[2023-06-19 08:42:21,708] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:42:21,729] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:42:21,729] [INFO] DQC Reference Directory: /var/lib/cwl/stgc459cc3c-456a-433d-893b-fe8b858b3f10/dqc_reference
[2023-06-19 08:42:26,554] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:42:26,555] [INFO] Task started: Prodigal
[2023-06-19 08:42:26,555] [INFO] Running command: gunzip -c /var/lib/cwl/stg08f62b3b-5e07-4cc1-b142-385efa0d6935/GCA_018900435.1_ASM1890043v1_genomic.fna.gz | prodigal -d GCA_018900435.1_ASM1890043v1_genomic.fna/cds.fna -a GCA_018900435.1_ASM1890043v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:42:35,525] [INFO] Task succeeded: Prodigal
[2023-06-19 08:42:35,526] [INFO] Task started: HMMsearch
[2023-06-19 08:42:35,526] [INFO] Running command: hmmsearch --tblout GCA_018900435.1_ASM1890043v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc459cc3c-456a-433d-893b-fe8b858b3f10/dqc_reference/reference_markers.hmm GCA_018900435.1_ASM1890043v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:42:35,940] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:42:35,942] [INFO] Found 6/6 markers.
[2023-06-19 08:42:36,002] [INFO] Query marker FASTA was written to GCA_018900435.1_ASM1890043v1_genomic.fna/markers.fasta
[2023-06-19 08:42:36,002] [INFO] Task started: Blastn
[2023-06-19 08:42:36,002] [INFO] Running command: blastn -query GCA_018900435.1_ASM1890043v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc459cc3c-456a-433d-893b-fe8b858b3f10/dqc_reference/reference_markers.fasta -out GCA_018900435.1_ASM1890043v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:42:39,722] [INFO] Task succeeded: Blastn
[2023-06-19 08:42:39,728] [INFO] Selected 21 target genomes.
[2023-06-19 08:42:39,729] [INFO] Target genome list was writen to GCA_018900435.1_ASM1890043v1_genomic.fna/target_genomes.txt
[2023-06-19 08:42:39,737] [INFO] Task started: fastANI
[2023-06-19 08:42:39,737] [INFO] Running command: fastANI --query /var/lib/cwl/stg08f62b3b-5e07-4cc1-b142-385efa0d6935/GCA_018900435.1_ASM1890043v1_genomic.fna.gz --refList GCA_018900435.1_ASM1890043v1_genomic.fna/target_genomes.txt --output GCA_018900435.1_ASM1890043v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:42:55,923] [INFO] Task succeeded: fastANI
[2023-06-19 08:42:55,924] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc459cc3c-456a-433d-893b-fe8b858b3f10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:42:55,924] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc459cc3c-456a-433d-893b-fe8b858b3f10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:42:55,957] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:42:55,957] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 08:42:55,958] [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 piscinae	strain=KCTC 42194	GCA_014230355.1	1507448	1507448	type	True	80.7106	441	948	95	below_threshold
Novosphingobium flavum	strain=NBRC 111647	GCA_014230315.1	1778672	1778672	type	True	80.6801	490	948	95	below_threshold
Novosphingobium aerophilum	strain=4Y4	GCA_014230305.1	2839843	2839843	type	True	80.6569	441	948	95	below_threshold
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	79.7152	408	948	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	79.47	399	948	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	79.4482	405	948	95	below_threshold
Novosphingobium naphthalenivorans	strain=NBRC 102051	GCA_001590985.1	273168	273168	type	True	79.3671	397	948	95	below_threshold
Novosphingobium olei	strain=TW-4	GCA_012927405.1	2728851	2728851	type	True	79.3071	385	948	95	below_threshold
Novosphingobium kunmingense	strain=CGMCC 1.12274	GCA_002813245.1	1211806	1211806	type	True	79.0805	381	948	95	below_threshold
Novosphingobium colocasiae	strain=KCTC 32255	GCA_014652555.1	1256513	1256513	type	True	79.0299	389	948	95	below_threshold
Novosphingobium taihuense	strain=DSM 17507	GCA_014199635.1	260085	260085	type	True	79.0286	356	948	95	below_threshold
Novosphingobium aromaticivorans	strain=DSM 12444	GCA_000013325.1	48935	48935	type	True	78.9804	359	948	95	below_threshold
Novosphingobium ginsenosidimutans	strain=FW-6	GCA_007954425.1	1176536	1176536	type	True	78.7353	338	948	95	below_threshold
Novosphingobium aureum	strain=YJ-S2-02	GCA_015865035.1	2792964	2792964	type	True	78.6742	332	948	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	78.5859	342	948	95	below_threshold
Novosphingobium profundi	strain=F72	GCA_018491765.1	1774954	1774954	type	True	78.4875	341	948	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	78.4517	314	948	95	below_threshold
Tsuneonella amylolytica	strain=NS1	GCA_003626915.1	2338327	2338327	type	True	78.2878	270	948	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	78.2524	255	948	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	78.1379	318	948	95	below_threshold
