[2023-03-16 06:12:34,968] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:12:34,968] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:12:34,968] [INFO] DQC Reference Directory: /var/lib/cwl/stg05a4f7ad-f563-4288-9344-d46265878b00/dqc_reference
[2023-03-16 06:12:36,637] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:12:36,637] [INFO] Task started: Prodigal
[2023-03-16 06:12:36,637] [INFO] Running command: cat /var/lib/cwl/stg607f0829-3630-41a8-afc5-26309af1dd14/OceanDNA-b31987.fa | prodigal -d OceanDNA-b31987/cds.fna -a OceanDNA-b31987/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:12:44,998] [INFO] Task succeeded: Prodigal
[2023-03-16 06:12:44,998] [INFO] Task started: HMMsearch
[2023-03-16 06:12:44,998] [INFO] Running command: hmmsearch --tblout OceanDNA-b31987/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05a4f7ad-f563-4288-9344-d46265878b00/dqc_reference/reference_markers.hmm OceanDNA-b31987/protein.faa > /dev/null
[2023-03-16 06:12:45,146] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:12:45,146] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg607f0829-3630-41a8-afc5-26309af1dd14/OceanDNA-b31987.fa]
[2023-03-16 06:12:45,184] [INFO] Query marker FASTA was written to OceanDNA-b31987/markers.fasta
[2023-03-16 06:12:45,185] [INFO] Task started: Blastn
[2023-03-16 06:12:45,185] [INFO] Running command: blastn -query OceanDNA-b31987/markers.fasta -db /var/lib/cwl/stg05a4f7ad-f563-4288-9344-d46265878b00/dqc_reference/reference_markers.fasta -out OceanDNA-b31987/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:12:45,760] [INFO] Task succeeded: Blastn
[2023-03-16 06:12:45,768] [INFO] Selected 21 target genomes.
[2023-03-16 06:12:45,768] [INFO] Target genome list was writen to OceanDNA-b31987/target_genomes.txt
[2023-03-16 06:12:45,782] [INFO] Task started: fastANI
[2023-03-16 06:12:45,782] [INFO] Running command: fastANI --query /var/lib/cwl/stg607f0829-3630-41a8-afc5-26309af1dd14/OceanDNA-b31987.fa --refList OceanDNA-b31987/target_genomes.txt --output OceanDNA-b31987/fastani_result.tsv --threads 1
[2023-03-16 06:12:59,495] [INFO] Task succeeded: fastANI
[2023-03-16 06:12:59,495] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05a4f7ad-f563-4288-9344-d46265878b00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:12:59,495] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05a4f7ad-f563-4288-9344-d46265878b00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:12:59,508] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:12:59,508] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 06:12:59,508] [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 aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	82.6808	250	327	95	below_threshold
Novosphingobium naphthalenivorans	strain=NBRC 102051	GCA_001590985.1	273168	273168	type	True	78.4607	133	327	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000767465.1	205844	205844	type	True	78.2841	133	327	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000235975.2	205844	205844	type	True	78.2375	130	327	95	below_threshold
Novosphingobium endophyticum	strain=CGMCC 1.15095	GCA_014640675.1	1955250	1955250	type	True	78.2044	128	327	95	below_threshold
Novosphingobium mathurense	strain=SM117	GCA_900168325.1	428990	428990	type	True	78.1654	124	327	95	below_threshold
Novosphingobium profundi	strain=F72	GCA_018491765.1	1774954	1774954	type	True	78.0362	134	327	95	below_threshold
Novosphingobium indicum	strain=CGMCC 1.6784	GCA_014645195.1	462949	462949	type	True	78.018	137	327	95	below_threshold
Novosphingobium malaysiense	strain=MUSC 273	GCA_000802225.1	1348853	1348853	type	True	77.9414	123	327	95	below_threshold
Novosphingobium fluoreni	strain=DSM 27568	GCA_014196615.1	1391222	1391222	type	True	77.9213	88	327	95	below_threshold
Novosphingobium marinum	strain=CGMCC 1.12918	GCA_014640055.1	1514948	1514948	type	True	77.8201	119	327	95	below_threshold
Novosphingobium marinum	strain=DSM 29043	GCA_013408095.1	1514948	1514948	type	True	77.8109	120	327	95	below_threshold
Novosphingobium aureum	strain=YJ-S2-02	GCA_015865035.1	2792964	2792964	type	True	77.7788	145	327	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	77.7243	117	327	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	77.7004	117	327	95	below_threshold
Novosphingobium lindaniclasticum	strain=LE124	GCA_000445125.1	1329895	1329895	type	True	77.6679	121	327	95	below_threshold
Novosphingobium colocasiae	strain=KCTC 32255	GCA_014652555.1	1256513	1256513	type	True	77.5554	119	327	95	below_threshold
Novosphingobium silvae	strain=FGD1	GCA_009856825.1	2692619	2692619	type	True	77.2919	124	327	95	below_threshold
Novosphingobium olei	strain=TW-4	GCA_012927405.1	2728851	2728851	type	True	77.2012	102	327	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	77.1475	106	327	95	below_threshold
