[2023-03-17 02:31:12,847] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:31:12,847] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:31:12,847] [INFO] DQC Reference Directory: /var/lib/cwl/stg3fc946ed-4248-4264-a67a-7fca8ccaa0d6/dqc_reference
[2023-03-17 02:31:14,378] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:31:14,379] [INFO] Task started: Prodigal
[2023-03-17 02:31:14,379] [INFO] Running command: cat /var/lib/cwl/stg6182138b-6051-4139-82eb-6fe678222ff8/OceanDNA-b31979.fa | prodigal -d OceanDNA-b31979/cds.fna -a OceanDNA-b31979/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:31:31,044] [INFO] Task succeeded: Prodigal
[2023-03-17 02:31:31,045] [INFO] Task started: HMMsearch
[2023-03-17 02:31:31,045] [INFO] Running command: hmmsearch --tblout OceanDNA-b31979/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3fc946ed-4248-4264-a67a-7fca8ccaa0d6/dqc_reference/reference_markers.hmm OceanDNA-b31979/protein.faa > /dev/null
[2023-03-17 02:31:31,228] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:31:31,229] [INFO] Found 6/6 markers.
[2023-03-17 02:31:31,245] [INFO] Query marker FASTA was written to OceanDNA-b31979/markers.fasta
[2023-03-17 02:31:31,246] [INFO] Task started: Blastn
[2023-03-17 02:31:31,246] [INFO] Running command: blastn -query OceanDNA-b31979/markers.fasta -db /var/lib/cwl/stg3fc946ed-4248-4264-a67a-7fca8ccaa0d6/dqc_reference/reference_markers.fasta -out OceanDNA-b31979/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:31:32,078] [INFO] Task succeeded: Blastn
[2023-03-17 02:31:32,078] [INFO] Selected 30 target genomes.
[2023-03-17 02:31:32,079] [INFO] Target genome list was writen to OceanDNA-b31979/target_genomes.txt
[2023-03-17 02:31:32,099] [INFO] Task started: fastANI
[2023-03-17 02:31:32,099] [INFO] Running command: fastANI --query /var/lib/cwl/stg6182138b-6051-4139-82eb-6fe678222ff8/OceanDNA-b31979.fa --refList OceanDNA-b31979/target_genomes.txt --output OceanDNA-b31979/fastani_result.tsv --threads 1
[2023-03-17 02:31:52,717] [INFO] Task succeeded: fastANI
[2023-03-17 02:31:52,717] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3fc946ed-4248-4264-a67a-7fca8ccaa0d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:31:52,717] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3fc946ed-4248-4264-a67a-7fca8ccaa0d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:31:52,733] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:31:52,733] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 02:31:52,733] [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
Novosphingobium naphthalenivorans	strain=NBRC 102051	GCA_001590985.1	273168	273168	type	True	79.0083	362	885	95	below_threshold
Novosphingobium colocasiae	strain=KCTC 32255	GCA_014652555.1	1256513	1256513	type	True	78.9416	362	885	95	below_threshold
Novosphingobium endophyticum	strain=CGMCC 1.15095	GCA_014640675.1	1955250	1955250	type	True	78.919	327	885	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000767465.1	205844	205844	type	True	78.7628	370	885	95	below_threshold
Novosphingobium marinum	strain=DSM 29043	GCA_013408095.1	1514948	1514948	type	True	78.7018	335	885	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000235975.2	205844	205844	type	True	78.6802	364	885	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	78.6782	377	885	95	below_threshold
Novosphingobium marinum	strain=CGMCC 1.12918	GCA_014640055.1	1514948	1514948	type	True	78.6779	333	885	95	below_threshold
Novosphingobium mathurense	strain=SM117	GCA_900168325.1	428990	428990	type	True	78.6496	338	885	95	below_threshold
Novosphingobium lentum	strain=NBRC 107847	GCA_001590965.1	145287	145287	type	True	78.5749	350	885	95	below_threshold
