[2023-03-19 04:11:06,927] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:11:06,927] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:11:06,927] [INFO] DQC Reference Directory: /var/lib/cwl/stg97b1d7b8-ca11-4a4f-b77c-64701831eaf5/dqc_reference
[2023-03-19 04:11:08,646] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:11:08,646] [INFO] Task started: Prodigal
[2023-03-19 04:11:08,647] [INFO] Running command: cat /var/lib/cwl/stgf31a1d39-9f18-4147-a917-0fcc54021e65/OceanDNA-b31530.fa | prodigal -d OceanDNA-b31530/cds.fna -a OceanDNA-b31530/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:11:22,175] [INFO] Task succeeded: Prodigal
[2023-03-19 04:11:22,175] [INFO] Task started: HMMsearch
[2023-03-19 04:11:22,175] [INFO] Running command: hmmsearch --tblout OceanDNA-b31530/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97b1d7b8-ca11-4a4f-b77c-64701831eaf5/dqc_reference/reference_markers.hmm OceanDNA-b31530/protein.faa > /dev/null
[2023-03-19 04:11:22,365] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:11:22,365] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf31a1d39-9f18-4147-a917-0fcc54021e65/OceanDNA-b31530.fa]
[2023-03-19 04:11:22,382] [INFO] Query marker FASTA was written to OceanDNA-b31530/markers.fasta
[2023-03-19 04:11:22,382] [INFO] Task started: Blastn
[2023-03-19 04:11:22,382] [INFO] Running command: blastn -query OceanDNA-b31530/markers.fasta -db /var/lib/cwl/stg97b1d7b8-ca11-4a4f-b77c-64701831eaf5/dqc_reference/reference_markers.fasta -out OceanDNA-b31530/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:11:22,994] [INFO] Task succeeded: Blastn
[2023-03-19 04:11:22,995] [INFO] Selected 27 target genomes.
[2023-03-19 04:11:22,995] [INFO] Target genome list was writen to OceanDNA-b31530/target_genomes.txt
[2023-03-19 04:11:23,011] [INFO] Task started: fastANI
[2023-03-19 04:11:23,011] [INFO] Running command: fastANI --query /var/lib/cwl/stgf31a1d39-9f18-4147-a917-0fcc54021e65/OceanDNA-b31530.fa --refList OceanDNA-b31530/target_genomes.txt --output OceanDNA-b31530/fastani_result.tsv --threads 1
[2023-03-19 04:11:37,360] [INFO] Task succeeded: fastANI
[2023-03-19 04:11:37,360] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97b1d7b8-ca11-4a4f-b77c-64701831eaf5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:11:37,360] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97b1d7b8-ca11-4a4f-b77c-64701831eaf5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:11:37,375] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:11:37,375] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:11:37,375] [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
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	79.5889	370	742	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	79.4425	376	742	95	below_threshold
Alteriqipengyuania lutimaris	strain=CECT 8624	GCA_014191645.1	1538146	1538146	type	True	79.4173	383	742	95	below_threshold
Alteriqipengyuania lutimaris	strain=S-5	GCA_003363135.1	1538146	1538146	type	True	79.4153	381	742	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	79.3447	365	742	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	79.315	390	742	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	79.2904	361	742	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	79.2892	349	742	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	79.2134	349	742	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_001719165.1	39960	39960	type	True	79.0942	358	742	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_000714795.1	39960	39960	type	True	79.0575	350	742	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	79.0501	382	742	95	below_threshold
Aurantiacibacter luteus	strain=KA37	GCA_001010945.1	1581420	1581420	type	True	78.9003	318	742	95	below_threshold
Tsuneonella amylolytica	strain=NS1	GCA_003626915.1	2338327	2338327	type	True	78.8319	329	742	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	78.7535	309	742	95	below_threshold
Pelagerythrobacter marensis	strain=KCTC 22370	GCA_001028625.1	543877	543877	type	True	78.6792	304	742	95	below_threshold
Tsuneonella troitsensis	strain=JCM 17037	GCA_001441535.1	292222	292222	type	True	78.6787	301	742	95	below_threshold
Tsuneonella troitsensis	strain=KMM 6042	GCA_003730315.1	292222	292222	type	True	78.6517	300	742	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	78.633	364	742	95	below_threshold
Qipengyuania aquimaris	strain=JCM 12189	GCA_009827445.1	255984	255984	suspected-type	True	78.5588	326	742	95	below_threshold
Erythrobacter tepidarius	strain=DSM 10594	GCA_002155695.1	60454	60454	type	True	78.5314	331	742	95	below_threshold
Pelagerythrobacter marensis	strain=DSM 21428	GCA_001461885.1	543877	543877	type	True	78.5184	315	742	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	78.5	324	742	95	below_threshold
Erythrobacter dokdonensis	strain=DSM 17193	GCA_002155305.1	328225	328225	type	True	78.4684	326	742	95	below_threshold
Novosphingobium flavum	strain=NBRC 111647	GCA_014230315.1	1778672	1778672	type	True	78.261	286	742	95	below_threshold
