[2023-03-15 05:29:10,768] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:29:10,768] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:29:10,768] [INFO] DQC Reference Directory: /var/lib/cwl/stg863d901b-8071-4f41-bb1e-6e39b164f04d/dqc_reference
[2023-03-15 05:29:12,380] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:29:12,381] [INFO] Task started: Prodigal
[2023-03-15 05:29:12,382] [INFO] Running command: cat /var/lib/cwl/stg056abe16-8edd-4d74-98c0-514832d4539f/OceanDNA-b31726.fa | prodigal -d OceanDNA-b31726/cds.fna -a OceanDNA-b31726/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:29:22,972] [INFO] Task succeeded: Prodigal
[2023-03-15 05:29:22,973] [INFO] Task started: HMMsearch
[2023-03-15 05:29:22,973] [INFO] Running command: hmmsearch --tblout OceanDNA-b31726/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg863d901b-8071-4f41-bb1e-6e39b164f04d/dqc_reference/reference_markers.hmm OceanDNA-b31726/protein.faa > /dev/null
[2023-03-15 05:29:23,156] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:29:23,157] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg056abe16-8edd-4d74-98c0-514832d4539f/OceanDNA-b31726.fa]
[2023-03-15 05:29:23,172] [INFO] Query marker FASTA was written to OceanDNA-b31726/markers.fasta
[2023-03-15 05:29:23,173] [INFO] Task started: Blastn
[2023-03-15 05:29:23,173] [INFO] Running command: blastn -query OceanDNA-b31726/markers.fasta -db /var/lib/cwl/stg863d901b-8071-4f41-bb1e-6e39b164f04d/dqc_reference/reference_markers.fasta -out OceanDNA-b31726/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:29:23,752] [INFO] Task succeeded: Blastn
[2023-03-15 05:29:23,752] [INFO] Selected 20 target genomes.
[2023-03-15 05:29:23,753] [INFO] Target genome list was writen to OceanDNA-b31726/target_genomes.txt
[2023-03-15 05:29:23,762] [INFO] Task started: fastANI
[2023-03-15 05:29:23,762] [INFO] Running command: fastANI --query /var/lib/cwl/stg056abe16-8edd-4d74-98c0-514832d4539f/OceanDNA-b31726.fa --refList OceanDNA-b31726/target_genomes.txt --output OceanDNA-b31726/fastani_result.tsv --threads 1
[2023-03-15 05:29:35,024] [INFO] Task succeeded: fastANI
[2023-03-15 05:29:35,025] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg863d901b-8071-4f41-bb1e-6e39b164f04d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:29:35,025] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg863d901b-8071-4f41-bb1e-6e39b164f04d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:29:35,050] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:29:35,050] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 05:29:35,050] [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	80.3797	363	550	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	80.0009	306	550	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	79.9352	340	550	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	79.8534	312	550	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	79.765	333	550	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	79.749	302	550	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	79.6855	297	550	95	below_threshold
Qipengyuania nanhaisediminis	strain=CGMCC 1.7715	GCA_900115585.1	604088	604088	type	True	79.4789	291	550	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	79.4708	303	550	95	below_threshold
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	79.4418	291	550	95	below_threshold
Qipengyuania pacifica	strain=NZ-96	GCA_019857205.1	2860199	2860199	type	True	79.3663	311	550	95	below_threshold
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	79.3154	308	550	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	79.2162	280	550	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	78.6904	259	550	95	below_threshold
Qipengyuania algicida	strain=KEMB 9005-328	GCA_009828025.1	1836209	1836209	type	True	78.1934	168	550	95	below_threshold
Qipengyuania psychrotolerans	strain=1XM2-8	GCA_019711355.1	2867238	2867238	type	True	78.1825	234	550	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	77.688	184	550	95	below_threshold
Erythrobacter tepidarius	strain=DSM 10594	GCA_002155695.1	60454	60454	type	True	77.3632	149	550	95	below_threshold
Croceibacterium atlanticum	strain=26DY36	GCA_001008165.2	1267766	1267766	type	True	77.0798	118	550	95	below_threshold
Croceibacterium atlanticum	strain=DSM 100738	GCA_014199315.1	1267766	1267766	type	True	77.0458	118	550	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 05:29:35,050] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31726/tc_result.tsv
