[2023-03-15 13:45:07,858] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:45:07,858] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:45:07,858] [INFO] DQC Reference Directory: /var/lib/cwl/stg9033d2cb-63eb-4805-b469-7961f28e5aff/dqc_reference
[2023-03-15 13:45:09,270] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:45:09,271] [INFO] Task started: Prodigal
[2023-03-15 13:45:09,271] [INFO] Running command: cat /var/lib/cwl/stgf55ac817-cb2f-4b74-a10a-c91aea92c19c/OceanDNA-b31865.fa | prodigal -d OceanDNA-b31865/cds.fna -a OceanDNA-b31865/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:45:29,308] [INFO] Task succeeded: Prodigal
[2023-03-15 13:45:29,308] [INFO] Task started: HMMsearch
[2023-03-15 13:45:29,309] [INFO] Running command: hmmsearch --tblout OceanDNA-b31865/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9033d2cb-63eb-4805-b469-7961f28e5aff/dqc_reference/reference_markers.hmm OceanDNA-b31865/protein.faa > /dev/null
[2023-03-15 13:45:29,501] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:45:29,501] [INFO] Found 6/6 markers.
[2023-03-15 13:45:29,522] [INFO] Query marker FASTA was written to OceanDNA-b31865/markers.fasta
[2023-03-15 13:45:29,524] [INFO] Task started: Blastn
[2023-03-15 13:45:29,524] [INFO] Running command: blastn -query OceanDNA-b31865/markers.fasta -db /var/lib/cwl/stg9033d2cb-63eb-4805-b469-7961f28e5aff/dqc_reference/reference_markers.fasta -out OceanDNA-b31865/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:45:30,344] [INFO] Task succeeded: Blastn
[2023-03-15 13:45:30,345] [INFO] Selected 11 target genomes.
[2023-03-15 13:45:30,346] [INFO] Target genome list was writen to OceanDNA-b31865/target_genomes.txt
[2023-03-15 13:45:30,353] [INFO] Task started: fastANI
[2023-03-15 13:45:30,353] [INFO] Running command: fastANI --query /var/lib/cwl/stgf55ac817-cb2f-4b74-a10a-c91aea92c19c/OceanDNA-b31865.fa --refList OceanDNA-b31865/target_genomes.txt --output OceanDNA-b31865/fastani_result.tsv --threads 1
[2023-03-15 13:45:37,773] [INFO] Task succeeded: fastANI
[2023-03-15 13:45:37,773] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9033d2cb-63eb-4805-b469-7961f28e5aff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:45:37,774] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9033d2cb-63eb-4805-b469-7961f28e5aff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:45:37,782] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2023-03-15 13:45:37,782] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-03-15 13:45:37,782] [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 aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	97.0339	889	1060	95	inconclusive
Qipengyuania pacifica	strain=NZ-96	GCA_019857205.1	2860199	2860199	type	True	96.9933	931	1060	95	inconclusive
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	81.3388	625	1060	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	80.6439	548	1060	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	80.1759	509	1060	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	79.5353	427	1060	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	79.5183	445	1060	95	below_threshold
Qipengyuania aestuarii	strain=GH1	GCA_019711535.1	2867241	2867241	type	True	79.4498	403	1060	95	below_threshold
Qipengyuania seohaensis	strain=SW-135	GCA_002795865.1	266951	266951	type	True	79.3907	428	1060	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	79.2391	407	1060	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	78.9851	432	1060	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:45:37,782] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31865/tc_result.tsv
[2023-03-15 13:45:37,782] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:45:37,783] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:45:37,783] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9033d2cb-63eb-4805-b469-7961f28e5aff/dqc_reference/checkm_data
[2023-03-15 13:45:37,783] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:45:37,795] [INFO] Task started: CheckM
[2023-03-15 13:45:37,795] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31865/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31865/checkm_input OceanDNA-b31865/checkm_result
[2023-03-15 13:46:27,761] [INFO] Task succeeded: CheckM
[2023-03-15 13:46:27,762] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:46:27,765] [INFO] ===== Completeness check finished =====
[2023-03-15 13:46:27,765] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:46:27,765] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31865/markers.fasta)
[2023-03-15 13:46:27,766] [INFO] Task started: Blastn
[2023-03-15 13:46:27,766] [INFO] Running command: blastn -query OceanDNA-b31865/markers.fasta -db /var/lib/cwl/stg9033d2cb-63eb-4805-b469-7961f28e5aff/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31865/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:46:29,319] [INFO] Task succeeded: Blastn
[2023-03-15 13:46:29,321] [INFO] Selected 16 target genomes.
[2023-03-15 13:46:29,321] [INFO] Target genome list was writen to OceanDNA-b31865/target_genomes_gtdb.txt
[2023-03-15 13:46:29,338] [INFO] Task started: fastANI
[2023-03-15 13:46:29,338] [INFO] Running command: fastANI --query /var/lib/cwl/stgf55ac817-cb2f-4b74-a10a-c91aea92c19c/OceanDNA-b31865.fa --refList OceanDNA-b31865/target_genomes_gtdb.txt --output OceanDNA-b31865/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:46:38,612] [INFO] Task succeeded: fastANI
[2023-03-15 13:46:38,622] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 13:46:38,622] [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_015767595.1	s__Qipengyuania sp002895025	96.9793	925	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.29	96.55	0.87	0.78	16	conclusive
GCA_016764075.1	s__Qipengyuania sp016764075	81.2587	436	1060	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	81.1757	568	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.07	97.03	0.89	0.88	4	-
GCF_009828015.1	s__Qipengyuania citrea	80.9464	572	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.91	97.49	0.87	0.80	20	-
GCF_011762005.1	s__Qipengyuania flava	80.6439	548	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.04	96.57	0.91	0.85	10	-
GCF_003355455.1	s__Qipengyuania aurea	80.3545	551	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.67	97.64	0.83	0.82	3	-
GCF_009827315.1	s__Qipengyuania gaetbuli	79.713	465	1060	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	79.5007	447	1060	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	79.489	436	1060	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	79.4162	336	1060	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	79.3907	428	1060	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	79.2764	367	1060	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	78.9957	431	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009993605.1	s__Qipengyuania sp009993605	78.7675	396	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793865.1	s__Qipengyuania sp016793865	78.0718	301	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308255.1	s__Croceibacterium sp001897135	77.8515	243	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	99.96	99.96	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2023-03-15 13:46:38,623] [INFO] GTDB search result was written to OceanDNA-b31865/result_gtdb.tsv
[2023-03-15 13:46:38,623] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:46:38,625] [INFO] DFAST_QC result json was written to OceanDNA-b31865/dqc_result.json
[2023-03-15 13:46:38,625] [INFO] DFAST_QC completed!
[2023-03-15 13:46:38,625] [INFO] Total running time: 0h1m31s