[2023-03-17 11:52:51,154] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:52:51,156] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:52:51,156] [INFO] DQC Reference Directory: /var/lib/cwl/stgc340efb3-4aeb-4b79-be3f-70ec8dee4712/dqc_reference
[2023-03-17 11:52:52,827] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:52:52,828] [INFO] Task started: Prodigal
[2023-03-17 11:52:52,828] [INFO] Running command: cat /var/lib/cwl/stga3853388-9b74-4dab-90ce-4cc745a9318d/OceanDNA-b31555.fa | prodigal -d OceanDNA-b31555/cds.fna -a OceanDNA-b31555/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:53:02,866] [INFO] Task succeeded: Prodigal
[2023-03-17 11:53:02,867] [INFO] Task started: HMMsearch
[2023-03-17 11:53:02,867] [INFO] Running command: hmmsearch --tblout OceanDNA-b31555/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc340efb3-4aeb-4b79-be3f-70ec8dee4712/dqc_reference/reference_markers.hmm OceanDNA-b31555/protein.faa > /dev/null
[2023-03-17 11:53:03,027] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:53:03,027] [WARNING] Found 4/6 markers. [/var/lib/cwl/stga3853388-9b74-4dab-90ce-4cc745a9318d/OceanDNA-b31555.fa]
[2023-03-17 11:53:03,078] [INFO] Query marker FASTA was written to OceanDNA-b31555/markers.fasta
[2023-03-17 11:53:03,078] [INFO] Task started: Blastn
[2023-03-17 11:53:03,079] [INFO] Running command: blastn -query OceanDNA-b31555/markers.fasta -db /var/lib/cwl/stgc340efb3-4aeb-4b79-be3f-70ec8dee4712/dqc_reference/reference_markers.fasta -out OceanDNA-b31555/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:53:03,603] [INFO] Task succeeded: Blastn
[2023-03-17 11:53:03,607] [INFO] Selected 19 target genomes.
[2023-03-17 11:53:03,607] [INFO] Target genome list was writen to OceanDNA-b31555/target_genomes.txt
[2023-03-17 11:53:03,616] [INFO] Task started: fastANI
[2023-03-17 11:53:03,616] [INFO] Running command: fastANI --query /var/lib/cwl/stga3853388-9b74-4dab-90ce-4cc745a9318d/OceanDNA-b31555.fa --refList OceanDNA-b31555/target_genomes.txt --output OceanDNA-b31555/fastani_result.tsv --threads 1
[2023-03-17 11:53:13,120] [INFO] Task succeeded: fastANI
[2023-03-17 11:53:13,120] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc340efb3-4aeb-4b79-be3f-70ec8dee4712/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:53:13,120] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc340efb3-4aeb-4b79-be3f-70ec8dee4712/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:53:13,132] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:53:13,132] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 11:53:13,132] [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 lutimaris	strain=JGD-16	GCA_013371495.1	2743979	2743979	type	True	79.3698	293	517	95	below_threshold
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	78.0786	167	517	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	77.9474	177	517	95	below_threshold
Qipengyuania seohaensis	strain=SW-135	GCA_002795865.1	266951	266951	type	True	77.9107	150	517	95	below_threshold
Qipengyuania nanhaisediminis	strain=CGMCC 1.7715	GCA_900115585.1	604088	604088	type	True	77.7951	173	517	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	77.7615	167	517	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	77.6512	159	517	95	below_threshold
Qipengyuania intermedia	strain=GH38	GCA_019711615.1	2867244	2867244	type	True	77.5473	170	517	95	below_threshold
Erythrobacter rubeus	strain=KMU-140	GCA_014705715.1	2760803	2760803	type	True	77.5099	162	517	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	77.4702	135	517	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	77.3673	131	517	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	77.3191	159	517	95	below_threshold
Altererythrobacter ishigakiensis	strain=NBRC 107699	GCA_001663155.1	476157	476157	type	True	77.2544	157	517	95	below_threshold
Altererythrobacter ishigakiensis	strain=ATCC BAA-2084	GCA_007830695.1	476157	476157	type	True	77.2359	159	517	95	below_threshold
Novosphingobium sediminis	strain=NBRC 106119	GCA_007991615.1	707214	707214	type	True	76.9729	90	517	95	below_threshold
Erythrobacter longus	strain=DSM 6997	GCA_000715015.1	1044	1044	type	True	76.761	109	517	95	below_threshold
Tsuneonella flava	strain=MS1-4	GCA_002870965.1	2055955	2055955	type	True	76.6183	98	517	95	below_threshold
Aurantiacibacter marinus	strain=KCTC 23554	GCA_001021555.1	874156	874156	type	True	76.5515	94	517	95	below_threshold
