7fad-4b18-b2f8-a66752d85469/dqc_reference/checkm_data
[2023-03-14 14:40:00,344] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:40:00,407] [INFO] Task started: CheckM
[2023-03-14 14:40:00,407] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31705/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31705/checkm_input OceanDNA-b31705/checkm_result
[2023-03-14 14:40:48,324] [INFO] Task succeeded: CheckM
[2023-03-14 14:40:48,324] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.89%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 14:40:48,326] [INFO] ===== Completeness check finished =====
[2023-03-14 14:40:48,326] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:40:48,326] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31705/markers.fasta)
[2023-03-14 14:40:48,327] [INFO] Task started: Blastn
[2023-03-14 14:40:48,327] [INFO] Running command: blastn -query OceanDNA-b31705/markers.fasta -db /var/lib/cwl/stgaa193647-7fad-4b18-b2f8-a66752d85469/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31705/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:40:49,585] [INFO] Task succeeded: Blastn
[2023-03-14 14:40:49,585] [INFO] Selected 17 target genomes.
[2023-03-14 14:40:49,586] [INFO] Target genome list was writen to OceanDNA-b31705/target_genomes_gtdb.txt
[2023-03-14 14:40:49,680] [INFO] Task started: fastANI
[2023-03-14 14:40:49,680] [INFO] Running command: fastANI --query /var/lib/cwl/stg602e3c85-a745-4fb6-bf85-bd7fc4107e0f/OceanDNA-b31705.fa --refList OceanDNA-b31705/target_genomes_gtdb.txt --output OceanDNA-b31705/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:40:59,678] [INFO] Task succeeded: fastANI
[2023-03-14 14:40:59,688] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 14:40:59,689] [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_009827295.1	s__Qipengyuania pelagi	96.9922	706	749	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009993605.1	s__Qipengyuania sp009993605	91.4423	679	749	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	87.3327	629	749	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	80.3395	393	749	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	80.1581	443	749	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.91	97.49	0.87	0.80	20	-
GCA_016764075.1	s__Qipengyuania sp016764075	79.9908	353	749	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	79.9457	451	749	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.07	97.03	0.89	0.88	4	-
GCF_009827315.1	s__Qipengyuania gaetbuli	79.81	440	749	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	79.733	328	749	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.48	99.48	0.85	0.85	2	-
GCA_003248395.1	s__Qipengyuania sp003248395	79.3416	345	749	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827515.1	s__Pelagerythrobacter marinus	79.3308	430	749	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827535.1	s__Altererythrobacter_F oceanensis	79.2082	376	749	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Altererythrobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001719165.1	s__Erythrobacter litoralis	79.2031	379	749	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015529805.1	s__Qipengyuania soli	79.0758	389	749	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011054555.1	s__Erythrobacter sp011054555	78.981	302	749	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015767595.1	s__Qipengyuania sp002895025	78.5716	373	749	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.29	96.55	0.87	0.78	16	-
GCF_001687545.1	s__Paraurantiacibacter namhicola	78.5536	319	749	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Paraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 14:40:59,689] [INFO] GTDB search result was written to OceanDNA-b31705/result_gtdb.tsv
[2023-03-14 14:40:59,689] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:40:59,691] [INFO] DFAST_QC result json was written to OceanDNA-b31705/dqc_result.json
[2023-03-14 14:40:59,691] [INFO] DFAST_QC completed!
[2023-03-14 14:40:59,691] [INFO] Total running time: 0h1m40s