Novosphingobium aerophilum	strain=4Y4	GCA_014230305.1	2839843	2839843	type	True	78.559	305	885	95	below_threshold
Novosphingobium lindaniclasticum	strain=LE124	GCA_000445125.1	1329895	1329895	type	True	78.5121	322	885	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	78.4778	321	885	95	below_threshold
Novosphingobium profundi	strain=F72	GCA_018491765.1	1774954	1774954	type	True	78.4592	327	885	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	78.395	313	885	95	below_threshold
Novosphingobium kunmingense	strain=CGMCC 1.12274	GCA_002813245.1	1211806	1211806	type	True	78.3645	323	885	95	below_threshold
Aurantiacibacter xanthus	strain=CCTCC AB 2015396	GCA_003584015.1	1784712	1784712	type	True	78.3172	271	885	95	below_threshold
Novosphingobium piscinae	strain=KCTC 42194	GCA_014230355.1	1507448	1507448	type	True	78.3081	304	885	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	78.2921	321	885	95	below_threshold
Novosphingobium silvae	strain=FGD1	GCA_009856825.1	2692619	2692619	type	True	78.198	312	885	95	below_threshold
Novosphingobium guangzhouense	strain=SA925	GCA_002896965.1	1850347	1850347	type	True	78.1971	331	885	95	below_threshold
Croceicoccus gelatinilyticus	strain=1NDH52	GCA_018398395.1	2835536	2835536	type	True	78.1723	282	885	95	below_threshold
Novosphingobium flavum	strain=NBRC 111647	GCA_014230315.1	1778672	1778672	type	True	78.1291	300	885	95	below_threshold
Tsuneonella aeria	strain=100921-2	GCA_009827495.1	1837929	1837929	type	True	78.1147	274	885	95	below_threshold
Croceicoccus sediminis	strain=S2-4-2	GCA_007570835.1	2571150	2571150	type	True	78.0949	282	885	95	below_threshold
Novosphingobium capsulatum	strain=NBRC 12533	GCA_001598375.1	13688	13688	type	True	78.0801	286	885	95	below_threshold
Novosphingobium ginsenosidimutans	strain=FW-6	GCA_007954425.1	1176536	1176536	type	True	78.0287	264	885	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	78.0073	293	885	95	below_threshold
Croceicoccus pelagius	strain=Ery9	GCA_001661915.1	1703341	1703341	type	True	77.9703	266	885	95	below_threshold
Qipengyuania thermophila	strain=CFH 74456	GCA_004153605.1	2509361	2509361	type	True	77.4277	181	885	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 02:31:52,733] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31979/tc_result.tsv
[2023-03-17 02:31:52,734] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:31:52,734] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:31:52,734] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3fc946ed-4248-4264-a67a-7fca8ccaa0d6/dqc_reference/checkm_data
[2023-03-17 02:31:52,734] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:31:52,738] [INFO] Task started: CheckM
[2023-03-17 02:31:52,738] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31979/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31979/checkm_input OceanDNA-b31979/checkm_result
[2023-03-17 02:32:35,428] [INFO] Task succeeded: CheckM
[2023-03-17 02:32:35,429] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.81%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:32:35,431] [INFO] ===== Completeness check finished =====
[2023-03-17 02:32:35,431] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:32:35,432] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31979/markers.fasta)
[2023-03-17 02:32:35,432] [INFO] Task started: Blastn
[2023-03-17 02:32:35,432] [INFO] Running command: blastn -query OceanDNA-b31979/markers.fasta -db /var/lib/cwl/stg3fc946ed-4248-4264-a67a-7fca8ccaa0d6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31979/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:32:36,986] [INFO] Task succeeded: Blastn
[2023-03-17 02:32:36,987] [INFO] Selected 33 target genomes.
