[2023-03-16 04:54:07,047] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:54:07,047] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:54:07,048] [INFO] DQC Reference Directory: /var/lib/cwl/stg18f13063-c95e-4107-b82c-be98a9e45c2c/dqc_reference
[2023-03-16 04:54:08,362] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:54:08,363] [INFO] Task started: Prodigal
[2023-03-16 04:54:08,363] [INFO] Running command: cat /var/lib/cwl/stg053dddbb-d476-43ef-b559-d3ded5cf2710/OceanDNA-b31853.fa | prodigal -d OceanDNA-b31853/cds.fna -a OceanDNA-b31853/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:54:25,361] [INFO] Task succeeded: Prodigal
[2023-03-16 04:54:25,361] [INFO] Task started: HMMsearch
[2023-03-16 04:54:25,361] [INFO] Running command: hmmsearch --tblout OceanDNA-b31853/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18f13063-c95e-4107-b82c-be98a9e45c2c/dqc_reference/reference_markers.hmm OceanDNA-b31853/protein.faa > /dev/null
[2023-03-16 04:54:25,631] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:54:25,632] [INFO] Found 6/6 markers.
[2023-03-16 04:54:25,650] [INFO] Query marker FASTA was written to OceanDNA-b31853/markers.fasta
[2023-03-16 04:54:25,651] [INFO] Task started: Blastn
[2023-03-16 04:54:25,651] [INFO] Running command: blastn -query OceanDNA-b31853/markers.fasta -db /var/lib/cwl/stg18f13063-c95e-4107-b82c-be98a9e45c2c/dqc_reference/reference_markers.fasta -out OceanDNA-b31853/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:54:26,431] [INFO] Task succeeded: Blastn
[2023-03-16 04:54:26,432] [INFO] Selected 12 target genomes.
[2023-03-16 04:54:26,432] [INFO] Target genome list was writen to OceanDNA-b31853/target_genomes.txt
[2023-03-16 04:54:26,441] [INFO] Task started: fastANI
[2023-03-16 04:54:26,441] [INFO] Running command: fastANI --query /var/lib/cwl/stg053dddbb-d476-43ef-b559-d3ded5cf2710/OceanDNA-b31853.fa --refList OceanDNA-b31853/target_genomes.txt --output OceanDNA-b31853/fastani_result.tsv --threads 1
[2023-03-16 04:54:34,364] [INFO] Task succeeded: fastANI
[2023-03-16 04:54:34,364] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18f13063-c95e-4107-b82c-be98a9e45c2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:54:34,365] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18f13063-c95e-4107-b82c-be98a9e45c2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:54:34,372] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:54:34,372] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:54:34,372] [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 aestuarii	strain=GH1	GCA_019711535.1	2867241	2867241	type	True	84.763	650	904	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	80.8962	457	904	95	below_threshold
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	80.8954	482	904	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	80.8793	500	904	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	80.628	461	904	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	80.6088	463	904	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	80.3759	412	904	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	80.3383	452	904	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	80.1582	442	904	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	80.0318	422	904	95	below_threshold
Qipengyuania intermedia	strain=GH38	GCA_019711615.1	2867244	2867244	type	True	79.9813	395	904	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	79.4062	345	904	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:54:34,372] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31853/tc_result.tsv
[2023-03-16 04:54:34,373] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:54:34,373] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:54:34,373] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18f13063-c95e-4107-b82c-be98a9e45c2c/dqc_reference/checkm_data
[2023-03-16 04:54:34,373] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:54:34,379] [INFO] Task started: CheckM
[2023-03-16 04:54:34,379] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31853/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31853/checkm_input OceanDNA-b31853/checkm_result
[2023-03-16 04:55:19,130] [INFO] Task succeeded: CheckM
[2023-03-16 04:55:19,131] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.59%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:55:19,133] [INFO] ===== Completeness check finished =====
[2023-03-16 04:55:19,134] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:55:19,134] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31853/markers.fasta)
[2023-03-16 04:55:19,135] [INFO] Task started: Blastn
[2023-03-16 04:55:19,135] [INFO] Running command: blastn -query OceanDNA-b31853/markers.fasta -db /var/lib/cwl/stg18f13063-c95e-4107-b82c-be98a9e45c2c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31853/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:55:20,504] [INFO] Task succeeded: Blastn
[2023-03-16 04:55:20,505] [INFO] Selected 13 target genomes.
[2023-03-16 04:55:20,505] [INFO] Target genome list was writen to OceanDNA-b31853/target_genomes_gtdb.txt
[2023-03-16 04:55:20,547] [INFO] Task started: fastANI
[2023-03-16 04:55:20,548] [INFO] Running command: fastANI --query /var/lib/cwl/stg053dddbb-d476-43ef-b559-d3ded5cf2710/OceanDNA-b31853.fa --refList OceanDNA-b31853/target_genomes_gtdb.txt --output OceanDNA-b31853/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:55:28,425] [INFO] Task succeeded: fastANI
[2023-03-16 04:55:28,433] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 04:55:28,433] [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_002695185.1	s__Qipengyuania sp002695185	96.5882	758	904	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	96.33	96.22	0.77	0.72	4	conclusive
GCF_000181515.1	s__Qipengyuania sp000181515	80.9373	471	904	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	80.732	464	904	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911865.1	s__Qipengyuania sp013911865	80.5075	361	904	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	80.3206	448	904	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	80.045	421	904	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001165.1	s__Qipengyuania sp013001165	80.0277	371	904	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115585.1	s__Qipengyuania nanhaisediminis	79.7738	411	904	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002795865.1	s__Qipengyuania seohaensis	79.6163	405	904	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827445.1	s__Qipengyuania aquimaris	79.5543	406	904	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	79.4204	344	904	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015529805.1	s__Qipengyuania soli	78.9282	320	904	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	78.136	281	904	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	98.10	96.53	0.93	0.90	11	-
--------------------------------------------------------------------------------
[2023-03-16 04:55:28,433] [INFO] GTDB search result was written to OceanDNA-b31853/result_gtdb.tsv
[2023-03-16 04:55:28,433] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:55:28,435] [INFO] DFAST_QC result json was written to OceanDNA-b31853/dqc_result.json
[2023-03-16 04:55:28,435] [INFO] DFAST_QC completed!
[2023-03-16 04:55:28,435] [INFO] Total running time: 0h1m21s