[2023-03-16 07:28:30,046] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:28:30,046] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:28:30,046] [INFO] DQC Reference Directory: /var/lib/cwl/stg4101b734-1400-4f10-b8d0-fb1f919273e9/dqc_reference
[2023-03-16 07:28:31,147] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:28:31,147] [INFO] Task started: Prodigal
[2023-03-16 07:28:31,147] [INFO] Running command: cat /var/lib/cwl/stg44ebab39-0fef-4984-899c-f1e37e688d8c/OceanDNA-b31662.fa | prodigal -d OceanDNA-b31662/cds.fna -a OceanDNA-b31662/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:28:51,508] [INFO] Task succeeded: Prodigal
[2023-03-16 07:28:51,508] [INFO] Task started: HMMsearch
[2023-03-16 07:28:51,508] [INFO] Running command: hmmsearch --tblout OceanDNA-b31662/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4101b734-1400-4f10-b8d0-fb1f919273e9/dqc_reference/reference_markers.hmm OceanDNA-b31662/protein.faa > /dev/null
[2023-03-16 07:28:51,694] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:28:51,694] [INFO] Found 6/6 markers.
[2023-03-16 07:28:51,719] [INFO] Query marker FASTA was written to OceanDNA-b31662/markers.fasta
[2023-03-16 07:28:51,720] [INFO] Task started: Blastn
[2023-03-16 07:28:51,720] [INFO] Running command: blastn -query OceanDNA-b31662/markers.fasta -db /var/lib/cwl/stg4101b734-1400-4f10-b8d0-fb1f919273e9/dqc_reference/reference_markers.fasta -out OceanDNA-b31662/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:28:52,366] [INFO] Task succeeded: Blastn
[2023-03-16 07:28:52,368] [INFO] Selected 29 target genomes.
[2023-03-16 07:28:52,369] [INFO] Target genome list was writen to OceanDNA-b31662/target_genomes.txt
[2023-03-16 07:28:52,388] [INFO] Task started: fastANI
[2023-03-16 07:28:52,388] [INFO] Running command: fastANI --query /var/lib/cwl/stg44ebab39-0fef-4984-899c-f1e37e688d8c/OceanDNA-b31662.fa --refList OceanDNA-b31662/target_genomes.txt --output OceanDNA-b31662/fastani_result.tsv --threads 1
[2023-03-16 07:29:07,099] [INFO] Task succeeded: fastANI
[2023-03-16 07:29:07,099] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4101b734-1400-4f10-b8d0-fb1f919273e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:29:07,099] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4101b734-1400-4f10-b8d0-fb1f919273e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:29:07,115] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:29:07,116] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 07:29:07,116] [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
Erythrobacter longus	strain=DSM 6997	GCA_000715015.1	1044	1044	type	True	79.8129	604	1032	95	below_threshold
Erythrobacter rubeus	strain=KMU-140	GCA_014705715.1	2760803	2760803	type	True	77.4152	234	1032	95	below_threshold
Erythrobacter sanguineus	strain=JCM 20691	GCA_002155655.1	198312	198312	type	True	77.2649	233	1032	95	below_threshold
Erythrobacter sanguineus	strain=DSM 11032	GCA_900143235.1	198312	198312	type	True	77.2602	233	1032	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	77.2552	189	1032	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	77.2231	256	1032	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	77.1766	232	1032	95	below_threshold
Erythrobacter dokdonensis	strain=DSM 17193	GCA_002155305.1	328225	328225	type	True	77.1656	236	1032	95	below_threshold
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	77.1296	194	1032	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	77.0239	168	1032	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	77.0039	183	1032	95	below_threshold
Erythrobacter neustonensis	strain=DSM 9434	GCA_001663175.1	1112	1112	type	True	76.9731	217	1032	95	below_threshold
Aurantiacibacter gangjinensis	strain=K7-2	GCA_001010925.1	502682	502682	type	True	76.9628	113	1032	95	below_threshold
Aurantiacibacter gangjinensis	strain=CGMCC 1.15024	GCA_001886695.1	502682	502682	type	True	76.9501	112	1032	95	below_threshold
Qipengyuania nanhaisediminis	strain=CGMCC 1.7715	GCA_900115585.1	604088	604088	type	True	76.9324	178	1032	95	below_threshold
Erythrobacter cryptus	strain=DSM 12079	GCA_000422985.1	196588	196588	type	True	76.9158	201	1032	95	below_threshold
Erythrobacter tepidarius	strain=DSM 10594	GCA_002155695.1	60454	60454	type	True	76.8651	218	1032	95	below_threshold
Erythrobacter insulae	strain=JBTF-M21	GCA_007004095.1	2584124	2584124	type	True	76.8484	199	1032	95	below_threshold
Altererythrobacter lutimaris	strain=JGD-16	GCA_013371495.1	2743979	2743979	type	True	76.8317	176	1032	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	76.7571	134	1032	95	below_threshold
Altererythrobacter ishigakiensis	strain=ATCC BAA-2084	GCA_007830695.1	476157	476157	type	True	76.7419	154	1032	95	below_threshold
Altererythrobacter ishigakiensis	strain=NBRC 107699	GCA_001663155.1	476157	476157	type	True	76.7002	156	1032	95	below_threshold
Tsuneonella suprasediminis	strain=Ery12	GCA_003605755.1	2306996	2306996	type	True	76.6782	94	1032	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	76.6779	134	1032	95	below_threshold
Tsuneonella flava	strain=MS1-4	GCA_002870965.1	2055955	2055955	type	True	76.6083	79	1032	95	below_threshold
