[2024-01-24 14:19:14,895] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:14,897] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:14,897] [INFO] DQC Reference Directory: /var/lib/cwl/stg6afdb53c-0969-400e-90f7-7327a41fbf8c/dqc_reference
[2024-01-24 14:19:16,066] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:16,067] [INFO] Task started: Prodigal
[2024-01-24 14:19:16,067] [INFO] Running command: gunzip -c /var/lib/cwl/stg9cc78f14-5763-4286-aa89-9bde69befc0a/GCF_009769755.1_ASM976975v1_genomic.fna.gz | prodigal -d GCF_009769755.1_ASM976975v1_genomic.fna/cds.fna -a GCF_009769755.1_ASM976975v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:25,686] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:25,686] [INFO] Task started: HMMsearch
[2024-01-24 14:19:25,687] [INFO] Running command: hmmsearch --tblout GCF_009769755.1_ASM976975v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6afdb53c-0969-400e-90f7-7327a41fbf8c/dqc_reference/reference_markers.hmm GCF_009769755.1_ASM976975v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:25,890] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:25,891] [INFO] Found 6/6 markers.
[2024-01-24 14:19:25,919] [INFO] Query marker FASTA was written to GCF_009769755.1_ASM976975v1_genomic.fna/markers.fasta
[2024-01-24 14:19:25,919] [INFO] Task started: Blastn
[2024-01-24 14:19:25,919] [INFO] Running command: blastn -query GCF_009769755.1_ASM976975v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6afdb53c-0969-400e-90f7-7327a41fbf8c/dqc_reference/reference_markers.fasta -out GCF_009769755.1_ASM976975v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:26,648] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:26,651] [INFO] Selected 18 target genomes.
[2024-01-24 14:19:26,652] [INFO] Target genome list was writen to GCF_009769755.1_ASM976975v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:26,658] [INFO] Task started: fastANI
[2024-01-24 14:19:26,658] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cc78f14-5763-4286-aa89-9bde69befc0a/GCF_009769755.1_ASM976975v1_genomic.fna.gz --refList GCF_009769755.1_ASM976975v1_genomic.fna/target_genomes.txt --output GCF_009769755.1_ASM976975v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:37,197] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:37,198] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6afdb53c-0969-400e-90f7-7327a41fbf8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:37,198] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6afdb53c-0969-400e-90f7-7327a41fbf8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:37,212] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:19:37,213] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:37,213] [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
Sphingorhabdus profundilacus	strain=IMCC26285	GCA_009769755.1	2509718	2509718	type	True	100.0	968	968	95	conclusive
Sphingorhabdus lacus	strain=IMCC1753	GCA_009768975.1	392610	392610	type	True	85.1742	631	968	95	below_threshold
Sphingorhabdus contaminans	strain=KCTC32445	GCA_007280415.1	1343899	1343899	type	True	82.4915	596	968	95	below_threshold
Sphingorhabdus rigui	strain=DSM 29050	GCA_014196595.1	1282858	1282858	type	True	78.7544	341	968	95	below_threshold
Sphingorhabdus wooponensis	strain=03SU3-P	GCA_003933235.1	940136	940136	type	True	78.5233	290	968	95	below_threshold
Sphingorhabdus pulchriflava	strain=GY_G	GCA_003367235.1	2292257	2292257	type	True	78.1022	248	968	95	below_threshold
Sphingobium cloacae	strain=JCM 10874	GCA_002355855.1	120107	120107	type	True	77.1654	123	968	95	below_threshold
Sphingobium sufflavum	strain=HL-25	GCA_021403115.1	1129547	1129547	type	True	77.0576	117	968	95	below_threshold
Sphingomonas koreensis	strain=NBRC 16723	GCA_001598395.1	93064	93064	type	True	77.0211	93	968	95	below_threshold
Sphingopyxis indica	strain=DS15	GCA_900188185.1	436663	436663	type	True	76.9621	146	968	95	below_threshold
Sphingomonas colocasiae	strain=JCM 31229	GCA_019880585.1	1848973	1848973	type	True	76.9552	136	968	95	below_threshold
Novosphingopyxis baekryungensis	strain=DSM 16222	GCA_000420305.1	279369	279369	type	True	76.7853	142	968	95	below_threshold
Sphingomicrobium astaxanthinifaciens	strain=JCM 18551	GCA_022865105.1	1227949	1227949	type	True	76.781	60	968	95	below_threshold
Novosphingobium umbonatum	strain=FSY-9	GCA_004005905.1	1908524	1908524	type	True	76.7595	119	968	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	76.7204	94	968	95	below_threshold
Novosphingobium pokkalii	strain=KCTC 42224	GCA_014652855.1	1770194	1770194	type	True	76.5223	110	968	95	below_threshold