Novosphingobium umbonatum	strain=FSY-9	GCA_004005905.1	1908524	1908524	type	True	75.878	57	517	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 11:53:13,135] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31555/tc_result.tsv
[2023-03-17 11:53:13,139] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:53:13,139] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:53:13,139] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc340efb3-4aeb-4b79-be3f-70ec8dee4712/dqc_reference/checkm_data
[2023-03-17 11:53:13,140] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:53:13,236] [INFO] Task started: CheckM
[2023-03-17 11:53:13,236] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31555/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31555/checkm_input OceanDNA-b31555/checkm_result
[2023-03-17 11:53:42,669] [INFO] Task succeeded: CheckM
[2023-03-17 11:53:42,669] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.09%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:53:42,762] [INFO] ===== Completeness check finished =====
[2023-03-17 11:53:42,762] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:53:42,762] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31555/markers.fasta)
[2023-03-17 11:53:42,763] [INFO] Task started: Blastn
[2023-03-17 11:53:42,763] [INFO] Running command: blastn -query OceanDNA-b31555/markers.fasta -db /var/lib/cwl/stgc340efb3-4aeb-4b79-be3f-70ec8dee4712/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31555/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:53:43,503] [INFO] Task succeeded: Blastn
[2023-03-17 11:53:43,510] [INFO] Selected 17 target genomes.
[2023-03-17 11:53:43,510] [INFO] Target genome list was writen to OceanDNA-b31555/target_genomes_gtdb.txt
[2023-03-17 11:53:43,528] [INFO] Task started: fastANI
[2023-03-17 11:53:43,528] [INFO] Running command: fastANI --query /var/lib/cwl/stga3853388-9b74-4dab-90ce-4cc745a9318d/OceanDNA-b31555.fa --refList OceanDNA-b31555/target_genomes_gtdb.txt --output OceanDNA-b31555/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:53:51,752] [INFO] Task succeeded: fastANI
[2023-03-17 11:53:51,762] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:53:51,762] [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_013371495.1	s__Erythrobacter sp013371495	79.3698	293	517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011047315.1	s__Erythrobacter sp011047315	78.2801	218	517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114695.1	s__Parerythrobacter sp004114695	78.2529	219	517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018205975.1	s__Erythrobacter sp018205975	78.2174	203	517	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	77.9689	231	517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013005.1	s__Altererythrobacter_D litoralis_A	77.6929	190	517	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_000756795.1	s__Qipengyuania vulgaris_A	77.6518	170	517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002155685.1	s__Erythrobacter colymbi	77.6512	159	517	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	77.6436	177	517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002295.1	s__Erythrobacter sp013002295	77.3301	120	517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.14	98.90	0.85	0.82	4	-
GCF_001663155.1	s__Erythrobacter ishigakiensis	77.2544	157	517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	97.03	96.25	0.95	0.94	6	-
GCF_013370205.1	s__Actirhodobacter atriluteus	77.1708	129	517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Actirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001516125.1	s__Erythrobacter sp001516125	77.1413	104	517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003149575.1	s__Erythrobacter sp003149575	77.114	155	517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	98.16	98.16	0.93	0.93	2	-
GCA_013822125.1	s__Erythrobacter sp013822125	76.9865	129	517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015661825.1	s__Novosphingobium capsulatum_A	76.6885	76	517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903834285.1	s__Novosphingobium sp903834285	76.2886	79	517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.71	99.71	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-03-17 11:53:51,765] [INFO] GTDB search result was written to OceanDNA-b31555/result_gtdb.tsv
[2023-03-17 11:53:51,769] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:53:51,774] [INFO] DFAST_QC result json was written to OceanDNA-b31555/dqc_result.json
[2023-03-17 11:53:51,774] [INFO] DFAST_QC completed!
[2023-03-17 11:53:51,775] [INFO] Total running time: 0h1m1s