[2023-03-16 03:47:34,644] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:47:34,644] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:47:34,644] [INFO] DQC Reference Directory: /var/lib/cwl/stg27d299c9-75b7-4406-b1d8-2d7371a209af/dqc_reference
[2023-03-16 03:47:35,723] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:47:35,723] [INFO] Task started: Prodigal
[2023-03-16 03:47:35,723] [INFO] Running command: cat /var/lib/cwl/stg9628be94-e9ed-4bf6-96ff-950413c33d7b/OceanDNA-b31676.fa | prodigal -d OceanDNA-b31676/cds.fna -a OceanDNA-b31676/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:47:55,637] [INFO] Task succeeded: Prodigal
[2023-03-16 03:47:55,638] [INFO] Task started: HMMsearch
[2023-03-16 03:47:55,638] [INFO] Running command: hmmsearch --tblout OceanDNA-b31676/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg27d299c9-75b7-4406-b1d8-2d7371a209af/dqc_reference/reference_markers.hmm OceanDNA-b31676/protein.faa > /dev/null
[2023-03-16 03:47:55,887] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:47:55,888] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg9628be94-e9ed-4bf6-96ff-950413c33d7b/OceanDNA-b31676.fa]
[2023-03-16 03:47:55,908] [INFO] Query marker FASTA was written to OceanDNA-b31676/markers.fasta
[2023-03-16 03:47:55,908] [INFO] Task started: Blastn
[2023-03-16 03:47:55,908] [INFO] Running command: blastn -query OceanDNA-b31676/markers.fasta -db /var/lib/cwl/stg27d299c9-75b7-4406-b1d8-2d7371a209af/dqc_reference/reference_markers.fasta -out OceanDNA-b31676/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:47:56,519] [INFO] Task succeeded: Blastn
[2023-03-16 03:47:56,519] [INFO] Selected 23 target genomes.
[2023-03-16 03:47:56,520] [INFO] Target genome list was writen to OceanDNA-b31676/target_genomes.txt
[2023-03-16 03:47:56,530] [INFO] Task started: fastANI
[2023-03-16 03:47:56,530] [INFO] Running command: fastANI --query /var/lib/cwl/stg9628be94-e9ed-4bf6-96ff-950413c33d7b/OceanDNA-b31676.fa --refList OceanDNA-b31676/target_genomes.txt --output OceanDNA-b31676/fastani_result.tsv --threads 1
[2023-03-16 03:48:09,104] [INFO] Task succeeded: fastANI
[2023-03-16 03:48:09,105] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg27d299c9-75b7-4406-b1d8-2d7371a209af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:48:09,105] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg27d299c9-75b7-4406-b1d8-2d7371a209af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:48:09,117] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:48:09,117] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 03:48:09,118] [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	78.2995	404	1030	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_000714795.1	39960	39960	type	True	78.2468	415	1030	95	below_threshold
Erythrobacter dokdonensis	strain=DSM 17193	GCA_002155305.1	328225	328225	type	True	78.2196	362	1030	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	78.1732	369	1030	95	below_threshold
Erythrobacter sanguineus	strain=JCM 20691	GCA_002155655.1	198312	198312	type	True	78.144	361	1030	95	below_threshold
Erythrobacter rubeus	strain=KMU-140	GCA_014705715.1	2760803	2760803	type	True	78.1341	328	1030	95	below_threshold
Erythrobacter sanguineus	strain=DSM 11032	GCA_900143235.1	198312	198312	type	True	78.0635	369	1030	95	below_threshold
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	78.0503	250	1030	95	below_threshold
Erythrobacter ramosus	strain=JCM 10282	GCA_009828055.1	35811	35811	type	True	77.9958	366	1030	95	below_threshold
Erythrobacter ramosus	strain=DSM 8510	GCA_014195675.1	35811	35811	type	True	77.9764	366	1030	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	77.9637	261	1030	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	77.9253	270	1030	95	below_threshold
Erythrobacter tepidarius	strain=DSM 10594	GCA_002155695.1	60454	60454	type	True	77.8934	356	1030	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	77.8706	261	1030	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	77.8436	289	1030	95	below_threshold
Croceicoccus sediminis	strain=S2-4-2	GCA_007570835.1	2571150	2571150	type	True	77.5629	156	1030	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	77.5456	249	1030	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	77.4976	224	1030	95	below_threshold
Aurantiacibacter zhengii	strain=V18	GCA_003584125.1	2307003	2307003	type	True	77.4904	205	1030	95	below_threshold
Croceicoccus marinus	strain=E4A9	GCA_001661675.2	450378	450378	type	True	77.1618	185	1030	95	below_threshold
Erythrobacter insulae	strain=JBTF-M21	GCA_007004095.1	2584124	2584124	type	True	77.1496	243	1030	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	77.0187	173	1030	95	below_threshold
