[2024-01-24 15:10:48,504] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:48,507] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:48,507] [INFO] DQC Reference Directory: /var/lib/cwl/stgd69368ed-1837-4e0a-89b4-a64fcbaadfc5/dqc_reference
[2024-01-24 15:10:49,973] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:49,974] [INFO] Task started: Prodigal
[2024-01-24 15:10:49,975] [INFO] Running command: gunzip -c /var/lib/cwl/stge1946c3d-bf9c-4219-bcda-a7f5fdcd1f02/GCF_014334095.1_ASM1433409v1_genomic.fna.gz | prodigal -d GCF_014334095.1_ASM1433409v1_genomic.fna/cds.fna -a GCF_014334095.1_ASM1433409v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:59,749] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:59,749] [INFO] Task started: HMMsearch
[2024-01-24 15:10:59,749] [INFO] Running command: hmmsearch --tblout GCF_014334095.1_ASM1433409v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd69368ed-1837-4e0a-89b4-a64fcbaadfc5/dqc_reference/reference_markers.hmm GCF_014334095.1_ASM1433409v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:00,046] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:00,048] [INFO] Found 6/6 markers.
[2024-01-24 15:11:00,085] [INFO] Query marker FASTA was written to GCF_014334095.1_ASM1433409v1_genomic.fna/markers.fasta
[2024-01-24 15:11:00,085] [INFO] Task started: Blastn
[2024-01-24 15:11:00,085] [INFO] Running command: blastn -query GCF_014334095.1_ASM1433409v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd69368ed-1837-4e0a-89b4-a64fcbaadfc5/dqc_reference/reference_markers.fasta -out GCF_014334095.1_ASM1433409v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:01,119] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:01,122] [INFO] Selected 25 target genomes.
[2024-01-24 15:11:01,123] [INFO] Target genome list was writen to GCF_014334095.1_ASM1433409v1_genomic.fna/target_genomes.txt
[2024-01-24 15:11:01,137] [INFO] Task started: fastANI
[2024-01-24 15:11:01,138] [INFO] Running command: fastANI --query /var/lib/cwl/stge1946c3d-bf9c-4219-bcda-a7f5fdcd1f02/GCF_014334095.1_ASM1433409v1_genomic.fna.gz --refList GCF_014334095.1_ASM1433409v1_genomic.fna/target_genomes.txt --output GCF_014334095.1_ASM1433409v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:20,263] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:20,263] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd69368ed-1837-4e0a-89b4-a64fcbaadfc5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:20,264] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd69368ed-1837-4e0a-89b4-a64fcbaadfc5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:20,290] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:20,291] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:20,291] [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
Novosphingopyxis iocasae	strain=PB63	GCA_014334095.1	2762729	2762729	type	True	100.0	1063	1063	95	conclusive
Novosphingopyxis baekryungensis	strain=DSM 16222	GCA_000420305.1	279369	279369	type	True	81.9678	642	1063	95	below_threshold
Qipengyuania intermedia	strain=GH38	GCA_019711615.1	2867244	2867244	type	True	78.6233	211	1063	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	78.5551	250	1063	95	below_threshold
Sphingomonas fennica	strain=K101	GCA_003034225.1	114404	114404	type	True	77.846	303	1063	95	below_threshold
Sphingomonas trueperi	strain=DSM 7225	GCA_011927635.1	53317	53317	type	True	77.8337	291	1063	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	77.7665	251	1063	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	77.6937	258	1063	95	below_threshold
Sphingomonas azotifigens	strain=NBRC 15497	GCA_002091475.1	330920	330920	type	True	77.6747	283	1063	95	below_threshold
Sphingobium scionense	strain=DSM 19371	GCA_014197035.1	1404341	1404341	type	True	77.6402	296	1063	95	below_threshold
Sphingomonas desiccabilis	strain=DSM 16792	GCA_014196135.1	429134	429134	type	True	77.5616	232	1063	95	below_threshold
Sphingomonas desiccabilis	strain=CP1D	GCA_004135605.1	429134	429134	type	True	77.5509	232	1063	95	below_threshold
Rhizorhabdus dicambivorans	strain=Ndbn-20	GCA_002355275.1	1850238	1850238	type	True	77.5268	276	1063	95	below_threshold
Sphingomonas formosensis	strain=CC-Nfb-2	GCA_009755815.1	861534	861534	type	True	77.4994	269	1063	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	77.4944	280	1063	95	below_threshold
Sphingomonas oleivorans	strain=FW-11	GCA_003050615.1	1735121	1735121	type	True	77.4714	266	1063	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	77.433	294	1063	95	below_threshold
Qipengyuania psychrotolerans	strain=1XM2-8	GCA_019711355.1	2867238	2867238	type	True	77.3969	139	1063	95	below_threshold
