[2024-01-24 10:47:22,629] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:22,632] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:22,632] [INFO] DQC Reference Directory: /var/lib/cwl/stg2944ad58-02c2-4af1-899a-e49463292f25/dqc_reference
[2024-01-24 10:47:26,177] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:26,184] [INFO] Task started: Prodigal
[2024-01-24 10:47:26,184] [INFO] Running command: gunzip -c /var/lib/cwl/stgbcde3b95-f6a4-49dc-8151-0b612c1eb2ac/GCF_020179425.1_ASM2017942v1_genomic.fna.gz | prodigal -d GCF_020179425.1_ASM2017942v1_genomic.fna/cds.fna -a GCF_020179425.1_ASM2017942v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:39,338] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:39,338] [INFO] Task started: HMMsearch
[2024-01-24 10:47:39,339] [INFO] Running command: hmmsearch --tblout GCF_020179425.1_ASM2017942v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2944ad58-02c2-4af1-899a-e49463292f25/dqc_reference/reference_markers.hmm GCF_020179425.1_ASM2017942v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:39,609] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:39,611] [INFO] Found 6/6 markers.
[2024-01-24 10:47:39,654] [INFO] Query marker FASTA was written to GCF_020179425.1_ASM2017942v1_genomic.fna/markers.fasta
[2024-01-24 10:47:39,654] [INFO] Task started: Blastn
[2024-01-24 10:47:39,654] [INFO] Running command: blastn -query GCF_020179425.1_ASM2017942v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2944ad58-02c2-4af1-899a-e49463292f25/dqc_reference/reference_markers.fasta -out GCF_020179425.1_ASM2017942v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:40,606] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:40,609] [INFO] Selected 14 target genomes.
[2024-01-24 10:47:40,610] [INFO] Target genome list was writen to GCF_020179425.1_ASM2017942v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:40,616] [INFO] Task started: fastANI
[2024-01-24 10:47:40,616] [INFO] Running command: fastANI --query /var/lib/cwl/stgbcde3b95-f6a4-49dc-8151-0b612c1eb2ac/GCF_020179425.1_ASM2017942v1_genomic.fna.gz --refList GCF_020179425.1_ASM2017942v1_genomic.fna/target_genomes.txt --output GCF_020179425.1_ASM2017942v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:53,703] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:53,704] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2944ad58-02c2-4af1-899a-e49463292f25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:53,704] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2944ad58-02c2-4af1-899a-e49463292f25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:53,715] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:53,715] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:53,716] [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 percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	100.0	1415	1416	95	conclusive
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	85.3796	914	1416	95	below_threshold
Novosphingobium olei	strain=TW-4	GCA_012927405.1	2728851	2728851	type	True	85.2624	967	1416	95	below_threshold
Novosphingobium jiangmenense	strain=1Y9A	GCA_015694345.1	2791981	2791981	type	True	81.7402	688	1416	95	below_threshold
Novosphingobium aromaticivorans	strain=DSM 12444	GCA_000013325.1	48935	48935	type	True	81.4583	709	1416	95	below_threshold
Novosphingobium lentum	strain=NBRC 107847	GCA_001590965.1	145287	145287	type	True	81.2193	636	1416	95	below_threshold
Novosphingobium taihuense	strain=DSM 17507	GCA_014199635.1	260085	260085	type	True	81.0592	668	1416	95	below_threshold
Novosphingobium subterraneum	strain=DSM 12447	GCA_000807925.1	48936	48936	type	True	80.9515	677	1416	95	below_threshold
Novosphingobium subterraneum	strain=NBRC 16086	GCA_001598575.1	48936	48936	type	True	80.9204	665	1416	95	below_threshold
Novosphingobium capsulatum	strain=NBRC 12533	GCA_001598375.1	13688	13688	type	True	80.7638	657	1416	95	below_threshold
Novosphingobium fuchskuhlense	strain=FNE08-7	GCA_001519075.1	1117702	1117702	type	True	80.5981	649	1416	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	79.2144	460	1416	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	78.9467	437	1416	95	below_threshold
Novosphingobium silvae	strain=FGD1	GCA_009856825.1	2692619	2692619	type	True	78.9379	439	1416	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:53,717] [INFO] DFAST Taxonomy check result was written to GCF_020179425.1_ASM2017942v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:53,717] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:53,718] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:53,718] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2944ad58-02c2-4af1-899a-e49463292f25/dqc_reference/checkm_data
[2024-01-24 10:47:53,719] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:53,762] [INFO] Task started: CheckM
[2024-01-24 10:47:53,763] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020179425.1_ASM2017942v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020179425.1_ASM2017942v1_genomic.fna/checkm_input GCF_020179425.1_ASM2017942v1_genomic.fna/checkm_result
[2024-01-24 10:48:35,334] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:35,335] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:35,362] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:35,363] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:35,363] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020179425.1_ASM2017942v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:35,364] [INFO] Task started: Blastn
[2024-01-24 10:48:35,364] [INFO] Running command: blastn -query GCF_020179425.1_ASM2017942v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2944ad58-02c2-4af1-899a-e49463292f25/dqc_reference/reference_markers_gtdb.fasta -out GCF_020179425.1_ASM2017942v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:37,171] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:37,175] [INFO] Selected 16 target genomes.
[2024-01-24 10:48:37,175] [INFO] Target genome list was writen to GCF_020179425.1_ASM2017942v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:37,224] [INFO] Task started: fastANI
[2024-01-24 10:48:37,224] [INFO] Running command: fastANI --query /var/lib/cwl/stgbcde3b95-f6a4-49dc-8151-0b612c1eb2ac/GCF_020179425.1_ASM2017942v1_genomic.fna.gz --refList GCF_020179425.1_ASM2017942v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020179425.1_ASM2017942v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:52,114] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:52,134] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:48:52,134] [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	85.2737	966	1416	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001725355.1	s__Novosphingobium sp001725355	82.3087	659	1416	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	82.0888	684	1416	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.66	97.51	0.82	0.80	4	-
GCF_005145025.1	s__Novosphingobium sp005145025	82.0134	692	1416	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015694345.1	s__Novosphingobium jiangmenense	81.744	687	1416	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	81.6275	656	1416	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.02	97.88	0.92	0.91	3	-
GCF_000013325.1	s__Novosphingobium aromaticivorans	81.4494	709	1416	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014652855.1	s__Novosphingobium pokkalii	81.1641	659	1416	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176395.1	s__Novosphingobium sp900176395	81.0864	624	1416	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	81.0454	630	1416	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007830315.1	s__Novosphingobium taihuense	81.0175	670	1416	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900117425.1	s__Novosphingobium sp900117425	81.0007	668	1416	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.26	96.76	0.88	0.87	3	-
GCF_000807925.1	s__Novosphingobium subterraneum	80.9734	677	1416	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.63	97.57	0.88	0.77	4	-
GCF_012641335.1	s__Novosphingobium sp012641335	80.9109	630	1416	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196055.1	s__Novosphingobium hassiacum	80.9034	613	1416	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	80.5919	649	1416	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 10:48:52,136] [INFO] GTDB search result was written to GCF_020179425.1_ASM2017942v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:52,136] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:52,141] [INFO] DFAST_QC result json was written to GCF_020179425.1_ASM2017942v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:52,141] [INFO] DFAST_QC completed!
[2024-01-24 10:48:52,141] [INFO] Total running time: 0h1m30s