[2023-03-17 02:32:36,987] [INFO] Target genome list was writen to OceanDNA-b31979/target_genomes_gtdb.txt
[2023-03-17 02:32:37,563] [INFO] Task started: fastANI
[2023-03-17 02:32:37,563] [INFO] Running command: fastANI --query /var/lib/cwl/stg6182138b-6051-4139-82eb-6fe678222ff8/OceanDNA-b31979.fa --refList OceanDNA-b31979/target_genomes_gtdb.txt --output OceanDNA-b31979/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:33:00,170] [INFO] Task succeeded: fastANI
[2023-03-17 02:33:00,188] [INFO] Found 33 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 02:33:00,188] [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_002556635.1	s__Novosphingobium sp002556635	79.1151	428	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001590985.1	s__Novosphingobium naphthalenivorans	79.0095	362	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652555.1	s__Novosphingobium colocasiae	78.954	361	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113255.1	s__Novosphingobium sp900113255	78.9391	358	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640675.1	s__Novosphingobium endophyticum	78.9335	326	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000802225.1	s__Novosphingobium malaysiense	78.8114	344	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000767465.1	s__Novosphingobium pentaromativorans	78.7507	372	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	96.84	95.17	0.76	0.62	4	-
GCF_014204535.1	s__Novosphingobium chloroacetimidivorans	78.7331	355	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408095.1	s__Novosphingobium marinum	78.6894	336	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900168325.1	s__Novosphingobium mathurense	78.6371	339	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.03	99.03	0.83	0.83	2	-
GCA_017745295.1	s__Novosphingobium sp017745295	78.5997	304	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719755.1	s__Novosphingobium sp016719755	78.5628	336	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.59	99.59	0.90	0.90	2	-
GCF_014230305.1	s__Novosphingobium aerophilum	78.5267	308	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.68	98.68	0.90	0.90	2	-
GCF_002855555.1	s__Novosphingobium sp002855555	78.502	284	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007993975.1	s__Novosphingobium barchaimii_B	78.4802	345	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302615.1	s__Novosphingobium sp017302615	78.4158	320	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001298105.1	s__Novosphingobium sp001298105	78.4079	334	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.11	98.61	0.92	0.87	4	-
GCF_002813245.1	s__Novosphingobium kunmingense	78.3772	323	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341845.1	s__Novosphingobium sp004341845	78.3588	350	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006874585.1	s__Novosphingobium sp006874585	78.3393	364	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.32	98.32	0.81	0.81	2	-
GCA_004211435.1	s__Novosphingobium sp004211435	78.3222	314	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018417475.1	s__Novosphingobium sp000813185	78.2921	321	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.53	97.53	0.86	0.86	2	-
GCA_013791705.1	s__Novosphingobium sp013791705	78.2429	244	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.87	99.87	0.91	0.91	2	-
GCF_018636735.1	s__Alteriqipengyuania sp018636735	78.2101	292	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828065.1	s__Croceibacterium soli	78.1784	282	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018398395.1	s__Croceicoccus sp018398395	78.1723	282	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014230315.1	s__Novosphingobium flavum	78.1417	299	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016745095.1	s__Croceicoccus sp016745095	78.1168	245	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007570835.1	s__Croceicoccus sediminis	78.1075	281	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827655.1	s__Alteraurantiacibacter buctensis	78.0821	289	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007954425.1	s__Novosphingobium ginsenosidimutans	78.0162	265	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822125.1	s__Erythrobacter sp013822125	77.6288	215	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004331795.1	s__CFH-75059 sp004331795	77.4277	181	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__CFH-75059	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-17 02:33:00,188] [INFO] GTDB search result was written to OceanDNA-b31979/result_gtdb.tsv
[2023-03-17 02:33:00,188] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:33:00,191] [INFO] DFAST_QC result json was written to OceanDNA-b31979/dqc_result.json
[2023-03-17 02:33:00,191] [INFO] DFAST_QC completed!
[2023-03-17 02:33:00,191] [INFO] Total running time: 0h1m47s