[2023-03-15 05:29:35,050] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:29:35,050] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:29:35,051] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg863d901b-8071-4f41-bb1e-6e39b164f04d/dqc_reference/checkm_data
[2023-03-15 05:29:35,051] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:29:35,055] [INFO] Task started: CheckM
[2023-03-15 05:29:35,055] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31726/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31726/checkm_input OceanDNA-b31726/checkm_result
[2023-03-15 05:30:05,446] [INFO] Task succeeded: CheckM
[2023-03-15 05:30:05,446] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.85%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:30:05,448] [INFO] ===== Completeness check finished =====
[2023-03-15 05:30:05,448] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:30:05,448] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31726/markers.fasta)
[2023-03-15 05:30:05,448] [INFO] Task started: Blastn
[2023-03-15 05:30:05,448] [INFO] Running command: blastn -query OceanDNA-b31726/markers.fasta -db /var/lib/cwl/stg863d901b-8071-4f41-bb1e-6e39b164f04d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31726/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:30:06,351] [INFO] Task succeeded: Blastn
[2023-03-15 05:30:06,352] [INFO] Selected 19 target genomes.
[2023-03-15 05:30:06,352] [INFO] Target genome list was writen to OceanDNA-b31726/target_genomes_gtdb.txt
[2023-03-15 05:30:06,369] [INFO] Task started: fastANI
[2023-03-15 05:30:06,369] [INFO] Running command: fastANI --query /var/lib/cwl/stg056abe16-8edd-4d74-98c0-514832d4539f/OceanDNA-b31726.fa --refList OceanDNA-b31726/target_genomes_gtdb.txt --output OceanDNA-b31726/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:30:16,673] [INFO] Task succeeded: fastANI
[2023-03-15 05:30:16,684] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 05:30:16,684] [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_009828015.1	s__Qipengyuania citrea	80.4849	373	550	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.91	97.49	0.87	0.80	20	-
GCF_001542855.1	s__Qipengyuania sp001542855	80.4246	374	550	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.07	97.03	0.89	0.88	4	-
GCF_011762005.1	s__Qipengyuania flava	80.3797	363	550	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	80.3531	352	550	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	80.0009	306	550	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	79.9115	289	550	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015767595.1	s__Qipengyuania sp002895025	79.4904	302	550	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.29	96.55	0.87	0.78	16	-
GCA_000756795.1	s__Qipengyuania vulgaris_A	79.4265	290	550	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	79.3165	293	550	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013260645.1	s__Qipengyuania mangrovi	78.9782	257	550	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	78.9249	247	550	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	78.8363	263	550	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	78.6978	220	550	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828025.1	s__Qipengyuania algicida	78.1934	168	550	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013005.1	s__Altererythrobacter_D litoralis_A	78.1301	213	550	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Altererythrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002377695.1	s__Alteriqipengyuania sp002377695	78.0993	178	550	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	99.97	99.97	1.00	1.00	2	-
GCF_005434975.1	s__Parerythrobacter lutipelagi	77.7417	167	550	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009993635.1	s__Alteriqipengyuania sp009993635	77.6132	175	550	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	99.91	99.91	0.97	0.97	2	-
GCA_006226465.1	s__Erythrobacter sp006226465	77.0713	76	550	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:30:16,684] [INFO] GTDB search result was written to OceanDNA-b31726/result_gtdb.tsv
[2023-03-15 05:30:16,684] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:30:16,687] [INFO] DFAST_QC result json was written to OceanDNA-b31726/dqc_result.json
[2023-03-15 05:30:16,687] [INFO] DFAST_QC completed!
[2023-03-15 05:30:16,687] [INFO] Total running time: 0h1m6s