[2023-03-17 09:05:02,519] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:05:02,519] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:05:02,519] [INFO] DQC Reference Directory: /var/lib/cwl/stg7820202f-531d-402b-9937-4e265e0691e1/dqc_reference
[2023-03-17 09:05:03,734] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:05:03,734] [INFO] Task started: Prodigal
[2023-03-17 09:05:03,734] [INFO] Running command: cat /var/lib/cwl/stg418739df-0fde-47f7-bb20-5f3793413a86/OceanDNA-b31857.fa | prodigal -d OceanDNA-b31857/cds.fna -a OceanDNA-b31857/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:05:13,730] [INFO] Task succeeded: Prodigal
[2023-03-17 09:05:13,730] [INFO] Task started: HMMsearch
[2023-03-17 09:05:13,730] [INFO] Running command: hmmsearch --tblout OceanDNA-b31857/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7820202f-531d-402b-9937-4e265e0691e1/dqc_reference/reference_markers.hmm OceanDNA-b31857/protein.faa > /dev/null
[2023-03-17 09:05:13,887] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:05:13,888] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg418739df-0fde-47f7-bb20-5f3793413a86/OceanDNA-b31857.fa]
[2023-03-17 09:05:13,902] [INFO] Query marker FASTA was written to OceanDNA-b31857/markers.fasta
[2023-03-17 09:05:13,902] [INFO] Task started: Blastn
[2023-03-17 09:05:13,902] [INFO] Running command: blastn -query OceanDNA-b31857/markers.fasta -db /var/lib/cwl/stg7820202f-531d-402b-9937-4e265e0691e1/dqc_reference/reference_markers.fasta -out OceanDNA-b31857/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:05:14,524] [INFO] Task succeeded: Blastn
[2023-03-17 09:05:14,524] [INFO] Selected 17 target genomes.
[2023-03-17 09:05:14,525] [INFO] Target genome list was writen to OceanDNA-b31857/target_genomes.txt
[2023-03-17 09:05:14,543] [INFO] Task started: fastANI
[2023-03-17 09:05:14,543] [INFO] Running command: fastANI --query /var/lib/cwl/stg418739df-0fde-47f7-bb20-5f3793413a86/OceanDNA-b31857.fa --refList OceanDNA-b31857/target_genomes.txt --output OceanDNA-b31857/fastani_result.tsv --threads 1
[2023-03-17 09:05:22,856] [INFO] Task succeeded: fastANI
[2023-03-17 09:05:22,856] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7820202f-531d-402b-9937-4e265e0691e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:05:22,856] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7820202f-531d-402b-9937-4e265e0691e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:05:22,939] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:05:22,939] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 09:05:22,939] [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 flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	81.3764	348	500	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	80.7891	326	500	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	80.6921	316	500	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	80.2244	274	500	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	79.9337	279	500	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	79.9018	273	500	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	79.9005	278	500	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	79.8393	269	500	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	79.7968	274	500	95	below_threshold
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	79.7662	271	500	95	below_threshold
Qipengyuania aquimaris	strain=JCM 12189	GCA_009827445.1	255984	255984	suspected-type	True	79.731	236	500	95	below_threshold
Qipengyuania pacifica	strain=NZ-96	GCA_019857205.1	2860199	2860199	type	True	79.7256	282	500	95	below_threshold
Qipengyuania nanhaisediminis	strain=CGMCC 1.7715	GCA_900115585.1	604088	604088	type	True	79.6801	258	500	95	below_threshold
Qipengyuania intermedia	strain=GH38	GCA_019711615.1	2867244	2867244	type	True	79.618	256	500	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	79.5355	212	500	95	below_threshold
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	79.5185	296	500	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	79.4959	262	500	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 09:05:22,939] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31857/tc_result.tsv
[2023-03-17 09:05:22,939] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:05:22,939] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:05:22,940] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7820202f-531d-402b-9937-4e265e0691e1/dqc_reference/checkm_data
[2023-03-17 09:05:22,940] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:05:22,944] [INFO] Task started: CheckM
[2023-03-17 09:05:22,944] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31857/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31857/checkm_input OceanDNA-b31857/checkm_result
[2023-03-17 09:05:54,088] [INFO] Task succeeded: CheckM
[2023-03-17 09:05:54,089] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.39%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 09:05:54,091] [INFO] ===== Completeness check finished =====
[2023-03-17 09:05:54,091] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:05:54,091] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31857/markers.fasta)
[2023-03-17 09:05:54,092] [INFO] Task started: Blastn
[2023-03-17 09:05:54,092] [INFO] Running command: blastn -query OceanDNA-b31857/markers.fasta -db /var/lib/cwl/stg7820202f-531d-402b-9937-4e265e0691e1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31857/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:05:55,452] [INFO] Task succeeded: Blastn
[2023-03-17 09:05:55,453] [INFO] Selected 9 target genomes.
[2023-03-17 09:05:55,453] [INFO] Target genome list was writen to OceanDNA-b31857/target_genomes_gtdb.txt
[2023-03-17 09:05:55,516] [INFO] Task started: fastANI
[2023-03-17 09:05:55,516] [INFO] Running command: fastANI --query /var/lib/cwl/stg418739df-0fde-47f7-bb20-5f3793413a86/OceanDNA-b31857.fa --refList OceanDNA-b31857/target_genomes_gtdb.txt --output OceanDNA-b31857/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:06:00,188] [INFO] Task succeeded: fastANI
[2023-03-17 09:06:00,194] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 09:06:00,195] [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_003355455.1	s__Qipengyuania aurea	98.0745	463	500	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.67	97.64	0.83	0.82	3	conclusive
GCF_001542855.1	s__Qipengyuania sp001542855	83.4033	381	500	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.07	97.03	0.89	0.88	4	-
GCA_016764075.1	s__Qipengyuania sp016764075	82.2784	301	500	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	81.5887	345	500	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	81.3764	348	500	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.04	96.57	0.91	0.85	10	-
GCA_000756795.1	s__Qipengyuania vulgaris_A	79.7525	256	500	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	79.7325	237	500	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	79.6764	259	500	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	78.9172	234	500	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 09:06:00,195] [INFO] GTDB search result was written to OceanDNA-b31857/result_gtdb.tsv
[2023-03-17 09:06:00,195] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:06:00,197] [INFO] DFAST_QC result json was written to OceanDNA-b31857/dqc_result.json
[2023-03-17 09:06:00,197] [INFO] DFAST_QC completed!
[2023-03-17 09:06:00,197] [INFO] Total running time: 0h0m58s