[2023-06-28 13:41:11,219] [INFO] DFAST_QC pipeline started.
[2023-06-28 13:41:11,221] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 13:41:11,221] [INFO] DQC Reference Directory: /var/lib/cwl/stg6990a8d9-1fc9-44bc-be34-baec2d667288/dqc_reference
[2023-06-28 13:41:12,418] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 13:41:12,419] [INFO] Task started: Prodigal
[2023-06-28 13:41:12,420] [INFO] Running command: gunzip -c /var/lib/cwl/stgd5c8694a-b33a-4b03-9c3e-db98dcf4e10f/GCA_020446565.1_ASM2044656v1_genomic.fna.gz | prodigal -d GCA_020446565.1_ASM2044656v1_genomic.fna/cds.fna -a GCA_020446565.1_ASM2044656v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 13:41:23,484] [INFO] Task succeeded: Prodigal
[2023-06-28 13:41:23,484] [INFO] Task started: HMMsearch
[2023-06-28 13:41:23,484] [INFO] Running command: hmmsearch --tblout GCA_020446565.1_ASM2044656v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6990a8d9-1fc9-44bc-be34-baec2d667288/dqc_reference/reference_markers.hmm GCA_020446565.1_ASM2044656v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 13:41:23,693] [INFO] Task succeeded: HMMsearch
[2023-06-28 13:41:23,694] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd5c8694a-b33a-4b03-9c3e-db98dcf4e10f/GCA_020446565.1_ASM2044656v1_genomic.fna.gz]
[2023-06-28 13:41:23,729] [INFO] Query marker FASTA was written to GCA_020446565.1_ASM2044656v1_genomic.fna/markers.fasta
[2023-06-28 13:41:23,729] [INFO] Task started: Blastn
[2023-06-28 13:41:23,729] [INFO] Running command: blastn -query GCA_020446565.1_ASM2044656v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6990a8d9-1fc9-44bc-be34-baec2d667288/dqc_reference/reference_markers.fasta -out GCA_020446565.1_ASM2044656v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:41:24,514] [INFO] Task succeeded: Blastn
[2023-06-28 13:41:24,518] [INFO] Selected 21 target genomes.
[2023-06-28 13:41:24,519] [INFO] Target genome list was writen to GCA_020446565.1_ASM2044656v1_genomic.fna/target_genomes.txt
[2023-06-28 13:41:24,520] [INFO] Task started: fastANI
[2023-06-28 13:41:24,520] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5c8694a-b33a-4b03-9c3e-db98dcf4e10f/GCA_020446565.1_ASM2044656v1_genomic.fna.gz --refList GCA_020446565.1_ASM2044656v1_genomic.fna/target_genomes.txt --output GCA_020446565.1_ASM2044656v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 13:41:39,743] [INFO] Task succeeded: fastANI
[2023-06-28 13:41:39,743] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6990a8d9-1fc9-44bc-be34-baec2d667288/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 13:41:39,744] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6990a8d9-1fc9-44bc-be34-baec2d667288/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 13:41:39,760] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 13:41:39,760] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 13:41:39,760] [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 naphthalenivorans	strain=NBRC 102051	GCA_001590985.1	273168	273168	type	True	78.663	337	1303	95	below_threshold
Novosphingobium endophyticum	strain=CGMCC 1.15095	GCA_014640675.1	1955250	1955250	type	True	78.5296	387	1303	95	below_threshold
Novosphingobium marinum	strain=CGMCC 1.12918	GCA_014640055.1	1514948	1514948	type	True	78.4728	317	1303	95	below_threshold
Novosphingobium marinum	strain=DSM 29043	GCA_013408095.1	1514948	1514948	type	True	78.4469	322	1303	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	78.2537	324	1303	95	below_threshold
Novosphingobium flavum	strain=NBRC 111647	GCA_014230315.1	1778672	1778672	type	True	78.1591	324	1303	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	78.1472	331	1303	95	below_threshold
Novosphingobium piscinae	strain=KCTC 42194	GCA_014230355.1	1507448	1507448	type	True	78.1366	320	1303	95	below_threshold
Novosphingobium malaysiense	strain=MUSC 273	GCA_000802225.1	1348853	1348853	type	True	78.098	400	1303	95	below_threshold
Novosphingobium aerophilum	strain=4Y4	GCA_014230305.1	2839843	2839843	type	True	78.0475	338	1303	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	78.001	318	1303	95	below_threshold
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	77.9611	310	1303	95	below_threshold
Novosphingobium aureum	strain=YJ-S2-02	GCA_015865035.1	2792964	2792964	type	True	77.8742	333	1303	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	77.7004	287	1303	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	77.6669	274	1303	95	below_threshold
Novosphingobium profundi	strain=F72	GCA_018491765.1	1774954	1774954	type	True	77.6658	307	1303	95	below_threshold
Novosphingobium pokkalii	strain=KCTC 42224	GCA_014652855.1	1770194	1770194	type	True	77.6298	283	1303	95	below_threshold
Novosphingobium silvae	strain=FGD1	GCA_009856825.1	2692619	2692619	type	True	77.5938	315	1303	95	below_threshold
Novosphingobium nitrogenifigens	strain=DSM 19370	GCA_000375445.1	378548	378548	type	True	77.214	232	1303	95	below_threshold
Sphingomonas desiccabilis	strain=CP1D	GCA_004135605.1	429134	429134	type	True	76.8474	176	1303	95	below_threshold
