[2023-03-17 22:50:15,915] [INFO] DFAST_QC pipeline started.
[2023-03-17 22:50:15,915] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 22:50:15,915] [INFO] DQC Reference Directory: /var/lib/cwl/stg20ce95cc-e397-49ee-bda9-3005b50c3b49/dqc_reference
[2023-03-17 22:50:17,070] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 22:50:17,071] [INFO] Task started: Prodigal
[2023-03-17 22:50:17,071] [INFO] Running command: cat /var/lib/cwl/stgac6e5c6c-42ae-487d-9ffc-d10ba6e4ab5d/OceanDNA-b31995.fa | prodigal -d OceanDNA-b31995/cds.fna -a OceanDNA-b31995/protein.faa -g 11 -q > /dev/null
[2023-03-17 22:50:34,099] [INFO] Task succeeded: Prodigal
[2023-03-17 22:50:34,099] [INFO] Task started: HMMsearch
[2023-03-17 22:50:34,099] [INFO] Running command: hmmsearch --tblout OceanDNA-b31995/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20ce95cc-e397-49ee-bda9-3005b50c3b49/dqc_reference/reference_markers.hmm OceanDNA-b31995/protein.faa > /dev/null
[2023-03-17 22:50:34,275] [INFO] Task succeeded: HMMsearch
[2023-03-17 22:50:34,275] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgac6e5c6c-42ae-487d-9ffc-d10ba6e4ab5d/OceanDNA-b31995.fa]
[2023-03-17 22:50:34,300] [INFO] Query marker FASTA was written to OceanDNA-b31995/markers.fasta
[2023-03-17 22:50:34,301] [INFO] Task started: Blastn
[2023-03-17 22:50:34,301] [INFO] Running command: blastn -query OceanDNA-b31995/markers.fasta -db /var/lib/cwl/stg20ce95cc-e397-49ee-bda9-3005b50c3b49/dqc_reference/reference_markers.fasta -out OceanDNA-b31995/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:50:34,945] [INFO] Task succeeded: Blastn
[2023-03-17 22:50:34,946] [INFO] Selected 14 target genomes.
[2023-03-17 22:50:34,946] [INFO] Target genome list was writen to OceanDNA-b31995/target_genomes.txt
[2023-03-17 22:50:34,951] [INFO] Task started: fastANI
[2023-03-17 22:50:34,951] [INFO] Running command: fastANI --query /var/lib/cwl/stgac6e5c6c-42ae-487d-9ffc-d10ba6e4ab5d/OceanDNA-b31995.fa --refList OceanDNA-b31995/target_genomes.txt --output OceanDNA-b31995/fastani_result.tsv --threads 1
[2023-03-17 22:50:45,629] [INFO] Task succeeded: fastANI
[2023-03-17 22:50:45,629] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20ce95cc-e397-49ee-bda9-3005b50c3b49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 22:50:45,629] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20ce95cc-e397-49ee-bda9-3005b50c3b49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 22:50:45,638] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 22:50:45,638] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 22:50:45,638] [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 decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	97.3056	678	834	95	conclusive
Novosphingobium profundi	strain=F72	GCA_018491765.1	1774954	1774954	type	True	83.4754	552	834	95	below_threshold
Novosphingobium aureum	strain=YJ-S2-02	GCA_015865035.1	2792964	2792964	type	True	82.434	473	834	95	below_threshold
Novosphingobium naphthalenivorans	strain=NBRC 102051	GCA_001590985.1	273168	273168	type	True	81.657	380	834	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000767465.1	205844	205844	type	True	80.2549	326	834	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000235975.2	205844	205844	type	True	80.1911	326	834	95	below_threshold
Novosphingobium malaysiense	strain=MUSC 273	GCA_000802225.1	1348853	1348853	type	True	79.9101	324	834	95	below_threshold
Novosphingobium indicum	strain=CGMCC 1.6784	GCA_014645195.1	462949	462949	type	True	79.752	366	834	95	below_threshold
Novosphingobium lindaniclasticum	strain=LE124	GCA_000445125.1	1329895	1329895	type	True	79.6626	322	834	95	below_threshold
Novosphingobium silvae	strain=FGD1	GCA_009856825.1	2692619	2692619	type	True	79.5212	325	834	95	below_threshold
