[2023-03-19 04:59:58,319] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:59:58,319] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:59:58,319] [INFO] DQC Reference Directory: /var/lib/cwl/stg20be87f0-7159-4b5d-bd77-664ab43dec4e/dqc_reference
[2023-03-19 04:59:59,404] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:59:59,404] [INFO] Task started: Prodigal
[2023-03-19 04:59:59,404] [INFO] Running command: cat /var/lib/cwl/stg859cfb26-9ef1-4fa5-a119-2952c189a087/OceanDNA-b31665.fa | prodigal -d OceanDNA-b31665/cds.fna -a OceanDNA-b31665/protein.faa -g 11 -q > /dev/null
[2023-03-19 05:00:14,636] [INFO] Task succeeded: Prodigal
[2023-03-19 05:00:14,636] [INFO] Task started: HMMsearch
[2023-03-19 05:00:14,637] [INFO] Running command: hmmsearch --tblout OceanDNA-b31665/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20be87f0-7159-4b5d-bd77-664ab43dec4e/dqc_reference/reference_markers.hmm OceanDNA-b31665/protein.faa > /dev/null
[2023-03-19 05:00:14,808] [INFO] Task succeeded: HMMsearch
[2023-03-19 05:00:14,809] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg859cfb26-9ef1-4fa5-a119-2952c189a087/OceanDNA-b31665.fa]
[2023-03-19 05:00:14,824] [INFO] Query marker FASTA was written to OceanDNA-b31665/markers.fasta
[2023-03-19 05:00:14,824] [INFO] Task started: Blastn
[2023-03-19 05:00:14,825] [INFO] Running command: blastn -query OceanDNA-b31665/markers.fasta -db /var/lib/cwl/stg20be87f0-7159-4b5d-bd77-664ab43dec4e/dqc_reference/reference_markers.fasta -out OceanDNA-b31665/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:00:15,381] [INFO] Task succeeded: Blastn
[2023-03-19 05:00:15,382] [INFO] Selected 23 target genomes.
[2023-03-19 05:00:15,382] [INFO] Target genome list was writen to OceanDNA-b31665/target_genomes.txt
[2023-03-19 05:00:15,396] [INFO] Task started: fastANI
[2023-03-19 05:00:15,396] [INFO] Running command: fastANI --query /var/lib/cwl/stg859cfb26-9ef1-4fa5-a119-2952c189a087/OceanDNA-b31665.fa --refList OceanDNA-b31665/target_genomes.txt --output OceanDNA-b31665/fastani_result.tsv --threads 1
[2023-03-19 05:00:28,280] [INFO] Task succeeded: fastANI
[2023-03-19 05:00:28,280] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20be87f0-7159-4b5d-bd77-664ab43dec4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 05:00:28,280] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20be87f0-7159-4b5d-bd77-664ab43dec4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 05:00:28,293] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 05:00:28,293] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 05:00:28,293] [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 litoralis	strain=DSM 8509	GCA_001719165.1	39960	39960	type	True	77.8364	262	785	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_000714795.1	39960	39960	type	True	77.8223	268	785	95	below_threshold
Erythrobacter sanguineus	strain=JCM 20691	GCA_002155655.1	198312	198312	type	True	77.7499	246	785	95	below_threshold
Erythrobacter rubeus	strain=KMU-140	GCA_014705715.1	2760803	2760803	type	True	77.7353	268	785	95	below_threshold
Erythrobacter sanguineus	strain=DSM 11032	GCA_900143235.1	198312	198312	type	True	77.7013	251	785	95	below_threshold
Qipengyuania nanhaisediminis	strain=CGMCC 1.7715	GCA_900115585.1	604088	604088	type	True	77.6128	160	785	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	77.6099	161	785	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	77.5592	227	785	95	below_threshold
Qipengyuania intermedia	strain=GH38	GCA_019711615.1	2867244	2867244	type	True	77.5198	153	785	95	below_threshold
Qipengyuania seohaensis	strain=SW-135	GCA_002795865.1	266951	266951	type	True	77.4736	141	785	95	below_threshold
Erythrobacter longus	strain=DSM 6997	GCA_000715015.1	1044	1044	type	True	77.4729	187	785	95	below_threshold
Altererythrobacter lutimaris	strain=JGD-16	GCA_013371495.1	2743979	2743979	type	True	77.4201	158	785	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	77.2066	156	785	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	77.103	144	785	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	77.0353	144	785	95	below_threshold
Qipengyuania aestuarii	strain=GH1	GCA_019711535.1	2867241	2867241	type	True	76.9528	142	785	95	below_threshold
Novosphingobium malaysiense	strain=MUSC 273	GCA_000802225.1	1348853	1348853	type	True	76.7068	93	785	95	below_threshold
Novosphingobium guangzhouense	strain=SA925	GCA_002896965.1	1850347	1850347	type	True	76.6456	81	785	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	76.5946	99	785	95	below_threshold
Allopontixanthobacter sediminis	strain=KCTC 42453	GCA_009828115.1	1689985	1689985	type	True	76.5678	117	785	95	below_threshold
Novosphingobium sediminis	strain=NBRC 106119	GCA_007991615.1	707214	707214	type	True	76.5342	100	785	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	76.529	102	785	95	below_threshold