Novosphingobium jiangmenense	strain=1Y9A	GCA_015694345.1	2791981	2791981	type	True	76.5182	109	1032	95	below_threshold
Allopontixanthobacter confluentis	strain=KCTC 52259	GCA_009827615.1	1849021	1849021	type	True	76.1798	108	1032	95	below_threshold
Sphingobium fluviale	strain=CHR27	GCA_004122115.1	2506423	2506423	type	True	76.146	53	1032	95	below_threshold
Novosphingobium aromaticivorans	strain=DSM 12444	GCA_000013325.1	48935	48935	type	True	76.0356	100	1032	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:29:07,117] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31662/tc_result.tsv
[2023-03-16 07:29:07,118] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:29:07,118] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:29:07,118] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4101b734-1400-4f10-b8d0-fb1f919273e9/dqc_reference/checkm_data
[2023-03-16 07:29:07,119] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:29:07,155] [INFO] Task started: CheckM
[2023-03-16 07:29:07,155] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31662/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31662/checkm_input OceanDNA-b31662/checkm_result
[2023-03-16 07:29:57,583] [INFO] Task succeeded: CheckM
[2023-03-16 07:29:57,583] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.40%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:29:57,586] [INFO] ===== Completeness check finished =====
[2023-03-16 07:29:57,586] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:29:57,586] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31662/markers.fasta)
[2023-03-16 07:29:57,587] [INFO] Task started: Blastn
[2023-03-16 07:29:57,587] [INFO] Running command: blastn -query OceanDNA-b31662/markers.fasta -db /var/lib/cwl/stg4101b734-1400-4f10-b8d0-fb1f919273e9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31662/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:29:58,651] [INFO] Task succeeded: Blastn
[2023-03-16 07:29:58,652] [INFO] Selected 19 target genomes.
[2023-03-16 07:29:58,652] [INFO] Target genome list was writen to OceanDNA-b31662/target_genomes_gtdb.txt
[2023-03-16 07:29:59,180] [INFO] Task started: fastANI
[2023-03-16 07:29:59,180] [INFO] Running command: fastANI --query /var/lib/cwl/stg44ebab39-0fef-4984-899c-f1e37e688d8c/OceanDNA-b31662.fa --refList OceanDNA-b31662/target_genomes_gtdb.txt --output OceanDNA-b31662/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:30:09,207] [INFO] Task succeeded: fastANI
[2023-03-16 07:30:09,217] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 07:30:09,218] [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_000715015.1	s__Erythrobacter longus	79.8129	604	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152865.1	s__Erythrobacter sp000152865	78.3249	379	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000714765.1	s__Erythrobacter sp000714765	77.8986	364	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003264115.1	s__Erythrobacter sp003264115	77.8903	343	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001542875.1	s__Erythrobacter sp001542875	77.7865	240	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214365.1	s__Erythrobacter sp013214365	77.6999	208	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706445.1	s__Erythrobacter sp002706445	77.6297	244	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363635.1	s__Erythrobacter sp009363635	77.4015	268	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001556995.1	s__Erythrobacter sp001556995	77.2936	214	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002952215.1	s__Erythrobacter sp002952215	77.2498	235	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001677335.1	s__Erythrobacter dokdonensis	77.1766	232	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900149685.1	s__Erythrobacter sp900149685	77.0881	195	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724215.1	s__Erythrobacter sp001724215	76.834	211	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013371495.1	s__Erythrobacter sp013371495	76.8317	176	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842735.1	s__Erythrobacter sp002842735	76.8289	191	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	95.33	95.33	0.91	0.91	2	-
GCF_003605755.1	s__Tsuneonella suprasediminis	76.6794	95	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002870965.1	s__Tsuneonella flava	76.6105	80	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	99.01	98.03	0.92	0.87	3	-
GCF_009827655.1	s__Alteraurantiacibacter buctensis	76.3749	115	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012979275.1	s__Pseudopontixanthobacter vadosimaris	76.2284	88	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pseudopontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 07:30:09,218] [INFO] GTDB search result was written to OceanDNA-b31662/result_gtdb.tsv
[2023-03-16 07:30:09,218] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:30:09,220] [INFO] DFAST_QC result json was written to OceanDNA-b31662/dqc_result.json
[2023-03-16 07:30:09,221] [INFO] DFAST_QC completed!
[2023-03-16 07:30:09,221] [INFO] Total running time: 0h1m39s