Sphingomonas desiccabilis	strain=DSM 16792	GCA_014196135.1	429134	429134	type	True	76.4997	82	968	95	below_threshold
Sphingomonas desiccabilis	strain=CP1D	GCA_004135605.1	429134	429134	type	True	76.4764	83	968	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:37,214] [INFO] DFAST Taxonomy check result was written to GCF_009769755.1_ASM976975v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:37,215] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:37,215] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:37,215] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6afdb53c-0969-400e-90f7-7327a41fbf8c/dqc_reference/checkm_data
[2024-01-24 14:19:37,217] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:37,245] [INFO] Task started: CheckM
[2024-01-24 14:19:37,246] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009769755.1_ASM976975v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009769755.1_ASM976975v1_genomic.fna/checkm_input GCF_009769755.1_ASM976975v1_genomic.fna/checkm_result
[2024-01-24 14:20:10,430] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:10,431] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:10,450] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:10,451] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:10,451] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009769755.1_ASM976975v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:10,451] [INFO] Task started: Blastn
[2024-01-24 14:20:10,452] [INFO] Running command: blastn -query GCF_009769755.1_ASM976975v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6afdb53c-0969-400e-90f7-7327a41fbf8c/dqc_reference/reference_markers_gtdb.fasta -out GCF_009769755.1_ASM976975v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:11,822] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:11,832] [INFO] Selected 14 target genomes.
[2024-01-24 14:20:11,832] [INFO] Target genome list was writen to GCF_009769755.1_ASM976975v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:11,852] [INFO] Task started: fastANI
[2024-01-24 14:20:11,853] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cc78f14-5763-4286-aa89-9bde69befc0a/GCF_009769755.1_ASM976975v1_genomic.fna.gz --refList GCF_009769755.1_ASM976975v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009769755.1_ASM976975v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:20,562] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:20,577] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:20,577] [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_009769755.1	s__Sphingorhabdus_B profundilacus	100.0	968	968	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009768975.1	s__Sphingorhabdus_B lacus	85.165	631	968	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823985.1	s__Sphingorhabdus_B sp013823985	83.1003	604	968	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007280415.1	s__Sphingorhabdus_B contaminans	82.498	595	968	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002282385.1	s__Sphingorhabdus_B sp002282385	78.763	335	968	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	99.98	99.95	0.99	0.98	4	-
GCF_014196595.1	s__Sphingorhabdus_B rigui	78.7421	342	968	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464315.1	s__Sphingorhabdus_B sp001464315	78.6681	351	968	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016742125.1	s__Sphingorhabdus_B sp016742125	78.5836	350	968	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016462305.1	s__Sphingorhabdus_B sp016462305	78.4162	244	968	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	98.63	98.63	0.82	0.82	2	-
GCA_002255985.1	s__Sphingorhabdus_B sp002255985	78.1716	338	968	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	98.49	98.44	0.89	0.89	3	-
GCA_903821685.1	s__Sphingorhabdus_B sp903821685	78.04	263	968	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	99.60	99.60	0.86	0.86	2	-
GCA_017987825.1	s__Sphingorhabdus_B sp017987825	77.6386	191	968	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013374095.1	s__Sphingomonas sp013374095	77.1421	107	968	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000251145.1	s__Sphingomonas sp000251145	76.3942	95	968	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.28	96.28	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:20,579] [INFO] GTDB search result was written to GCF_009769755.1_ASM976975v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:20,580] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:20,584] [INFO] DFAST_QC result json was written to GCF_009769755.1_ASM976975v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:20,585] [INFO] DFAST_QC completed!
[2024-01-24 14:20:20,585] [INFO] Total running time: 0h1m6s