Sphingomonas populi	strain=3-7	GCA_004208535.1	2484750	2484750	type	True	76.2301	72	785	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 05:00:28,294] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31665/tc_result.tsv
[2023-03-19 05:00:28,294] [INFO] ===== Taxonomy check completed =====
[2023-03-19 05:00:28,294] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 05:00:28,294] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20be87f0-7159-4b5d-bd77-664ab43dec4e/dqc_reference/checkm_data
[2023-03-19 05:00:28,295] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 05:00:28,439] [INFO] Task started: CheckM
[2023-03-19 05:00:28,439] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31665/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31665/checkm_input OceanDNA-b31665/checkm_result
[2023-03-19 05:01:09,937] [INFO] Task succeeded: CheckM
[2023-03-19 05:01:09,938] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 47.22%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 05:01:09,940] [INFO] ===== Completeness check finished =====
[2023-03-19 05:01:09,940] [INFO] ===== Start GTDB Search =====
[2023-03-19 05:01:09,940] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31665/markers.fasta)
[2023-03-19 05:01:09,941] [INFO] Task started: Blastn
[2023-03-19 05:01:09,941] [INFO] Running command: blastn -query OceanDNA-b31665/markers.fasta -db /var/lib/cwl/stg20be87f0-7159-4b5d-bd77-664ab43dec4e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31665/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:01:10,767] [INFO] Task succeeded: Blastn
[2023-03-19 05:01:10,767] [INFO] Selected 22 target genomes.
[2023-03-19 05:01:10,768] [INFO] Target genome list was writen to OceanDNA-b31665/target_genomes_gtdb.txt
[2023-03-19 05:01:10,787] [INFO] Task started: fastANI
[2023-03-19 05:01:10,787] [INFO] Running command: fastANI --query /var/lib/cwl/stg859cfb26-9ef1-4fa5-a119-2952c189a087/OceanDNA-b31665.fa --refList OceanDNA-b31665/target_genomes_gtdb.txt --output OceanDNA-b31665/fastani_result_gtdb.tsv --threads 1
[2023-03-19 05:01:23,475] [INFO] Task succeeded: fastANI
[2023-03-19 05:01:23,487] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 05:01:23,487] [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
GCA_000714765.1	s__Erythrobacter sp000714765	78.4448	356	785	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	78.4159	302	785	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	78.2272	304	785	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	78.2098	305	785	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	78.1981	193	785	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	77.8805	277	785	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	77.8014	171	785	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011765465.1	s__Erythrobacter sp011765465	77.7483	275	785	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	77.7455	214	785	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	77.7236	269	785	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019204025.1	s__Erythrobacter sp019204025	77.6397	252	785	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744895.1	s__Erythrobacter sp000744895	77.6075	267	785	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	77.4968	223	785	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000715015.1	s__Erythrobacter longus	77.4729	187	785	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001557115.1	s__Erythrobacter sp001557115	77.4453	184	785	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.84	99.84	0.90	0.90	2	-
GCF_001557325.1	s__Erythrobacter donghaensis_B	77.4102	194	785	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.70	99.64	0.86	0.85	7	-
GCA_003724185.1	s__Erythrobacter sp003724185	77.3902	251	785	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842925.1	s__Erythrobacter sp002842925	76.9878	181	785	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002269345.1	s__Tsuneonella mangrovi	76.9037	125	785	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002896965.1	s__Novosphingobium guangzhouense	76.6206	82	785	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009746585.1	s__Novosphingobium sp009746585	76.5746	100	785	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004208535.1	s__Sphingomonas populi	76.2301	72	785	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 05:01:23,487] [INFO] GTDB search result was written to OceanDNA-b31665/result_gtdb.tsv
[2023-03-19 05:01:23,487] [INFO] ===== GTDB Search completed =====
[2023-03-19 05:01:23,490] [INFO] DFAST_QC result json was written to OceanDNA-b31665/dqc_result.json
[2023-03-19 05:01:23,490] [INFO] DFAST_QC completed!
[2023-03-19 05:01:23,490] [INFO] Total running time: 0h1m25s