[2023-03-14 12:40:03,144] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:40:03,144] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:40:03,144] [INFO] DQC Reference Directory: /var/lib/cwl/stgb19816b2-0471-467d-8877-e61d6d54e094/dqc_reference
[2023-03-14 12:40:04,260] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:40:04,261] [INFO] Task started: Prodigal
[2023-03-14 12:40:04,261] [INFO] Running command: cat /var/lib/cwl/stgbf34f135-f772-4fa7-99c2-7b60bf018439/OceanDNA-b31551.fa | prodigal -d OceanDNA-b31551/cds.fna -a OceanDNA-b31551/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:40:11,729] [INFO] Task succeeded: Prodigal
[2023-03-14 12:40:11,730] [INFO] Task started: HMMsearch
[2023-03-14 12:40:11,730] [INFO] Running command: hmmsearch --tblout OceanDNA-b31551/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb19816b2-0471-467d-8877-e61d6d54e094/dqc_reference/reference_markers.hmm OceanDNA-b31551/protein.faa > /dev/null
[2023-03-14 12:40:11,929] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:40:11,930] [INFO] Found 6/6 markers.
[2023-03-14 12:40:11,942] [INFO] Query marker FASTA was written to OceanDNA-b31551/markers.fasta
[2023-03-14 12:40:11,944] [INFO] Task started: Blastn
[2023-03-14 12:40:11,944] [INFO] Running command: blastn -query OceanDNA-b31551/markers.fasta -db /var/lib/cwl/stgb19816b2-0471-467d-8877-e61d6d54e094/dqc_reference/reference_markers.fasta -out OceanDNA-b31551/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:40:12,592] [INFO] Task succeeded: Blastn
[2023-03-14 12:40:12,593] [INFO] Selected 33 target genomes.
[2023-03-14 12:40:12,593] [INFO] Target genome list was writen to OceanDNA-b31551/target_genomes.txt
[2023-03-14 12:40:12,613] [INFO] Task started: fastANI
[2023-03-14 12:40:12,613] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf34f135-f772-4fa7-99c2-7b60bf018439/OceanDNA-b31551.fa --refList OceanDNA-b31551/target_genomes.txt --output OceanDNA-b31551/fastani_result.tsv --threads 1
[2023-03-14 12:40:35,676] [INFO] Task succeeded: fastANI
[2023-03-14 12:40:35,676] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb19816b2-0471-467d-8877-e61d6d54e094/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:40:35,676] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb19816b2-0471-467d-8877-e61d6d54e094/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:40:35,691] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:40:35,691] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 12:40:35,691] [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
Altererythrobacter ishigakiensis	strain=ATCC BAA-2084	GCA_007830695.1	476157	476157	type	True	83.5858	268	400	95	below_threshold
Altererythrobacter ishigakiensis	strain=NBRC 107699	GCA_001663155.1	476157	476157	type	True	83.4868	273	400	95	below_threshold
Parerythrobacter jejuensis	strain=JCM 16677	GCA_009827995.1	795812	795812	type	True	77.6206	91	400	95	below_threshold
Altererythrobacter lutimaris	strain=JGD-16	GCA_013371495.1	2743979	2743979	type	True	77.5	131	400	95	below_threshold
Erythrobacter rubeus	strain=KMU-140	GCA_014705715.1	2760803	2760803	type	True	77.3785	103	400	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	77.2544	99	400	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	77.1424	95	400	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	77.1323	87	400	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	77.0539	100	400	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	76.9786	102	400	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	76.8707	72	400	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	76.8643	94	400	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	76.8623	102	400	95	below_threshold
Qipengyuania intermedia	strain=GH38	GCA_019711615.1	2867244	2867244	type	True	76.7497	85	400	95	below_threshold
Qipengyuania aestuarii	strain=GH1	GCA_019711535.1	2867241	2867241	type	True	76.7015	70	400	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	76.6803	76	400	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	76.6545	93	400	95	below_threshold
Erythrobacter longus	strain=DSM 6997	GCA_000715015.1	1044	1044	type	True	76.5877	80	400	95	below_threshold
Aurantiacibacter odishensis	strain=KCTC 23981	GCA_003605195.1	1155476	1155476	type	True	76.583	63	400	95	below_threshold
Erythrobacter tepidarius	strain=DSM 10594	GCA_002155695.1	60454	60454	type	True	76.5795	87	400	95	below_threshold
Qipengyuania aquimaris	strain=JCM 12189	GCA_009827445.1	255984	255984	suspected-type	True	76.5684	82	400	95	below_threshold
Novosphingobium ginsenosidimutans	strain=FW-6	GCA_007954425.1	1176536	1176536	type	True	76.5622	54	400	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	76.5133	89	400	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	76.2659	76	400	95	below_threshold
Novosphingobium kunmingense	strain=CGMCC 1.12274	GCA_002813245.1	1211806	1211806	type	True	76.1369	50	400	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:40:35,692] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31551/tc_result.tsv
