[2023-07-01 05:18:18,137] [INFO] DFAST_QC pipeline started.
[2023-07-01 05:18:18,139] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 05:18:18,140] [INFO] DQC Reference Directory: /var/lib/cwl/stgf931b84a-6103-496b-a431-fe68560b9e42/dqc_reference
[2023-07-01 05:18:20,500] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 05:18:20,501] [INFO] Task started: Prodigal
[2023-07-01 05:18:20,501] [INFO] Running command: gunzip -c /var/lib/cwl/stgd99ce9f3-3aa0-4741-b33e-6a213b117cb3/GCA_903862085.1_freshwater_MAG_---_AM-lipid-02-D4_bin-0854_genomic.fna.gz | prodigal -d GCA_903862085.1_freshwater_MAG_---_AM-lipid-02-D4_bin-0854_genomic.fna/cds.fna -a GCA_903862085.1_freshwater_MAG_---_AM-lipid-02-D4_bin-0854_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 05:18:34,600] [INFO] Task succeeded: Prodigal
[2023-07-01 05:18:34,600] [INFO] Task started: HMMsearch
[2023-07-01 05:18:34,601] [INFO] Running command: hmmsearch --tblout GCA_903862085.1_freshwater_MAG_---_AM-lipid-02-D4_bin-0854_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf931b84a-6103-496b-a431-fe68560b9e42/dqc_reference/reference_markers.hmm GCA_903862085.1_freshwater_MAG_---_AM-lipid-02-D4_bin-0854_genomic.fna/protein.faa > /dev/null
[2023-07-01 05:18:34,856] [INFO] Task succeeded: HMMsearch
[2023-07-01 05:18:34,858] [INFO] Found 6/6 markers.
[2023-07-01 05:18:34,896] [INFO] Query marker FASTA was written to GCA_903862085.1_freshwater_MAG_---_AM-lipid-02-D4_bin-0854_genomic.fna/markers.fasta
[2023-07-01 05:18:34,896] [INFO] Task started: Blastn
[2023-07-01 05:18:34,896] [INFO] Running command: blastn -query GCA_903862085.1_freshwater_MAG_---_AM-lipid-02-D4_bin-0854_genomic.fna/markers.fasta -db /var/lib/cwl/stgf931b84a-6103-496b-a431-fe68560b9e42/dqc_reference/reference_markers.fasta -out GCA_903862085.1_freshwater_MAG_---_AM-lipid-02-D4_bin-0854_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 05:18:35,837] [INFO] Task succeeded: Blastn
[2023-07-01 05:18:35,842] [INFO] Selected 15 target genomes.
[2023-07-01 05:18:35,842] [INFO] Target genome list was writen to GCA_903862085.1_freshwater_MAG_---_AM-lipid-02-D4_bin-0854_genomic.fna/target_genomes.txt
[2023-07-01 05:18:35,844] [INFO] Task started: fastANI
[2023-07-01 05:18:35,844] [INFO] Running command: fastANI --query /var/lib/cwl/stgd99ce9f3-3aa0-4741-b33e-6a213b117cb3/GCA_903862085.1_freshwater_MAG_---_AM-lipid-02-D4_bin-0854_genomic.fna.gz --refList GCA_903862085.1_freshwater_MAG_---_AM-lipid-02-D4_bin-0854_genomic.fna/target_genomes.txt --output GCA_903862085.1_freshwater_MAG_---_AM-lipid-02-D4_bin-0854_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 05:18:48,120] [INFO] Task succeeded: fastANI
[2023-07-01 05:18:48,121] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf931b84a-6103-496b-a431-fe68560b9e42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 05:18:48,121] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf931b84a-6103-496b-a431-fe68560b9e42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 05:18:48,136] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2023-07-01 05:18:48,137] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-07-01 05:18:48,139] [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 acidiphilum	strain=DSM 19966	GCA_000429005.1	505248	505248	type	True	98.9554	1087	1264	95	conclusive
Novosphingobium nitrogenifigens	strain=DSM 19370	GCA_000192575.1	378548	378548	type	True	79.563	568	1264	95	below_threshold
Novosphingobium nitrogenifigens	strain=DSM 19370	GCA_000375445.1	378548	378548	type	True	79.5061	570	1264	95	below_threshold
Novosphingobium pokkalii	strain=KCTC 42224	GCA_014652855.1	1770194	1770194	type	True	79.496	553	1264	95	below_threshold
Novosphingobium capsulatum	strain=NBRC 12533	GCA_001598375.1	13688	13688	type	True	79.4226	558	1264	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	79.2505	504	1264	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	78.6815	478	1264	95	below_threshold
Novosphingobium hassiacum	strain=DSM 14552	GCA_014196055.1	173676	173676	type	True	78.6259	403	1264	95	below_threshold
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	78.6095	423	1264	95	below_threshold
Novosphingobium meiothermophilum	strain=SYSU G00007	GCA_003171715.1	2202251	2202251	type	True	78.3494	417	1264	95	below_threshold
Novosphingobium jiangmenense	strain=1Y9A	GCA_015694345.1	2791981	2791981	type	True	78.3197	399	1264	95	below_threshold
Novosphingobium subterraneum	strain=DSM 12447	GCA_000807925.1	48936	48936	type	True	78.0467	380	1264	95	below_threshold
