[2023-03-18 04:04:53,892] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:04:53,892] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:04:53,892] [INFO] DQC Reference Directory: /var/lib/cwl/stge328fbca-0239-4077-a2c5-d7f4e6c780a7/dqc_reference
[2023-03-18 04:04:55,025] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:04:55,026] [INFO] Task started: Prodigal
[2023-03-18 04:04:55,026] [INFO] Running command: cat /var/lib/cwl/stga2ceb000-330d-4bac-ba61-5e76a0fd1fb3/OceanDNA-b31994.fa | prodigal -d OceanDNA-b31994/cds.fna -a OceanDNA-b31994/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:05:13,957] [INFO] Task succeeded: Prodigal
[2023-03-18 04:05:13,957] [INFO] Task started: HMMsearch
[2023-03-18 04:05:13,957] [INFO] Running command: hmmsearch --tblout OceanDNA-b31994/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge328fbca-0239-4077-a2c5-d7f4e6c780a7/dqc_reference/reference_markers.hmm OceanDNA-b31994/protein.faa > /dev/null
[2023-03-18 04:05:14,156] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:05:14,156] [INFO] Found 6/6 markers.
[2023-03-18 04:05:14,181] [INFO] Query marker FASTA was written to OceanDNA-b31994/markers.fasta
[2023-03-18 04:05:14,182] [INFO] Task started: Blastn
[2023-03-18 04:05:14,182] [INFO] Running command: blastn -query OceanDNA-b31994/markers.fasta -db /var/lib/cwl/stge328fbca-0239-4077-a2c5-d7f4e6c780a7/dqc_reference/reference_markers.fasta -out OceanDNA-b31994/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:05:15,037] [INFO] Task succeeded: Blastn
[2023-03-18 04:05:15,038] [INFO] Selected 19 target genomes.
[2023-03-18 04:05:15,039] [INFO] Target genome list was writen to OceanDNA-b31994/target_genomes.txt
[2023-03-18 04:05:15,072] [INFO] Task started: fastANI
[2023-03-18 04:05:15,073] [INFO] Running command: fastANI --query /var/lib/cwl/stga2ceb000-330d-4bac-ba61-5e76a0fd1fb3/OceanDNA-b31994.fa --refList OceanDNA-b31994/target_genomes.txt --output OceanDNA-b31994/fastani_result.tsv --threads 1
[2023-03-18 04:05:30,488] [INFO] Task succeeded: fastANI
[2023-03-18 04:05:30,488] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge328fbca-0239-4077-a2c5-d7f4e6c780a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:05:30,488] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge328fbca-0239-4077-a2c5-d7f4e6c780a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:05:30,499] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:05:30,499] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 04:05:30,499] [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	81.111	499	1030	95	below_threshold
Novosphingobium endophyticum	strain=CGMCC 1.15095	GCA_014640675.1	1955250	1955250	type	True	80.567	390	1030	95	below_threshold
Novosphingobium indicum	strain=CGMCC 1.6784	GCA_014645195.1	462949	462949	type	True	80.3947	453	1030	95	below_threshold
Novosphingobium malaysiense	strain=MUSC 273	GCA_000802225.1	1348853	1348853	type	True	80.3646	423	1030	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000235975.2	205844	205844	type	True	79.9666	416	1030	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000767465.1	205844	205844	type	True	79.9535	441	1030	95	below_threshold
Novosphingobium mathurense	strain=SM117	GCA_900168325.1	428990	428990	type	True	79.9296	395	1030	95	below_threshold
Novosphingobium colocasiae	strain=KCTC 32255	GCA_014652555.1	1256513	1256513	type	True	79.9161	388	1030	95	below_threshold
Novosphingobium lindaniclasticum	strain=LE124	GCA_000445125.1	1329895	1329895	type	True	79.8938	381	1030	95	below_threshold
Novosphingobium barchaimii	strain=LL02	GCA_001046635.1	1420591	1420591	type	True	79.6997	417	1030	95	below_threshold
Novosphingobium silvae	strain=FGD1	GCA_009856825.1	2692619	2692619	type	True	79.6311	396	1030	95	below_threshold
Novosphingobium guangzhouense	strain=SA925	GCA_002896965.1	1850347	1850347	type	True	79.518	397	1030	95	below_threshold
Novosphingobium aureum	strain=YJ-S2-02	GCA_015865035.1	2792964	2792964	type	True	79.4373	376	1030	95	below_threshold
Novosphingobium profundi	strain=F72	GCA_018491765.1	1774954	1774954	type	True	79.2638	400	1030	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	78.9607	376	1030	95	below_threshold
Novosphingobium piscinae	strain=KCTC 42194	GCA_014230355.1	1507448	1507448	type	True	78.867	313	1030	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	78.8203	357	1030	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	78.7897	316	1030	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	78.711	318	1030	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 04:05:30,549] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31994/tc_result.tsv
