[2023-06-28 18:01:21,170] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:01:21,172] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:01:21,172] [INFO] DQC Reference Directory: /var/lib/cwl/stg430ff433-9af5-47e4-a416-06247f57a741/dqc_reference
[2023-06-28 18:01:22,431] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:01:22,432] [INFO] Task started: Prodigal
[2023-06-28 18:01:22,432] [INFO] Running command: gunzip -c /var/lib/cwl/stgda64a3c0-dc99-41b9-8c60-44c9e9b1ec81/GCA_020446595.1_ASM2044659v1_genomic.fna.gz | prodigal -d GCA_020446595.1_ASM2044659v1_genomic.fna/cds.fna -a GCA_020446595.1_ASM2044659v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:01:30,313] [INFO] Task succeeded: Prodigal
[2023-06-28 18:01:30,314] [INFO] Task started: HMMsearch
[2023-06-28 18:01:30,314] [INFO] Running command: hmmsearch --tblout GCA_020446595.1_ASM2044659v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg430ff433-9af5-47e4-a416-06247f57a741/dqc_reference/reference_markers.hmm GCA_020446595.1_ASM2044659v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:01:30,546] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:01:30,548] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgda64a3c0-dc99-41b9-8c60-44c9e9b1ec81/GCA_020446595.1_ASM2044659v1_genomic.fna.gz]
[2023-06-28 18:01:30,580] [INFO] Query marker FASTA was written to GCA_020446595.1_ASM2044659v1_genomic.fna/markers.fasta
[2023-06-28 18:01:30,580] [INFO] Task started: Blastn
[2023-06-28 18:01:30,580] [INFO] Running command: blastn -query GCA_020446595.1_ASM2044659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg430ff433-9af5-47e4-a416-06247f57a741/dqc_reference/reference_markers.fasta -out GCA_020446595.1_ASM2044659v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:01:31,327] [INFO] Task succeeded: Blastn
[2023-06-28 18:01:31,332] [INFO] Selected 23 target genomes.
[2023-06-28 18:01:31,333] [INFO] Target genome list was writen to GCA_020446595.1_ASM2044659v1_genomic.fna/target_genomes.txt
[2023-06-28 18:01:31,334] [INFO] Task started: fastANI
[2023-06-28 18:01:31,334] [INFO] Running command: fastANI --query /var/lib/cwl/stgda64a3c0-dc99-41b9-8c60-44c9e9b1ec81/GCA_020446595.1_ASM2044659v1_genomic.fna.gz --refList GCA_020446595.1_ASM2044659v1_genomic.fna/target_genomes.txt --output GCA_020446595.1_ASM2044659v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:01:45,501] [INFO] Task succeeded: fastANI
[2023-06-28 18:01:45,502] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg430ff433-9af5-47e4-a416-06247f57a741/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:01:45,502] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg430ff433-9af5-47e4-a416-06247f57a741/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:01:45,528] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:01:45,529] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 18:01:45,529] [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 colocasiae	strain=KCTC 32255	GCA_014652555.1	1256513	1256513	type	True	77.927	225	841	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	77.8661	217	841	95	below_threshold
Novosphingobium marinum	strain=DSM 29043	GCA_013408095.1	1514948	1514948	type	True	77.8314	214	841	95	below_threshold
Novosphingobium marinum	strain=CGMCC 1.12918	GCA_014640055.1	1514948	1514948	type	True	77.8171	215	841	95	below_threshold
Novosphingobium mathurense	strain=SM117	GCA_900168325.1	428990	428990	type	True	77.8044	225	841	95	below_threshold
Novosphingobium piscinae	strain=KCTC 42194	GCA_014230355.1	1507448	1507448	type	True	77.7955	221	841	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	77.7738	228	841	95	below_threshold
Novosphingobium flavum	strain=NBRC 111647	GCA_014230315.1	1778672	1778672	type	True	77.6745	212	841	95	below_threshold
Novosphingobium fuchskuhlense	strain=FNE08-7	GCA_001519075.1	1117702	1117702	type	True	77.5581	180	841	95	below_threshold
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	77.531	208	841	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	77.5229	165	841	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	77.4989	199	841	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	77.4594	161	841	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	77.1893	180	841	95	below_threshold
Novosphingobium guangzhouense	strain=SA925	GCA_002896965.1	1850347	1850347	type	True	77.1487	201	841	95	below_threshold
Tsuneonella rigui	strain=KCTC 42620	GCA_003958625.1	1708790	1708790	type	True	77.1255	155	841	95	below_threshold
Pelagerythrobacter marensis	strain=KCTC 22370	GCA_001028625.1	543877	543877	type	True	77.1196	137	841	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	77.082	156	841	95	below_threshold
Pelagerythrobacter marensis	strain=DSM 21428	GCA_001461885.1	543877	543877	type	True	77.054	139	841	95	below_threshold
Aurantiacibacter odishensis	strain=KCTC 23981	GCA_003605195.1	1155476	1155476	type	True	76.9392	154	841	95	below_threshold
Tsuneonella amylolytica	strain=NS1	GCA_003626915.1	2338327	2338327	type	True	76.9079	163	841	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	76.7891	157	841	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	76.7378	148	841	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 18:01:45,532] [INFO] DFAST Taxonomy check result was written to GCA_020446595.1_ASM2044659v1_genomic.fna/tc_result.tsv