[2023-03-14 12:40:35,692] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:40:35,692] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:40:35,692] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb19816b2-0471-467d-8877-e61d6d54e094/dqc_reference/checkm_data
[2023-03-14 12:40:35,693] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:40:35,699] [INFO] Task started: CheckM
[2023-03-14 12:40:35,699] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31551/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31551/checkm_input OceanDNA-b31551/checkm_result
[2023-03-14 12:41:04,280] [INFO] Task succeeded: CheckM
[2023-03-14 12:41:04,281] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.42%
Contamintation: 6.25%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 12:41:04,284] [INFO] ===== Completeness check finished =====
[2023-03-14 12:41:04,284] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:41:04,284] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31551/markers.fasta)
[2023-03-14 12:41:04,285] [INFO] Task started: Blastn
[2023-03-14 12:41:04,285] [INFO] Running command: blastn -query OceanDNA-b31551/markers.fasta -db /var/lib/cwl/stgb19816b2-0471-467d-8877-e61d6d54e094/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31551/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:41:05,328] [INFO] Task succeeded: Blastn
[2023-03-14 12:41:05,329] [INFO] Selected 30 target genomes.
[2023-03-14 12:41:05,329] [INFO] Target genome list was writen to OceanDNA-b31551/target_genomes_gtdb.txt
[2023-03-14 12:41:05,359] [INFO] Task started: fastANI
[2023-03-14 12:41:05,359] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf34f135-f772-4fa7-99c2-7b60bf018439/OceanDNA-b31551.fa --refList OceanDNA-b31551/target_genomes_gtdb.txt --output OceanDNA-b31551/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:41:22,665] [INFO] Task succeeded: fastANI
[2023-03-14 12:41:22,680] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:41:22,680] [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_001663155.1	s__Erythrobacter ishigakiensis	83.4868	273	400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	97.03	96.25	0.95	0.94	6	-
GCA_013002295.1	s__Erythrobacter sp013002295	80.6317	189	400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.14	98.90	0.85	0.82	4	-
GCA_003149575.1	s__Erythrobacter sp003149575	80.3538	230	400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	98.16	98.16	0.93	0.93	2	-
GCF_011047315.1	s__Erythrobacter sp011047315	78.4347	197	400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177715.1	s__Erythrobacter xiamenensis	77.683	152	400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001515985.1	s__Erythrobacter sp001515985	77.6202	137	400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018205975.1	s__Erythrobacter sp018205975	77.5009	131	400	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	77.5	131	400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001281485.1	s__Erythrobacter epoxidivorans	77.4723	119	400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003483125.1	s__Erythrobacter sp003483125	77.4684	59	400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014705715.1	s__Erythrobacter sp014705715	77.3782	103	400	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	77.3298	134	400	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	77.3101	96	400	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	77.2283	104	400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005434975.1	s__Parerythrobacter lutipelagi	77.2237	95	400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002215495.1	s__Erythrobacter sp002215495	76.9963	67	400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822125.1	s__Erythrobacter sp013822125	76.9097	73	400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001165.1	s__Qipengyuania sp013001165	76.7782	78	400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214365.1	s__Erythrobacter sp013214365	76.717	60	400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001516125.1	s__Erythrobacter sp001516125	76.6985	81	400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827445.1	s__Qipengyuania aquimaris	76.5954	81	400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000715015.1	s__Erythrobacter longus	76.5877	80	400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007954425.1	s__Novosphingobium ginsenosidimutans	76.5622	54	400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009993605.1	s__Qipengyuania sp009993605	76.5425	87	400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900117425.1	s__Novosphingobium sp900117425	76.3897	58	400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.26	96.76	0.88	0.87	3	-
GCF_000181515.1	s__Qipengyuania sp000181515	76.3024	92	400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803135.1	s__Pelagerythrobacter sp016803135	76.2049	89	400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:41:22,680] [INFO] GTDB search result was written to OceanDNA-b31551/result_gtdb.tsv
[2023-03-14 12:41:22,680] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:41:22,683] [INFO] DFAST_QC result json was written to OceanDNA-b31551/dqc_result.json
[2023-03-14 12:41:22,683] [INFO] DFAST_QC completed!
[2023-03-14 12:41:22,683] [INFO] Total running time: 0h1m20s