Novosphingobium endophyticum	strain=CGMCC 1.15095	GCA_014640675.1	1955250	1955250	type	True	79.4217	296	834	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	79.1845	253	834	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	78.8437	253	834	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	78.2961	255	834	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 22:50:45,638] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31995/tc_result.tsv
[2023-03-17 22:50:45,638] [INFO] ===== Taxonomy check completed =====
[2023-03-17 22:50:45,638] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 22:50:45,638] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20ce95cc-e397-49ee-bda9-3005b50c3b49/dqc_reference/checkm_data
[2023-03-17 22:50:45,639] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 22:50:45,648] [INFO] Task started: CheckM
[2023-03-17 22:50:45,648] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31995/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31995/checkm_input OceanDNA-b31995/checkm_result
[2023-03-17 22:51:29,128] [INFO] Task succeeded: CheckM
[2023-03-17 22:51:29,128] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 22:51:29,131] [INFO] ===== Completeness check finished =====
[2023-03-17 22:51:29,131] [INFO] ===== Start GTDB Search =====
[2023-03-17 22:51:29,132] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31995/markers.fasta)
[2023-03-17 22:51:29,133] [INFO] Task started: Blastn
[2023-03-17 22:51:29,133] [INFO] Running command: blastn -query OceanDNA-b31995/markers.fasta -db /var/lib/cwl/stg20ce95cc-e397-49ee-bda9-3005b50c3b49/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31995/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:51:30,324] [INFO] Task succeeded: Blastn
[2023-03-17 22:51:30,324] [INFO] Selected 8 target genomes.
[2023-03-17 22:51:30,324] [INFO] Target genome list was writen to OceanDNA-b31995/target_genomes_gtdb.txt
[2023-03-17 22:51:30,335] [INFO] Task started: fastANI
[2023-03-17 22:51:30,335] [INFO] Running command: fastANI --query /var/lib/cwl/stgac6e5c6c-42ae-487d-9ffc-d10ba6e4ab5d/OceanDNA-b31995.fa --refList OceanDNA-b31995/target_genomes_gtdb.txt --output OceanDNA-b31995/fastani_result_gtdb.tsv --threads 1
[2023-03-17 22:51:37,454] [INFO] Task succeeded: fastANI
[2023-03-17 22:51:37,460] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 22:51:37,460] [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_018417475.1	s__Novosphingobium sp000813185	97.3056	678	834	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.53	97.53	0.86	0.86	2	conclusive
GCF_008107685.1	s__Novosphingobium sp008107685	91.0929	622	834	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	83.459	553	834	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	82.4341	473	834	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	80.5269	396	834	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.32	98.32	0.81	0.81	2	-
GCF_000767465.1	s__Novosphingobium pentaromativorans	80.2461	326	834	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	96.84	95.17	0.76	0.62	4	-
GCF_004342985.1	s__Novosphingobium sp004342985	79.8752	364	834	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.88	97.88	0.88	0.88	2	-
GCF_014645195.1	s__Novosphingobium indicum	79.7665	365	834	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.92	97.92	0.77	0.77	2	-
--------------------------------------------------------------------------------
[2023-03-17 22:51:37,460] [INFO] GTDB search result was written to OceanDNA-b31995/result_gtdb.tsv
[2023-03-17 22:51:37,460] [INFO] ===== GTDB Search completed =====
[2023-03-17 22:51:37,462] [INFO] DFAST_QC result json was written to OceanDNA-b31995/dqc_result.json
[2023-03-17 22:51:37,462] [INFO] DFAST_QC completed!
[2023-03-17 22:51:37,462] [INFO] Total running time: 0h1m22s