[2023-06-28 18:01:45,532] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:01:45,533] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:01:45,533] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg430ff433-9af5-47e4-a416-06247f57a741/dqc_reference/checkm_data
[2023-06-28 18:01:45,534] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:01:45,566] [INFO] Task started: CheckM
[2023-06-28 18:01:45,567] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020446595.1_ASM2044659v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020446595.1_ASM2044659v1_genomic.fna/checkm_input GCA_020446595.1_ASM2044659v1_genomic.fna/checkm_result
[2023-06-28 18:02:13,209] [INFO] Task succeeded: CheckM
[2023-06-28 18:02:13,211] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 46.30%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:02:13,237] [INFO] ===== Completeness check finished =====
[2023-06-28 18:02:13,237] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:02:13,238] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020446595.1_ASM2044659v1_genomic.fna/markers.fasta)
[2023-06-28 18:02:13,238] [INFO] Task started: Blastn
[2023-06-28 18:02:13,238] [INFO] Running command: blastn -query GCA_020446595.1_ASM2044659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg430ff433-9af5-47e4-a416-06247f57a741/dqc_reference/reference_markers_gtdb.fasta -out GCA_020446595.1_ASM2044659v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:02:14,496] [INFO] Task succeeded: Blastn
[2023-06-28 18:02:14,501] [INFO] Selected 23 target genomes.
[2023-06-28 18:02:14,501] [INFO] Target genome list was writen to GCA_020446595.1_ASM2044659v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:02:14,531] [INFO] Task started: fastANI
[2023-06-28 18:02:14,531] [INFO] Running command: fastANI --query /var/lib/cwl/stgda64a3c0-dc99-41b9-8c60-44c9e9b1ec81/GCA_020446595.1_ASM2044659v1_genomic.fna.gz --refList GCA_020446595.1_ASM2044659v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020446595.1_ASM2044659v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:02:29,183] [INFO] Task succeeded: fastANI
[2023-06-28 18:02:29,205] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 18:02:29,206] [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_002556635.1	s__Novosphingobium sp002556635	78.3585	300	841	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113255.1	s__Novosphingobium sp900113255	78.0434	233	841	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506425.1	s__Novosphingobium sp902506425	77.9327	206	841	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652555.1	s__Novosphingobium colocasiae	77.927	225	841	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	77.8577	208	841	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408095.1	s__Novosphingobium marinum	77.8002	216	841	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001298105.1	s__Novosphingobium sp001298105	77.7877	233	841	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.11	98.61	0.92	0.87	4	-
GCF_014204535.1	s__Novosphingobium chloroacetimidivorans	77.7666	213	841	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009746585.1	s__Novosphingobium sp009746585	77.7617	229	841	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002337385.1	s__Alteraurantiacibacter sp002337385	77.67	177	841	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719755.1	s__Novosphingobium sp016719755	77.6238	240	841	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.59	99.59	0.90	0.90	2	-
GCF_014652615.1	s__Novosphingobium arvoryzae	77.5159	209	841	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135625.1	s__Pelagerythrobacter rhizovicinus	77.4594	161	841	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001725355.1	s__Novosphingobium sp001725355	77.4121	198	841	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002279825.1	s__Croceibacterium sp002279825	77.3875	160	841	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	99.89	99.89	0.97	0.97	2	-
GCF_003569745.1	s__Croceibacterium sp003569745	77.368	173	841	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018971065.1	s__Novosphingobium sp018971065	77.2535	202	841	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018828205.1	s__Qipengyuania sp018828205	77.2494	154	841	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827515.1	s__Pelagerythrobacter marinus	77.1582	182	841	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003958625.1	s__Tsuneonella rigui	77.1255	155	841	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822005.1	s__Novosphingobium sp013822005	77.0839	158	841	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827295.1	s__Qipengyuania pelagi	77.082	156	841	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012979275.1	s__Pseudopontixanthobacter vadosimaris	76.8236	133	841	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pseudopontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 18:02:29,208] [INFO] GTDB search result was written to GCA_020446595.1_ASM2044659v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:02:29,208] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:02:29,214] [INFO] DFAST_QC result json was written to GCA_020446595.1_ASM2044659v1_genomic.fna/dqc_result.json
[2023-06-28 18:02:29,215] [INFO] DFAST_QC completed!
[2023-06-28 18:02:29,215] [INFO] Total running time: 0h1m8s