Novosphingobium umbonatum	strain=FSY-9	GCA_004005905.1	1908524	1908524	type	True	77.9718	324	1264	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	77.6245	252	1264	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	77.1704	261	1264	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 05:18:48,142] [INFO] DFAST Taxonomy check result was written to GCA_903862085.1_freshwater_MAG_---_AM-lipid-02-D4_bin-0854_genomic.fna/tc_result.tsv
[2023-07-01 05:18:48,143] [INFO] ===== Taxonomy check completed =====
[2023-07-01 05:18:48,144] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 05:18:48,144] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf931b84a-6103-496b-a431-fe68560b9e42/dqc_reference/checkm_data
[2023-07-01 05:18:48,148] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 05:18:48,189] [INFO] Task started: CheckM
[2023-07-01 05:18:48,189] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903862085.1_freshwater_MAG_---_AM-lipid-02-D4_bin-0854_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903862085.1_freshwater_MAG_---_AM-lipid-02-D4_bin-0854_genomic.fna/checkm_input GCA_903862085.1_freshwater_MAG_---_AM-lipid-02-D4_bin-0854_genomic.fna/checkm_result
[2023-07-01 05:19:38,116] [INFO] Task succeeded: CheckM
[2023-07-01 05:19:38,117] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 05:19:38,135] [INFO] ===== Completeness check finished =====
[2023-07-01 05:19:38,136] [INFO] ===== Start GTDB Search =====
[2023-07-01 05:19:38,136] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903862085.1_freshwater_MAG_---_AM-lipid-02-D4_bin-0854_genomic.fna/markers.fasta)
[2023-07-01 05:19:38,137] [INFO] Task started: Blastn
[2023-07-01 05:19:38,137] [INFO] Running command: blastn -query GCA_903862085.1_freshwater_MAG_---_AM-lipid-02-D4_bin-0854_genomic.fna/markers.fasta -db /var/lib/cwl/stgf931b84a-6103-496b-a431-fe68560b9e42/dqc_reference/reference_markers_gtdb.fasta -out GCA_903862085.1_freshwater_MAG_---_AM-lipid-02-D4_bin-0854_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 05:19:39,811] [INFO] Task succeeded: Blastn
[2023-07-01 05:19:39,816] [INFO] Selected 10 target genomes.
[2023-07-01 05:19:39,816] [INFO] Target genome list was writen to GCA_903862085.1_freshwater_MAG_---_AM-lipid-02-D4_bin-0854_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 05:19:39,818] [INFO] Task started: fastANI
[2023-07-01 05:19:39,818] [INFO] Running command: fastANI --query /var/lib/cwl/stgd99ce9f3-3aa0-4741-b33e-6a213b117cb3/GCA_903862085.1_freshwater_MAG_---_AM-lipid-02-D4_bin-0854_genomic.fna.gz --refList GCA_903862085.1_freshwater_MAG_---_AM-lipid-02-D4_bin-0854_genomic.fna/target_genomes_gtdb.txt --output GCA_903862085.1_freshwater_MAG_---_AM-lipid-02-D4_bin-0854_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 05:19:48,058] [INFO] Task succeeded: fastANI
[2023-07-01 05:19:48,073] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 05:19:48,073] [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_000429005.1	s__Novosphingobium acidiphilum	98.9554	1087	1264	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.82	98.58	0.89	0.82	13	conclusive
GCF_001519065.1	s__Novosphingobium sp001519065	83.8845	918	1264	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903832325.1	s__Novosphingobium sp903832325	83.6318	901	1264	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.98	99.94	0.97	0.96	4	-
GCF_001519055.1	s__Novosphingobium sp001519055	82.1024	809	1264	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903893935.1	s__Novosphingobium sp903893935	81.6461	444	1264	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903868655.1	s__Novosphingobium sp903868655	81.579	464	1264	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903848655.1	s__Novosphingobium sp903848655	80.6914	564	1264	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001014975.1	s__Novosphingobium sp002336885	79.3092	518	1264	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.66	97.51	0.82	0.80	4	-
GCA_001725355.1	s__Novosphingobium sp001725355	79.1858	476	1264	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002256985.1	s__Novosphingobium sp002256985	78.726	439	1264	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.95	99.92	0.97	0.95	3	-
--------------------------------------------------------------------------------
[2023-07-01 05:19:48,075] [INFO] GTDB search result was written to GCA_903862085.1_freshwater_MAG_---_AM-lipid-02-D4_bin-0854_genomic.fna/result_gtdb.tsv
[2023-07-01 05:19:48,076] [INFO] ===== GTDB Search completed =====
[2023-07-01 05:19:48,080] [INFO] DFAST_QC result json was written to GCA_903862085.1_freshwater_MAG_---_AM-lipid-02-D4_bin-0854_genomic.fna/dqc_result.json
[2023-07-01 05:19:48,080] [INFO] DFAST_QC completed!
[2023-07-01 05:19:48,080] [INFO] Total running time: 0h1m30s