Sphingomonas colocasiae	strain=JCM 31229	GCA_019880585.1	1848973	1848973	type	True	76.6503	238	1303	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 13:41:39,762] [INFO] DFAST Taxonomy check result was written to GCA_020446565.1_ASM2044656v1_genomic.fna/tc_result.tsv
[2023-06-28 13:41:39,763] [INFO] ===== Taxonomy check completed =====
[2023-06-28 13:41:39,763] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 13:41:39,763] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6990a8d9-1fc9-44bc-be34-baec2d667288/dqc_reference/checkm_data
[2023-06-28 13:41:39,764] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 13:41:39,804] [INFO] Task started: CheckM
[2023-06-28 13:41:39,804] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020446565.1_ASM2044656v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020446565.1_ASM2044656v1_genomic.fna/checkm_input GCA_020446565.1_ASM2044656v1_genomic.fna/checkm_result
[2023-06-28 13:42:15,475] [INFO] Task succeeded: CheckM
[2023-06-28 13:42:15,476] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.34%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 13:42:15,495] [INFO] ===== Completeness check finished =====
[2023-06-28 13:42:15,495] [INFO] ===== Start GTDB Search =====
[2023-06-28 13:42:15,496] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020446565.1_ASM2044656v1_genomic.fna/markers.fasta)
[2023-06-28 13:42:15,496] [INFO] Task started: Blastn
[2023-06-28 13:42:15,496] [INFO] Running command: blastn -query GCA_020446565.1_ASM2044656v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6990a8d9-1fc9-44bc-be34-baec2d667288/dqc_reference/reference_markers_gtdb.fasta -out GCA_020446565.1_ASM2044656v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:42:16,885] [INFO] Task succeeded: Blastn
[2023-06-28 13:42:16,889] [INFO] Selected 24 target genomes.
[2023-06-28 13:42:16,889] [INFO] Target genome list was writen to GCA_020446565.1_ASM2044656v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 13:42:16,892] [INFO] Task started: fastANI
[2023-06-28 13:42:16,892] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5c8694a-b33a-4b03-9c3e-db98dcf4e10f/GCA_020446565.1_ASM2044656v1_genomic.fna.gz --refList GCA_020446565.1_ASM2044656v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020446565.1_ASM2044656v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 13:42:34,050] [INFO] Task succeeded: fastANI
[2023-06-28 13:42:34,069] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 13:42:34,069] [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	78.8463	456	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001590985.1	s__Novosphingobium naphthalenivorans	78.6635	337	1303	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	78.6381	441	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640675.1	s__Novosphingobium endophyticum	78.5286	387	1303	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	78.459	321	1303	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	78.2121	306	1303	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	78.172	325	1303	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	78.1579	324	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014230355.1	s__Novosphingobium piscinae	78.1439	320	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000802225.1	s__Novosphingobium malaysiense	78.1162	398	1303	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	78.1114	352	1303	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	77.9998	323	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204535.1	s__Novosphingobium chloroacetimidivorans	77.9909	345	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007993975.1	s__Novosphingobium barchaimii_B	77.8886	336	1303	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	77.8371	295	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002855555.1	s__Novosphingobium sp002855555	77.8213	331	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015661825.1	s__Novosphingobium capsulatum_A	77.6725	243	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018491765.1	s__Novosphingobium profundi	77.6658	307	1303	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	77.5506	353	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001742225.1	s__Novosphingobium resinovorum	77.541	369	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.22	97.83	0.80	0.78	4	-
GCF_015999305.1	s__Alteriqipengyuania sp015999305	77.2788	231	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001519065.1	s__Novosphingobium sp001519065	77.0082	213	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003240855.1	s__Sphingomonas_L sanxanigenens_A	76.8469	183	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135605.1	s__Sphingomonas desiccabilis	76.8318	177	1303	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-28 13:42:34,071] [INFO] GTDB search result was written to GCA_020446565.1_ASM2044656v1_genomic.fna/result_gtdb.tsv
[2023-06-28 13:42:34,072] [INFO] ===== GTDB Search completed =====
[2023-06-28 13:42:34,076] [INFO] DFAST_QC result json was written to GCA_020446565.1_ASM2044656v1_genomic.fna/dqc_result.json
[2023-06-28 13:42:34,077] [INFO] DFAST_QC completed!
[2023-06-28 13:42:34,077] [INFO] Total running time: 0h1m23s