[2023-03-18 09:53:10,295] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:53:10,295] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:53:10,295] [INFO] DQC Reference Directory: /var/lib/cwl/stg56561d1f-3054-45d1-8bba-0ceea6d9406a/dqc_reference
[2023-03-18 09:53:11,379] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:53:11,379] [INFO] Task started: Prodigal
[2023-03-18 09:53:11,379] [INFO] Running command: cat /var/lib/cwl/stg473e5ff5-072c-4455-9b98-8edef9bdde2b/OceanDNA-b31692.fa | prodigal -d OceanDNA-b31692/cds.fna -a OceanDNA-b31692/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:53:18,513] [INFO] Task succeeded: Prodigal
[2023-03-18 09:53:18,514] [INFO] Task started: HMMsearch
[2023-03-18 09:53:18,514] [INFO] Running command: hmmsearch --tblout OceanDNA-b31692/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56561d1f-3054-45d1-8bba-0ceea6d9406a/dqc_reference/reference_markers.hmm OceanDNA-b31692/protein.faa > /dev/null
[2023-03-18 09:53:18,664] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:53:18,665] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg473e5ff5-072c-4455-9b98-8edef9bdde2b/OceanDNA-b31692.fa]
[2023-03-18 09:53:18,674] [INFO] Query marker FASTA was written to OceanDNA-b31692/markers.fasta
[2023-03-18 09:53:18,675] [INFO] Task started: Blastn
[2023-03-18 09:53:18,675] [INFO] Running command: blastn -query OceanDNA-b31692/markers.fasta -db /var/lib/cwl/stg56561d1f-3054-45d1-8bba-0ceea6d9406a/dqc_reference/reference_markers.fasta -out OceanDNA-b31692/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:53:19,396] [INFO] Task succeeded: Blastn
[2023-03-18 09:53:19,396] [INFO] Selected 16 target genomes.
[2023-03-18 09:53:19,397] [INFO] Target genome list was writen to OceanDNA-b31692/target_genomes.txt
[2023-03-18 09:53:19,406] [INFO] Task started: fastANI
[2023-03-18 09:53:19,406] [INFO] Running command: fastANI --query /var/lib/cwl/stg473e5ff5-072c-4455-9b98-8edef9bdde2b/OceanDNA-b31692.fa --refList OceanDNA-b31692/target_genomes.txt --output OceanDNA-b31692/fastani_result.tsv --threads 1
[2023-03-18 09:53:26,890] [INFO] Task succeeded: fastANI
[2023-03-18 09:53:26,891] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56561d1f-3054-45d1-8bba-0ceea6d9406a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:53:26,891] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56561d1f-3054-45d1-8bba-0ceea6d9406a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:53:26,901] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:53:26,901] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 09:53:26,901] [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	79.4362	248	385	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	79.3606	250	385	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	79.1976	231	385	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	79.1	249	385	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	79.0078	247	385	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	78.9052	216	385	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	78.8307	208	385	95	below_threshold
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	78.8102	246	385	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	78.8052	192	385	95	below_threshold
Qipengyuania vulgaris	strain=DSM 17792	GCA_009827325.1	291985	291985	type	True	78.6268	207	385	95	below_threshold
Qipengyuania intermedia	strain=GH38	GCA_019711615.1	2867244	2867244	type	True	78.5746	224	385	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	78.3625	219	385	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	78.3026	209	385	95	below_threshold
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	78.1784	167	385	95	below_threshold
Erythrobacter dokdonensis	strain=DSM 17193	GCA_002155305.1	328225	328225	type	True	77.6997	169	385	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	77.682	167	385	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 09:53:26,901] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31692/tc_result.tsv
[2023-03-18 09:53:26,901] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:53:26,901] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:53:26,901] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56561d1f-3054-45d1-8bba-0ceea6d9406a/dqc_reference/checkm_data
[2023-03-18 09:53:26,902] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:53:26,906] [INFO] Task started: CheckM
[2023-03-18 09:53:26,906] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31692/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31692/checkm_input OceanDNA-b31692/checkm_result
[2023-03-18 09:53:49,405] [INFO] Task succeeded: CheckM
[2023-03-18 09:53:49,405] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:53:49,407] [INFO] ===== Completeness check finished =====
[2023-03-18 09:53:49,407] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:53:49,407] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31692/markers.fasta)
[2023-03-18 09:53:49,408] [INFO] Task started: Blastn
[2023-03-18 09:53:49,408] [INFO] Running command: blastn -query OceanDNA-b31692/markers.fasta -db /var/lib/cwl/stg56561d1f-3054-45d1-8bba-0ceea6d9406a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31692/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:53:50,687] [INFO] Task succeeded: Blastn
[2023-03-18 09:53:50,688] [INFO] Selected 17 target genomes.
[2023-03-18 09:53:50,688] [INFO] Target genome list was writen to OceanDNA-b31692/target_genomes_gtdb.txt
[2023-03-18 09:53:50,699] [INFO] Task started: fastANI
[2023-03-18 09:53:50,699] [INFO] Running command: fastANI --query /var/lib/cwl/stg473e5ff5-072c-4455-9b98-8edef9bdde2b/OceanDNA-b31692.fa --refList OceanDNA-b31692/target_genomes_gtdb.txt --output OceanDNA-b31692/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:53:58,689] [INFO] Task succeeded: fastANI
[2023-03-18 09:53:58,699] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 09:53:58,700] [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	79.4183	238	385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827315.1	s__Qipengyuania gaetbuli	79.3606	250	385	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	79.1184	248	385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000181515.1	s__Qipengyuania sp000181515	79.1044	247	385	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	78.9618	226	385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.58	97.35	0.92	0.89	12	-
GCF_900115585.1	s__Qipengyuania nanhaisediminis	78.8976	218	385	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	78.8669	184	385	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	78.8236	247	385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.91	97.49	0.87	0.80	20	-
GCA_013911865.1	s__Qipengyuania sp013911865	78.6713	171	385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827325.1	s__Qipengyuania vulgaris	78.6268	207	385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000756795.1	s__Qipengyuania vulgaris_A	78.6013	235	385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248395.1	s__Qipengyuania sp003248395	78.5399	194	385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176355.1	s__Alteriqipengyuania bathyomarina	78.2317	192	385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	98.10	96.53	0.93	0.90	11	-
GCF_009827535.1	s__Altererythrobacter_F oceanensis	78.2247	194	385	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_015999305.1	s__Alteriqipengyuania sp015999305	78.0395	207	385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002377695.1	s__Alteriqipengyuania sp002377695	77.8911	182	385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	99.97	99.97	1.00	1.00	2	-
GCF_001677335.1	s__Erythrobacter dokdonensis	77.6664	168	385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-18 09:53:58,700] [INFO] GTDB search result was written to OceanDNA-b31692/result_gtdb.tsv
[2023-03-18 09:53:58,700] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:53:58,702] [INFO] DFAST_QC result json was written to OceanDNA-b31692/dqc_result.json
[2023-03-18 09:53:58,702] [INFO] DFAST_QC completed!
[2023-03-18 09:53:58,702] [INFO] Total running time: 0h0m48s