Novosphingobium umbonatum	strain=FSY-9	GCA_004005905.1	1908524	1908524	type	True	77.7284	221	948	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 08:42:55,963] [INFO] DFAST Taxonomy check result was written to GCA_018900435.1_ASM1890043v1_genomic.fna/tc_result.tsv
[2023-06-19 08:42:55,964] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:42:55,965] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:42:55,965] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc459cc3c-456a-433d-893b-fe8b858b3f10/dqc_reference/checkm_data
[2023-06-19 08:42:55,967] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:42:56,014] [INFO] Task started: CheckM
[2023-06-19 08:42:56,014] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018900435.1_ASM1890043v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018900435.1_ASM1890043v1_genomic.fna/checkm_input GCA_018900435.1_ASM1890043v1_genomic.fna/checkm_result
[2023-06-19 08:43:29,290] [INFO] Task succeeded: CheckM
[2023-06-19 08:43:29,291] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.97%
Contamintation: 5.56%
Strain heterogeneity: 20.00%
--------------------------------------------------------------------------------
[2023-06-19 08:43:29,325] [INFO] ===== Completeness check finished =====
[2023-06-19 08:43:29,325] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:43:29,326] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018900435.1_ASM1890043v1_genomic.fna/markers.fasta)
[2023-06-19 08:43:29,326] [INFO] Task started: Blastn
[2023-06-19 08:43:29,326] [INFO] Running command: blastn -query GCA_018900435.1_ASM1890043v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc459cc3c-456a-433d-893b-fe8b858b3f10/dqc_reference/reference_markers_gtdb.fasta -out GCA_018900435.1_ASM1890043v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:43:30,943] [INFO] Task succeeded: Blastn
[2023-06-19 08:43:30,948] [INFO] Selected 18 target genomes.
[2023-06-19 08:43:30,948] [INFO] Target genome list was writen to GCA_018900435.1_ASM1890043v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:43:30,956] [INFO] Task started: fastANI
[2023-06-19 08:43:30,957] [INFO] Running command: fastANI --query /var/lib/cwl/stg08f62b3b-5e07-4cc1-b142-385efa0d6935/GCA_018900435.1_ASM1890043v1_genomic.fna.gz --refList GCA_018900435.1_ASM1890043v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018900435.1_ASM1890043v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:43:44,311] [INFO] Task succeeded: fastANI
[2023-06-19 08:43:44,327] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 08:43:44,327] [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
GCA_013791705.1	s__Novosphingobium sp013791705	99.7602	815	948	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.87	99.87	0.91	0.91	2	conclusive
GCF_014230355.1	s__Novosphingobium piscinae	80.7236	439	948	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014230315.1	s__Novosphingobium flavum	80.6931	490	948	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014230305.1	s__Novosphingobium aerophilum	80.6604	439	948	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.68	98.68	0.90	0.90	2	-
GCF_014652615.1	s__Novosphingobium arvoryzae	79.7274	407	948	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719755.1	s__Novosphingobium sp016719755	79.3922	393	948	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.59	99.59	0.90	0.90	2	-
GCA_001725355.1	s__Novosphingobium sp001725355	79.2769	376	948	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302615.1	s__Novosphingobium sp017302615	79.2752	374	948	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004211435.1	s__Novosphingobium sp004211435	79.1278	373	948	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002556635.1	s__Novosphingobium sp002556635	79.1045	395	948	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013325.1	s__Novosphingobium aromaticivorans	78.951	362	948	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007993975.1	s__Novosphingobium barchaimii_B	78.9377	352	948	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	78.9033	332	948	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018971065.1	s__Novosphingobium sp018971065	78.8775	332	948	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002198665.1	s__Novosphingobium sp002198665	78.7372	338	948	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	78.6742	332	948	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240895.1	s__Novosphingobium sp018240895	78.3411	293	948	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	78.1944	247	948	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 08:43:44,330] [INFO] GTDB search result was written to GCA_018900435.1_ASM1890043v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:43:44,331] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:43:44,336] [INFO] DFAST_QC result json was written to GCA_018900435.1_ASM1890043v1_genomic.fna/dqc_result.json
[2023-06-19 08:43:44,337] [INFO] DFAST_QC completed!
[2023-06-19 08:43:44,337] [INFO] Total running time: 0h1m23s