Qipengyuania aestuarii	strain=GH1	GCA_019711535.1	2867241	2867241	type	True	76.6925	50	327	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 06:12:59,510] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31987/tc_result.tsv
[2023-03-16 06:12:59,514] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:12:59,514] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:12:59,514] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05a4f7ad-f563-4288-9344-d46265878b00/dqc_reference/checkm_data
[2023-03-16 06:12:59,515] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:12:59,522] [INFO] Task started: CheckM
[2023-03-16 06:12:59,522] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31987/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31987/checkm_input OceanDNA-b31987/checkm_result
[2023-03-16 06:13:25,193] [INFO] Task succeeded: CheckM
[2023-03-16 06:13:25,194] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.59%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:13:25,233] [INFO] ===== Completeness check finished =====
[2023-03-16 06:13:25,233] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:13:25,233] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31987/markers.fasta)
[2023-03-16 06:13:25,233] [INFO] Task started: Blastn
[2023-03-16 06:13:25,234] [INFO] Running command: blastn -query OceanDNA-b31987/markers.fasta -db /var/lib/cwl/stg05a4f7ad-f563-4288-9344-d46265878b00/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31987/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:13:26,092] [INFO] Task succeeded: Blastn
[2023-03-16 06:13:26,099] [INFO] Selected 18 target genomes.
[2023-03-16 06:13:26,099] [INFO] Target genome list was writen to OceanDNA-b31987/target_genomes_gtdb.txt
[2023-03-16 06:13:26,116] [INFO] Task started: fastANI
[2023-03-16 06:13:26,116] [INFO] Running command: fastANI --query /var/lib/cwl/stg607f0829-3630-41a8-afc5-26309af1dd14/OceanDNA-b31987.fa --refList OceanDNA-b31987/target_genomes_gtdb.txt --output OceanDNA-b31987/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:13:39,239] [INFO] Task succeeded: fastANI
[2023-03-16 06:13:39,250] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 06:13:39,250] [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_009746585.1	s__Novosphingobium sp009746585	82.6808	250	327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002556635.1	s__Novosphingobium sp002556635	80.8367	211	327	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	78.2841	133	327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	96.84	95.17	0.76	0.62	4	-
GCF_006874585.1	s__Novosphingobium sp006874585	78.2345	129	327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.32	98.32	0.81	0.81	2	-
GCF_900168325.1	s__Novosphingobium mathurense	78.1654	124	327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.03	99.03	0.83	0.83	2	-
GCF_900113255.1	s__Novosphingobium sp900113255	78.0989	136	327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506425.1	s__Novosphingobium sp902506425	78.0919	130	327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645195.1	s__Novosphingobium indicum	78.018	137	327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.92	97.92	0.77	0.77	2	-
GCA_004211435.1	s__Novosphingobium sp004211435	77.9862	127	327	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	77.9777	127	327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001742225.1	s__Novosphingobium resinovorum	77.9552	152	327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.22	97.83	0.80	0.78	4	-
GCF_000802225.1	s__Novosphingobium malaysiense	77.9414	123	327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002149965.1	s__Novosphingobium panipatense	77.8994	135	327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.24	97.74	0.85	0.82	3	-
GCF_015865035.1	s__Novosphingobium sp015865035	77.7788	145	327	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	77.7004	117	327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.53	97.53	0.86	0.86	2	-
GCF_016803135.1	s__Pelagerythrobacter sp016803135	77.4322	96	327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009856825.1	s__Novosphingobium sp009856825	77.3138	123	327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176355.1	s__Alteriqipengyuania bathyomarina	76.9018	68	327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	98.10	96.53	0.93	0.90	11	-
--------------------------------------------------------------------------------
[2023-03-16 06:13:39,253] [INFO] GTDB search result was written to OceanDNA-b31987/result_gtdb.tsv
[2023-03-16 06:13:39,257] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:13:39,261] [INFO] DFAST_QC result json was written to OceanDNA-b31987/dqc_result.json
[2023-03-16 06:13:39,261] [INFO] DFAST_QC completed!
[2023-03-16 06:13:39,261] [INFO] Total running time: 0h1m4s