[2023-03-18 04:05:30,550] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:05:30,550] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:05:30,550] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge328fbca-0239-4077-a2c5-d7f4e6c780a7/dqc_reference/checkm_data
[2023-03-18 04:05:30,551] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:05:30,572] [INFO] Task started: CheckM
[2023-03-18 04:05:30,572] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31994/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31994/checkm_input OceanDNA-b31994/checkm_result
[2023-03-18 04:06:18,615] [INFO] Task succeeded: CheckM
[2023-03-18 04:06:18,615] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.93%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:06:18,618] [INFO] ===== Completeness check finished =====
[2023-03-18 04:06:18,618] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:06:18,618] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31994/markers.fasta)
[2023-03-18 04:06:18,619] [INFO] Task started: Blastn
[2023-03-18 04:06:18,619] [INFO] Running command: blastn -query OceanDNA-b31994/markers.fasta -db /var/lib/cwl/stge328fbca-0239-4077-a2c5-d7f4e6c780a7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31994/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:06:20,238] [INFO] Task succeeded: Blastn
[2023-03-18 04:06:20,239] [INFO] Selected 21 target genomes.
[2023-03-18 04:06:20,239] [INFO] Target genome list was writen to OceanDNA-b31994/target_genomes_gtdb.txt
[2023-03-18 04:06:20,613] [INFO] Task started: fastANI
[2023-03-18 04:06:20,613] [INFO] Running command: fastANI --query /var/lib/cwl/stga2ceb000-330d-4bac-ba61-5e76a0fd1fb3/OceanDNA-b31994.fa --refList OceanDNA-b31994/target_genomes_gtdb.txt --output OceanDNA-b31994/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:06:38,077] [INFO] Task succeeded: fastANI
[2023-03-18 04:06:38,089] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 04:06:38,089] [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_900113255.1	s__Novosphingobium sp900113255	81.8967	472	1030	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	81.0981	500	1030	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	80.5575	391	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017745295.1	s__Novosphingobium sp017745295	80.4554	366	1030	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	80.3906	453	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.92	97.92	0.77	0.77	2	-
GCF_000802225.1	s__Novosphingobium malaysiense	80.3646	423	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000281975.1	s__Novosphingobium sp000281975	80.3625	426	1030	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	80.1924	404	1030	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	80.1175	437	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.32	98.32	0.81	0.81	2	-
GCF_001742225.1	s__Novosphingobium resinovorum	80.0975	437	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.22	97.83	0.80	0.78	4	-
GCF_000767465.1	s__Novosphingobium pentaromativorans	79.9534	441	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	96.84	95.17	0.76	0.62	4	-
GCF_014652555.1	s__Novosphingobium colocasiae	79.9305	387	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168325.1	s__Novosphingobium mathurense	79.9296	395	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.03	99.03	0.83	0.83	2	-
GCF_000445125.1	s__Novosphingobium lindaniclasticum	79.8926	381	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000272475.1	s__Novosphingobium sp000272475	79.6706	342	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009856825.1	s__Novosphingobium sp009856825	79.6182	397	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421325.1	s__Novosphingobium sp001421325	79.536	347	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002896965.1	s__Novosphingobium guangzhouense	79.5243	396	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015865035.1	s__Novosphingobium sp015865035	79.4376	376	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018491765.1	s__Novosphingobium profundi	79.2703	399	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014230355.1	s__Novosphingobium piscinae	78.853	314	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 04:06:38,089] [INFO] GTDB search result was written to OceanDNA-b31994/result_gtdb.tsv
[2023-03-18 04:06:38,089] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:06:38,091] [INFO] DFAST_QC result json was written to OceanDNA-b31994/dqc_result.json
[2023-03-18 04:06:38,091] [INFO] DFAST_QC completed!
[2023-03-18 04:06:38,092] [INFO] Total running time: 0h1m44s