[2023-03-15 12:33:51,660] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:33:51,660] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:33:51,660] [INFO] DQC Reference Directory: /var/lib/cwl/stg94b98f56-03aa-49bd-af9a-c8cdc90ad579/dqc_reference
[2023-03-15 12:33:52,797] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:33:52,797] [INFO] Task started: Prodigal
[2023-03-15 12:33:52,797] [INFO] Running command: cat /var/lib/cwl/stg6ce344c2-b5e6-49f2-8f5c-dc9671590d0d/OceanDNA-b31989.fa | prodigal -d OceanDNA-b31989/cds.fna -a OceanDNA-b31989/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:34:10,252] [INFO] Task succeeded: Prodigal
[2023-03-15 12:34:10,252] [INFO] Task started: HMMsearch
[2023-03-15 12:34:10,252] [INFO] Running command: hmmsearch --tblout OceanDNA-b31989/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg94b98f56-03aa-49bd-af9a-c8cdc90ad579/dqc_reference/reference_markers.hmm OceanDNA-b31989/protein.faa > /dev/null
[2023-03-15 12:34:10,444] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:34:10,444] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg6ce344c2-b5e6-49f2-8f5c-dc9671590d0d/OceanDNA-b31989.fa]
[2023-03-15 12:34:10,469] [INFO] Query marker FASTA was written to OceanDNA-b31989/markers.fasta
[2023-03-15 12:34:10,469] [INFO] Task started: Blastn
[2023-03-15 12:34:10,469] [INFO] Running command: blastn -query OceanDNA-b31989/markers.fasta -db /var/lib/cwl/stg94b98f56-03aa-49bd-af9a-c8cdc90ad579/dqc_reference/reference_markers.fasta -out OceanDNA-b31989/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:34:11,087] [INFO] Task succeeded: Blastn
[2023-03-15 12:34:11,093] [INFO] Selected 13 target genomes.
[2023-03-15 12:34:11,093] [INFO] Target genome list was writen to OceanDNA-b31989/target_genomes.txt
[2023-03-15 12:34:11,101] [INFO] Task started: fastANI
[2023-03-15 12:34:11,101] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ce344c2-b5e6-49f2-8f5c-dc9671590d0d/OceanDNA-b31989.fa --refList OceanDNA-b31989/target_genomes.txt --output OceanDNA-b31989/fastani_result.tsv --threads 1
[2023-03-15 12:34:20,987] [INFO] Task succeeded: fastANI
[2023-03-15 12:34:20,987] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg94b98f56-03aa-49bd-af9a-c8cdc90ad579/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:34:20,987] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg94b98f56-03aa-49bd-af9a-c8cdc90ad579/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:34:20,996] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 12:34:20,996] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 12:34:20,996] [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 profundi	strain=F72	GCA_018491765.1	1774954	1774954	type	True	80.8274	527	902	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	80.673	521	902	95	below_threshold
Novosphingobium naphthalenivorans	strain=NBRC 102051	GCA_001590985.1	273168	273168	type	True	79.8416	455	902	95	below_threshold
Novosphingobium aureum	strain=YJ-S2-02	GCA_015865035.1	2792964	2792964	type	True	79.7362	445	902	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000235975.2	205844	205844	type	True	79.4142	335	902	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000767465.1	205844	205844	type	True	79.3572	342	902	95	below_threshold
Novosphingobium indicum	strain=CGMCC 1.6784	GCA_014645195.1	462949	462949	type	True	79.2856	356	902	95	below_threshold
Novosphingobium mathurense	strain=SM117	GCA_900168325.1	428990	428990	type	True	79.1195	355	902	95	below_threshold
Novosphingobium malaysiense	strain=MUSC 273	GCA_000802225.1	1348853	1348853	type	True	78.9437	357	902	95	below_threshold
Novosphingobium silvae	strain=FGD1	GCA_009856825.1	2692619	2692619	type	True	78.4991	319	902	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	78.0131	281	902	95	below_threshold
Novosphingobium umbonatum	strain=FSY-9	GCA_004005905.1	1908524	1908524	type	True	77.1656	168	902	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	77.1109	166	902	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 12:34:20,998] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31989/tc_result.tsv
[2023-03-15 12:34:20,999] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:34:20,999] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:34:20,999] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg94b98f56-03aa-49bd-af9a-c8cdc90ad579/dqc_reference/checkm_data
[2023-03-15 12:34:21,000] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:34:21,006] [INFO] Task started: CheckM
[2023-03-15 12:34:21,006] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31989/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31989/checkm_input OceanDNA-b31989/checkm_result
[2023-03-15 12:35:06,549] [INFO] Task succeeded: CheckM
[2023-03-15 12:35:06,550] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 12:35:06,570] [INFO] ===== Completeness check finished =====
[2023-03-15 12:35:06,570] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:35:06,570] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31989/markers.fasta)
[2023-03-15 12:35:06,571] [INFO] Task started: Blastn
[2023-03-15 12:35:06,571] [INFO] Running command: blastn -query OceanDNA-b31989/markers.fasta -db /var/lib/cwl/stg94b98f56-03aa-49bd-af9a-c8cdc90ad579/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31989/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:35:07,569] [INFO] Task succeeded: Blastn
[2023-03-15 12:35:07,576] [INFO] Selected 11 target genomes.
[2023-03-15 12:35:07,576] [INFO] Target genome list was writen to OceanDNA-b31989/target_genomes_gtdb.txt
[2023-03-15 12:35:07,685] [INFO] Task started: fastANI
[2023-03-15 12:35:07,685] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ce344c2-b5e6-49f2-8f5c-dc9671590d0d/OceanDNA-b31989.fa --refList OceanDNA-b31989/target_genomes_gtdb.txt --output OceanDNA-b31989/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:35:17,132] [INFO] Task succeeded: fastANI
[2023-03-15 12:35:17,139] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 12:35:17,139] [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_018491765.1	s__Novosphingobium profundi	80.8156	528	902	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	80.6848	520	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.53	97.53	0.86	0.86	2	-
GCF_008107685.1	s__Novosphingobium sp008107685	79.8745	466	902	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	79.8416	455	902	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	79.7362	445	902	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	79.3572	342	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	96.84	95.17	0.76	0.62	4	-
GCF_014645195.1	s__Novosphingobium indicum	79.2652	358	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.92	97.92	0.77	0.77	2	-
GCF_006874585.1	s__Novosphingobium sp006874585	79.0817	411	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.32	98.32	0.81	0.81	2	-
GCA_017745295.1	s__Novosphingobium sp017745295	79.0012	351	902	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	78.9566	356	902	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	78.2344	313	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 12:35:17,141] [INFO] GTDB search result was written to OceanDNA-b31989/result_gtdb.tsv
[2023-03-15 12:35:17,142] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:35:17,145] [INFO] DFAST_QC result json was written to OceanDNA-b31989/dqc_result.json
[2023-03-15 12:35:17,146] [INFO] DFAST_QC completed!
[2023-03-15 12:35:17,146] [INFO] Total running time: 0h1m25s