[2023-03-18 10:46:22,171] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:46:22,171] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:46:22,171] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e58774f-2093-44db-95a9-97547979ce0e/dqc_reference
[2023-03-18 10:46:23,265] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:46:23,266] [INFO] Task started: Prodigal
[2023-03-18 10:46:23,267] [INFO] Running command: cat /var/lib/cwl/stg60a8efa3-d23f-4e26-92dc-0c2e359310a9/OceanDNA-b32000.fa | prodigal -d OceanDNA-b32000/cds.fna -a OceanDNA-b32000/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:46:48,592] [INFO] Task succeeded: Prodigal
[2023-03-18 10:46:48,592] [INFO] Task started: HMMsearch
[2023-03-18 10:46:48,592] [INFO] Running command: hmmsearch --tblout OceanDNA-b32000/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e58774f-2093-44db-95a9-97547979ce0e/dqc_reference/reference_markers.hmm OceanDNA-b32000/protein.faa > /dev/null
[2023-03-18 10:46:48,800] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:46:48,801] [INFO] Found 6/6 markers.
[2023-03-18 10:46:48,830] [INFO] Query marker FASTA was written to OceanDNA-b32000/markers.fasta
[2023-03-18 10:46:48,831] [INFO] Task started: Blastn
[2023-03-18 10:46:48,831] [INFO] Running command: blastn -query OceanDNA-b32000/markers.fasta -db /var/lib/cwl/stg8e58774f-2093-44db-95a9-97547979ce0e/dqc_reference/reference_markers.fasta -out OceanDNA-b32000/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:46:49,763] [INFO] Task succeeded: Blastn
[2023-03-18 10:46:49,765] [INFO] Selected 15 target genomes.
[2023-03-18 10:46:49,765] [INFO] Target genome list was writen to OceanDNA-b32000/target_genomes.txt
[2023-03-18 10:46:49,773] [INFO] Task started: fastANI
[2023-03-18 10:46:49,773] [INFO] Running command: fastANI --query /var/lib/cwl/stg60a8efa3-d23f-4e26-92dc-0c2e359310a9/OceanDNA-b32000.fa --refList OceanDNA-b32000/target_genomes.txt --output OceanDNA-b32000/fastani_result.tsv --threads 1
[2023-03-18 10:47:04,271] [INFO] Task succeeded: fastANI
[2023-03-18 10:47:04,271] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e58774f-2093-44db-95a9-97547979ce0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:47:04,271] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e58774f-2093-44db-95a9-97547979ce0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:47:04,281] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 10:47:04,281] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 10:47:04,281] [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 indicum	strain=CGMCC 1.6784	GCA_014645195.1	462949	462949	type	True	98.4052	1221	1346	95	conclusive
Novosphingobium malaysiense	strain=MUSC 273	GCA_000802225.1	1348853	1348853	type	True	86.8058	1002	1346	95	below_threshold
Novosphingobium naphthalenivorans	strain=NBRC 102051	GCA_001590985.1	273168	273168	type	True	83.4933	798	1346	95	below_threshold
Novosphingobium mathurense	strain=SM117	GCA_900168325.1	428990	428990	type	True	81.6016	627	1346	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000767465.1	205844	205844	type	True	81.5569	660	1346	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000235975.2	205844	205844	type	True	81.4948	649	1346	95	below_threshold
Novosphingobium endophyticum	strain=CGMCC 1.15095	GCA_014640675.1	1955250	1955250	type	True	81.1505	655	1346	95	below_threshold
Novosphingobium aureum	strain=YJ-S2-02	GCA_015865035.1	2792964	2792964	type	True	80.8543	642	1346	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	80.4989	627	1346	95	below_threshold
Novosphingobium profundi	strain=F72	GCA_018491765.1	1774954	1774954	type	True	80.4636	629	1346	95	below_threshold
Novosphingobium silvae	strain=FGD1	GCA_009856825.1	2692619	2692619	type	True	80.2661	590	1346	95	below_threshold
Novosphingobium guangzhouense	strain=SA925	GCA_002896965.1	1850347	1850347	type	True	80.2361	649	1346	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	79.4787	464	1346	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	79.4285	535	1346	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	79.3957	451	1346	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 10:47:04,283] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32000/tc_result.tsv
[2023-03-18 10:47:04,287] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:47:04,287] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:47:04,287] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e58774f-2093-44db-95a9-97547979ce0e/dqc_reference/checkm_data
[2023-03-18 10:47:04,287] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:47:04,351] [INFO] Task started: CheckM
[2023-03-18 10:47:04,351] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32000/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32000/checkm_input OceanDNA-b32000/checkm_result
[2023-03-18 10:48:05,577] [INFO] Task succeeded: CheckM
[2023-03-18 10:48:05,577] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 10:48:05,610] [INFO] ===== Completeness check finished =====
[2023-03-18 10:48:05,610] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:48:05,610] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32000/markers.fasta)
[2023-03-18 10:48:05,611] [INFO] Task started: Blastn
[2023-03-18 10:48:05,611] [INFO] Running command: blastn -query OceanDNA-b32000/markers.fasta -db /var/lib/cwl/stg8e58774f-2093-44db-95a9-97547979ce0e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32000/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:48:07,417] [INFO] Task succeeded: Blastn
[2023-03-18 10:48:07,421] [INFO] Selected 13 target genomes.
[2023-03-18 10:48:07,422] [INFO] Target genome list was writen to OceanDNA-b32000/target_genomes_gtdb.txt
[2023-03-18 10:48:07,433] [INFO] Task started: fastANI
[2023-03-18 10:48:07,433] [INFO] Running command: fastANI --query /var/lib/cwl/stg60a8efa3-d23f-4e26-92dc-0c2e359310a9/OceanDNA-b32000.fa --refList OceanDNA-b32000/target_genomes_gtdb.txt --output OceanDNA-b32000/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:48:21,740] [INFO] Task succeeded: fastANI
[2023-03-18 10:48:21,748] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 10:48:21,748] [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_014645195.1	s__Novosphingobium indicum	98.3857	1222	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.92	97.92	0.77	0.77	2	conclusive
GCF_000802225.1	s__Novosphingobium malaysiense	86.8058	1002	1346	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	83.4933	798	1346	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	81.5797	630	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.03	99.03	0.83	0.83	2	-
GCF_000767465.1	s__Novosphingobium pentaromativorans	81.5569	660	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	96.84	95.17	0.76	0.62	4	-
GCF_900113255.1	s__Novosphingobium sp900113255	81.4968	650	1346	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	81.1243	706	1346	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	80.9839	683	1346	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	80.8545	642	1346	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	80.8476	735	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.22	97.83	0.80	0.78	4	-
GCF_018417475.1	s__Novosphingobium sp000813185	80.4863	627	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.53	97.53	0.86	0.86	2	-
GCF_018491765.1	s__Novosphingobium profundi	80.4728	628	1346	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	80.2855	588	1346	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 10:48:21,752] [INFO] GTDB search result was written to OceanDNA-b32000/result_gtdb.tsv
[2023-03-18 10:48:21,756] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:48:21,760] [INFO] DFAST_QC result json was written to OceanDNA-b32000/dqc_result.json
[2023-03-18 10:48:21,760] [INFO] DFAST_QC completed!
[2023-03-18 10:48:21,760] [INFO] Total running time: 0h1m60s