Croceicoccus hydrothermalis	strain=JLT1	GCA_022378335.1	2867964	2867964	type	True	76.5928	142	1030	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 03:48:09,176] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31676/tc_result.tsv
[2023-03-16 03:48:09,176] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:48:09,176] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:48:09,176] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg27d299c9-75b7-4406-b1d8-2d7371a209af/dqc_reference/checkm_data
[2023-03-16 03:48:09,177] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:48:09,190] [INFO] Task started: CheckM
[2023-03-16 03:48:09,190] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31676/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31676/checkm_input OceanDNA-b31676/checkm_result
[2023-03-16 03:48:58,453] [INFO] Task succeeded: CheckM
[2023-03-16 03:48:58,453] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 03:48:58,456] [INFO] ===== Completeness check finished =====
[2023-03-16 03:48:58,456] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:48:58,456] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31676/markers.fasta)
[2023-03-16 03:48:58,456] [INFO] Task started: Blastn
[2023-03-16 03:48:58,456] [INFO] Running command: blastn -query OceanDNA-b31676/markers.fasta -db /var/lib/cwl/stg27d299c9-75b7-4406-b1d8-2d7371a209af/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31676/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:48:59,394] [INFO] Task succeeded: Blastn
[2023-03-16 03:48:59,395] [INFO] Selected 23 target genomes.
[2023-03-16 03:48:59,395] [INFO] Target genome list was writen to OceanDNA-b31676/target_genomes_gtdb.txt
[2023-03-16 03:48:59,489] [INFO] Task started: fastANI
[2023-03-16 03:48:59,490] [INFO] Running command: fastANI --query /var/lib/cwl/stg9628be94-e9ed-4bf6-96ff-950413c33d7b/OceanDNA-b31676.fa --refList OceanDNA-b31676/target_genomes_gtdb.txt --output OceanDNA-b31676/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:49:12,450] [INFO] Task succeeded: fastANI
[2023-03-16 03:49:12,463] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 03:49:12,464] [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_000152865.1	s__Erythrobacter sp000152865	78.7041	425	1030	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	78.668	420	1030	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	78.5836	389	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002155685.1	s__Erythrobacter colymbi	78.5158	376	1030	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	78.51	276	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105095.1	s__Erythrobacter sp900105095	78.5075	414	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004114695.1	s__Parerythrobacter sp004114695	78.362	290	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011765465.1	s__Erythrobacter sp011765465	78.3308	439	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001719165.1	s__Erythrobacter litoralis	78.2995	404	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_903934325.1	s__Erythrobacter sp903934325	78.25	374	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_016125555.1	s__Erythrobacter sp016125555	78.2168	380	1030	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	78.1949	359	1030	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	78.1138	330	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827315.1	s__Qipengyuania gaetbuli	77.8706	261	1030	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	77.8485	277	1030	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_019204025.1	s__Erythrobacter sp019204025	77.8219	300	1030	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	77.693	303	1030	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	77.6468	171	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827295.1	s__Qipengyuania pelagi	77.5427	250	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019204045.1	s__Erythrobacter sp019204045	77.5275	214	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009993635.1	s__Alteriqipengyuania sp009993635	77.3886	256	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	99.91	99.91	0.97	0.97	2	-
GCF_007004095.1	s__Erythrobacter insulae	77.1483	244	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009926135.1	s__Novosphingobium sp009926135	76.8209	167	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 03:49:12,464] [INFO] GTDB search result was written to OceanDNA-b31676/result_gtdb.tsv
[2023-03-16 03:49:12,464] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:49:12,466] [INFO] DFAST_QC result json was written to OceanDNA-b31676/dqc_result.json
[2023-03-16 03:49:12,466] [INFO] DFAST_QC completed!
[2023-03-16 03:49:12,466] [INFO] Total running time: 0h1m38s