[2024-01-24 11:59:22,958] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:22,960] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:22,961] [INFO] DQC Reference Directory: /var/lib/cwl/stg4498fbba-a92a-41e5-9c57-4f2cdb9e05cf/dqc_reference
[2024-01-24 11:59:25,640] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:25,641] [INFO] Task started: Prodigal
[2024-01-24 11:59:25,641] [INFO] Running command: gunzip -c /var/lib/cwl/stgaad959fa-1017-4d5e-a3e9-b7f857df45b0/GCF_020179475.1_ASM2017947v1_genomic.fna.gz | prodigal -d GCF_020179475.1_ASM2017947v1_genomic.fna/cds.fna -a GCF_020179475.1_ASM2017947v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:36,153] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:36,154] [INFO] Task started: HMMsearch
[2024-01-24 11:59:36,154] [INFO] Running command: hmmsearch --tblout GCF_020179475.1_ASM2017947v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4498fbba-a92a-41e5-9c57-4f2cdb9e05cf/dqc_reference/reference_markers.hmm GCF_020179475.1_ASM2017947v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:36,405] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:36,407] [INFO] Found 6/6 markers.
[2024-01-24 11:59:36,448] [INFO] Query marker FASTA was written to GCF_020179475.1_ASM2017947v1_genomic.fna/markers.fasta
[2024-01-24 11:59:36,448] [INFO] Task started: Blastn
[2024-01-24 11:59:36,449] [INFO] Running command: blastn -query GCF_020179475.1_ASM2017947v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4498fbba-a92a-41e5-9c57-4f2cdb9e05cf/dqc_reference/reference_markers.fasta -out GCF_020179475.1_ASM2017947v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:37,506] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:37,510] [INFO] Selected 13 target genomes.
[2024-01-24 11:59:37,510] [INFO] Target genome list was writen to GCF_020179475.1_ASM2017947v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:37,522] [INFO] Task started: fastANI
[2024-01-24 11:59:37,522] [INFO] Running command: fastANI --query /var/lib/cwl/stgaad959fa-1017-4d5e-a3e9-b7f857df45b0/GCF_020179475.1_ASM2017947v1_genomic.fna.gz --refList GCF_020179475.1_ASM2017947v1_genomic.fna/target_genomes.txt --output GCF_020179475.1_ASM2017947v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:48,834] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:48,835] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4498fbba-a92a-41e5-9c57-4f2cdb9e05cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:48,835] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4498fbba-a92a-41e5-9c57-4f2cdb9e05cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:48,847] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:48,847] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:48,848] [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 huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	100.0	1214	1214	95	conclusive
Novosphingobium olei	strain=TW-4	GCA_012927405.1	2728851	2728851	type	True	87.3873	925	1214	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	85.4927	906	1214	95	below_threshold
Novosphingobium jiangmenense	strain=1Y9A	GCA_015694345.1	2791981	2791981	type	True	81.7225	675	1214	95	below_threshold
Novosphingobium aromaticivorans	strain=DSM 12444	GCA_000013325.1	48935	48935	type	True	81.7078	628	1214	95	below_threshold
Novosphingobium subterraneum	strain=DSM 12447	GCA_000807925.1	48936	48936	type	True	81.0329	632	1214	95	below_threshold
Novosphingobium lentum	strain=NBRC 107847	GCA_001590965.1	145287	145287	type	True	80.9191	640	1214	95	below_threshold
Novosphingobium fuchskuhlense	strain=FNE08-7	GCA_001519075.1	1117702	1117702	type	True	80.9025	622	1214	95	below_threshold
Novosphingobium sediminis	strain=NBRC 106119	GCA_007991615.1	707214	707214	type	True	80.8043	647	1214	95	below_threshold
Novosphingobium meiothermophilum	strain=SYSU G00007	GCA_003171715.1	2202251	2202251	type	True	80.2316	547	1214	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	79.3435	478	1214	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	79.2743	461	1214	95	below_threshold
Novosphingobium silvae	strain=FGD1	GCA_009856825.1	2692619	2692619	type	True	79.1787	451	1214	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:49,008] [INFO] DFAST Taxonomy check result was written to GCF_020179475.1_ASM2017947v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:49,009] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:49,009] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:49,010] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4498fbba-a92a-41e5-9c57-4f2cdb9e05cf/dqc_reference/checkm_data
[2024-01-24 11:59:49,012] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:49,055] [INFO] Task started: CheckM
[2024-01-24 11:59:49,055] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020179475.1_ASM2017947v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020179475.1_ASM2017947v1_genomic.fna/checkm_input GCF_020179475.1_ASM2017947v1_genomic.fna/checkm_result
[2024-01-24 12:00:24,083] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:24,084] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:24,107] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:24,108] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:24,109] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020179475.1_ASM2017947v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:24,110] [INFO] Task started: Blastn
[2024-01-24 12:00:24,110] [INFO] Running command: blastn -query GCF_020179475.1_ASM2017947v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4498fbba-a92a-41e5-9c57-4f2cdb9e05cf/dqc_reference/reference_markers_gtdb.fasta -out GCF_020179475.1_ASM2017947v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:26,164] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:26,169] [INFO] Selected 16 target genomes.
[2024-01-24 12:00:26,169] [INFO] Target genome list was writen to GCF_020179475.1_ASM2017947v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:26,184] [INFO] Task started: fastANI
[2024-01-24 12:00:26,184] [INFO] Running command: fastANI --query /var/lib/cwl/stgaad959fa-1017-4d5e-a3e9-b7f857df45b0/GCF_020179475.1_ASM2017947v1_genomic.fna.gz --refList GCF_020179475.1_ASM2017947v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020179475.1_ASM2017947v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:39,752] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:39,770] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:00:39,771] [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_012927405.1	s__Novosphingobium olei	87.3873	925	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005145025.1	s__Novosphingobium sp005145025	81.9211	671	1214	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	81.7957	668	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.66	97.51	0.82	0.80	4	-
GCF_015694345.1	s__Novosphingobium jiangmenense	81.7408	674	1214	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	81.7106	628	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001725355.1	s__Novosphingobium sp001725355	81.6369	609	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003454795.1	s__Novosphingobium sp003454795	81.3934	645	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.02	97.88	0.92	0.91	3	-
GCF_900117425.1	s__Novosphingobium sp900117425	81.2228	676	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.26	96.76	0.88	0.87	3	-
GCF_007830315.1	s__Novosphingobium taihuense	81.0932	638	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000807925.1	s__Novosphingobium subterraneum	81.0291	632	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.63	97.57	0.88	0.77	4	-
GCF_001590965.1	s__Novosphingobium lentum	80.934	638	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001519075.1	s__Novosphingobium fuchskuhlense	80.9275	619	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364785.1	s__Novosphingobium sp004364785	80.8517	614	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007991615.1	s__Novosphingobium sediminis	80.8139	646	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003171715.1	s__Novosphingobium meiothermophilum	80.2526	545	1214	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	79.9276	533	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:39,772] [INFO] GTDB search result was written to GCF_020179475.1_ASM2017947v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:39,773] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:39,778] [INFO] DFAST_QC result json was written to GCF_020179475.1_ASM2017947v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:39,778] [INFO] DFAST_QC completed!
[2024-01-24 12:00:39,779] [INFO] Total running time: 0h1m17s