Novosphingobium marinum	strain=CGMCC 1.12918	GCA_014640055.1	1514948	1514948	type	True	78.1128	268	742	95	below_threshold
Novosphingobium marinum	strain=DSM 29043	GCA_013408095.1	1514948	1514948	type	True	78.0247	273	742	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:11:37,375] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31530/tc_result.tsv
[2023-03-19 04:11:37,375] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:11:37,375] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:11:37,376] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97b1d7b8-ca11-4a4f-b77c-64701831eaf5/dqc_reference/checkm_data
[2023-03-19 04:11:37,376] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:11:37,380] [INFO] Task started: CheckM
[2023-03-19 04:11:37,380] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31530/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31530/checkm_input OceanDNA-b31530/checkm_result
[2023-03-19 04:12:13,543] [INFO] Task succeeded: CheckM
[2023-03-19 04:12:13,543] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.53%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:12:13,545] [INFO] ===== Completeness check finished =====
[2023-03-19 04:12:13,545] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:12:13,545] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31530/markers.fasta)
[2023-03-19 04:12:13,546] [INFO] Task started: Blastn
[2023-03-19 04:12:13,546] [INFO] Running command: blastn -query OceanDNA-b31530/markers.fasta -db /var/lib/cwl/stg97b1d7b8-ca11-4a4f-b77c-64701831eaf5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31530/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:12:14,519] [INFO] Task succeeded: Blastn
[2023-03-19 04:12:14,520] [INFO] Selected 21 target genomes.
[2023-03-19 04:12:14,520] [INFO] Target genome list was writen to OceanDNA-b31530/target_genomes_gtdb.txt
[2023-03-19 04:12:14,641] [INFO] Task started: fastANI
[2023-03-19 04:12:14,641] [INFO] Running command: fastANI --query /var/lib/cwl/stgf31a1d39-9f18-4147-a917-0fcc54021e65/OceanDNA-b31530.fa --refList OceanDNA-b31530/target_genomes_gtdb.txt --output OceanDNA-b31530/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:12:26,261] [INFO] Task succeeded: fastANI
[2023-03-19 04:12:26,274] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 04:12:26,274] [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_014641655.1	s__Alteriqipengyuania_A marina	98.1178	701	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania_A	95.0	98.02	98.02	0.89	0.89	2	conclusive
GCF_009827575.1	s__Alteriqipengyuania_A halimionae	82.4318	575	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114695.1	s__Parerythrobacter sp004114695	79.7105	390	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827315.1	s__Qipengyuania gaetbuli	79.5749	371	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018828205.1	s__Qipengyuania sp018828205	79.4196	323	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827515.1	s__Pelagerythrobacter marinus	79.3322	389	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002712945.1	s__Alteriqipengyuania sp002712945	79.2699	224	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011765465.1	s__Erythrobacter sp011765465	79.2543	372	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001678665.1	s__Qipengyuania sp001678665	79.2205	382	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000186705.1	s__Alteriqipengyuania sp000186705	79.2086	347	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003355455.1	s__Qipengyuania aurea	79.1075	323	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.67	97.64	0.83	0.82	3	-
GCF_900177715.1	s__Erythrobacter xiamenensis	79.0226	342	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015529805.1	s__Qipengyuania soli	78.9852	323	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001010945.1	s__Alteraurantiacibacter luteus	78.8988	318	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011320115.1	s__Croceibacterium segetis	78.8059	293	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001028625.1	s__Pelagerythrobacter marensis	78.7068	302	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002155695.1	s__Erythrobacter tepidarius	78.5366	330	742	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	78.5	324	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014230315.1	s__Novosphingobium flavum	78.2349	288	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013370205.1	s__Actirhodobacter atriluteus	78.2066	282	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Actirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003958635.1	s__Altericroceibacterium_A xinjiangense	77.692	198	742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Altericroceibacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:12:26,274] [INFO] GTDB search result was written to OceanDNA-b31530/result_gtdb.tsv
[2023-03-19 04:12:26,274] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:12:26,277] [INFO] DFAST_QC result json was written to OceanDNA-b31530/dqc_result.json
[2023-03-19 04:12:26,277] [INFO] DFAST_QC completed!
[2023-03-19 04:12:26,277] [INFO] Total running time: 0h1m19s