[2023-03-18 09:01:40,999] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:01:41,001] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:01:41,001] [INFO] DQC Reference Directory: /var/lib/cwl/stg56a7952a-ad05-4c0e-b0f8-910a2078ca78/dqc_reference
[2023-03-18 09:01:42,188] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:01:42,189] [INFO] Task started: Prodigal
[2023-03-18 09:01:42,189] [INFO] Running command: cat /var/lib/cwl/stg459deaf4-71bc-4d4c-b73e-b531c3f6454c/OceanDNA-b31711.fa | prodigal -d OceanDNA-b31711/cds.fna -a OceanDNA-b31711/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:01:58,704] [INFO] Task succeeded: Prodigal
[2023-03-18 09:01:58,705] [INFO] Task started: HMMsearch
[2023-03-18 09:01:58,705] [INFO] Running command: hmmsearch --tblout OceanDNA-b31711/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56a7952a-ad05-4c0e-b0f8-910a2078ca78/dqc_reference/reference_markers.hmm OceanDNA-b31711/protein.faa > /dev/null
[2023-03-18 09:01:58,882] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:01:58,883] [INFO] Found 6/6 markers.
[2023-03-18 09:01:58,915] [INFO] Query marker FASTA was written to OceanDNA-b31711/markers.fasta
[2023-03-18 09:01:58,916] [INFO] Task started: Blastn
[2023-03-18 09:01:58,917] [INFO] Running command: blastn -query OceanDNA-b31711/markers.fasta -db /var/lib/cwl/stg56a7952a-ad05-4c0e-b0f8-910a2078ca78/dqc_reference/reference_markers.fasta -out OceanDNA-b31711/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:01:59,754] [INFO] Task succeeded: Blastn
[2023-03-18 09:01:59,755] [INFO] Selected 16 target genomes.
[2023-03-18 09:01:59,756] [INFO] Target genome list was writen to OceanDNA-b31711/target_genomes.txt
[2023-03-18 09:01:59,764] [INFO] Task started: fastANI
[2023-03-18 09:01:59,764] [INFO] Running command: fastANI --query /var/lib/cwl/stg459deaf4-71bc-4d4c-b73e-b531c3f6454c/OceanDNA-b31711.fa --refList OceanDNA-b31711/target_genomes.txt --output OceanDNA-b31711/fastani_result.tsv --threads 1
[2023-03-18 09:02:10,785] [INFO] Task succeeded: fastANI
[2023-03-18 09:02:10,785] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56a7952a-ad05-4c0e-b0f8-910a2078ca78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:02:10,786] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56a7952a-ad05-4c0e-b0f8-910a2078ca78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:02:10,796] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 09:02:10,796] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 09:02:10,796] [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 gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	95.65	822	877	95	conclusive
Qipengyuania intermedia	strain=GH38	GCA_019711615.1	2867244	2867244	type	True	83.0411	642	877	95	below_threshold
Qipengyuania nanhaisediminis	strain=CGMCC 1.7715	GCA_900115585.1	604088	604088	type	True	82.9477	648	877	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	82.8246	627	877	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	82.807	630	877	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	82.7096	594	877	95	below_threshold
Qipengyuania seohaensis	strain=SW-135	GCA_002795865.1	266951	266951	type	True	82.6819	620	877	95	below_threshold
Qipengyuania aquimaris	strain=JCM 12189	GCA_009827445.1	255984	255984	suspected-type	True	82.6264	642	877	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	82.5012	632	877	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	82.481	626	877	95	below_threshold
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	82.4615	620	877	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	81.9278	567	877	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	81.5118	575	877	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	81.0197	531	877	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	80.5607	497	877	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	80.2262	488	877	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 09:02:10,799] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31711/tc_result.tsv
[2023-03-18 09:02:10,801] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:02:10,801] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:02:10,801] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56a7952a-ad05-4c0e-b0f8-910a2078ca78/dqc_reference/checkm_data
[2023-03-18 09:02:10,802] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:02:10,811] [INFO] Task started: CheckM
[2023-03-18 09:02:10,812] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31711/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31711/checkm_input OceanDNA-b31711/checkm_result
[2023-03-18 09:02:52,995] [INFO] Task succeeded: CheckM
[2023-03-18 09:02:52,996] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:02:53,034] [INFO] ===== Completeness check finished =====
[2023-03-18 09:02:53,035] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:02:53,035] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31711/markers.fasta)
[2023-03-18 09:02:53,036] [INFO] Task started: Blastn
[2023-03-18 09:02:53,036] [INFO] Running command: blastn -query OceanDNA-b31711/markers.fasta -db /var/lib/cwl/stg56a7952a-ad05-4c0e-b0f8-910a2078ca78/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31711/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:02:54,657] [INFO] Task succeeded: Blastn
[2023-03-18 09:02:54,665] [INFO] Selected 12 target genomes.
[2023-03-18 09:02:54,665] [INFO] Target genome list was writen to OceanDNA-b31711/target_genomes_gtdb.txt
[2023-03-18 09:02:54,789] [INFO] Task started: fastANI
[2023-03-18 09:02:54,789] [INFO] Running command: fastANI --query /var/lib/cwl/stg459deaf4-71bc-4d4c-b73e-b531c3f6454c/OceanDNA-b31711.fa --refList OceanDNA-b31711/target_genomes_gtdb.txt --output OceanDNA-b31711/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:03:02,251] [INFO] Task succeeded: fastANI
[2023-03-18 09:03:02,259] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 09:03:02,259] [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_009827315.1	s__Qipengyuania gaetbuli	95.65	822	877	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_900115585.1	s__Qipengyuania nanhaisediminis	82.9385	649	877	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	82.6819	620	877	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	82.6176	643	877	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	82.5228	589	877	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	82.2028	603	877	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	81.833	507	877	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	81.492	577	877	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	81.4498	421	877	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	81.3589	579	877	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.07	97.03	0.89	0.88	4	-
GCA_003248395.1	s__Qipengyuania sp003248395	80.531	449	877	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	80.226	488	877	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:03:02,260] [INFO] GTDB search result was written to OceanDNA-b31711/result_gtdb.tsv
[2023-03-18 09:03:02,264] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:03:02,267] [INFO] DFAST_QC result json was written to OceanDNA-b31711/dqc_result.json
[2023-03-18 09:03:02,267] [INFO] DFAST_QC completed!
[2023-03-18 09:03:02,267] [INFO] Total running time: 0h1m21s