Sphingomonas mucosissima	strain=DSM 17494	GCA_002197665.1	370959	370959	type	True	77.3861	199	1063	95	below_threshold
Sphingomonas hengshuiensis	strain=WHSC-8	GCA_000935025.1	1609977	1609977	type	True	77.3808	260	1063	95	below_threshold
Novosphingobium profundi	strain=F72	GCA_018491765.1	1774954	1774954	type	True	77.3794	211	1063	95	below_threshold
Novosphingobium piscinae	strain=KCTC 42194	GCA_014230355.1	1507448	1507448	type	True	77.3315	220	1063	95	below_threshold
Sphingomonas ginsengisoli An et al. 2013	strain=KACC 16858	GCA_009363895.1	363835	363835	type	True	77.2947	188	1063	95	below_threshold
Erythrobacter cryptus	strain=DSM 12079	GCA_000422985.1	196588	196588	type	True	77.2659	221	1063	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	76.9568	251	1063	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:20,293] [INFO] DFAST Taxonomy check result was written to GCF_014334095.1_ASM1433409v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:20,293] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:20,294] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:20,294] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd69368ed-1837-4e0a-89b4-a64fcbaadfc5/dqc_reference/checkm_data
[2024-01-24 15:11:20,295] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:20,329] [INFO] Task started: CheckM
[2024-01-24 15:11:20,329] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014334095.1_ASM1433409v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014334095.1_ASM1433409v1_genomic.fna/checkm_input GCF_014334095.1_ASM1433409v1_genomic.fna/checkm_result
[2024-01-24 15:11:53,819] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:53,821] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:53,843] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:53,843] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:53,844] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014334095.1_ASM1433409v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:53,844] [INFO] Task started: Blastn
[2024-01-24 15:11:53,844] [INFO] Running command: blastn -query GCF_014334095.1_ASM1433409v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd69368ed-1837-4e0a-89b4-a64fcbaadfc5/dqc_reference/reference_markers_gtdb.fasta -out GCF_014334095.1_ASM1433409v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:55,772] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:55,778] [INFO] Selected 22 target genomes.
[2024-01-24 15:11:55,778] [INFO] Target genome list was writen to GCF_014334095.1_ASM1433409v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:55,796] [INFO] Task started: fastANI
[2024-01-24 15:11:55,797] [INFO] Running command: fastANI --query /var/lib/cwl/stge1946c3d-bf9c-4219-bcda-a7f5fdcd1f02/GCF_014334095.1_ASM1433409v1_genomic.fna.gz --refList GCF_014334095.1_ASM1433409v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014334095.1_ASM1433409v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:13,146] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:13,171] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:13,171] [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_014334095.1	s__Novosphingopyxis sp002683755	100.0	1062	1063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingopyxis	95.0	96.10	95.99	0.84	0.79	3	conclusive
GCF_000420305.1	s__Novosphingopyxis baekryungensis	81.9484	641	1063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815535.1	s__Alteraurantiacibacter spongiae	79.0903	248	1063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016745095.1	s__Croceicoccus sp016745095	78.343	260	1063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001555775.1	s__Blastomonas delafieldii_A	78.1448	348	1063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Blastomonas	95.0	99.74	98.25	0.90	0.81	22	-
GCF_003201955.1	s__Blastomonas natatoria	77.8986	307	1063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Blastomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355855.1	s__Sphingobium cloacae	77.8634	265	1063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003034225.1	s__Sphingomonas_E fennica	77.8351	304	1063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_E	95.0	98.08	97.94	0.82	0.81	3	-
GCA_000503195.1	s__Blastomonas sp000503195	77.8283	353	1063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Blastomonas	95.0	97.00	97.00	0.84	0.84	2	-
GCF_900177405.1	s__Allosphingosinicella indica	77.6881	260	1063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003240855.1	s__Sphingomonas_L sanxanigenens_A	77.611	259	1063	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_006874585.1	s__Novosphingobium sp006874585	77.5594	265	1063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.32	98.32	0.81	0.81	2	-
GCF_000016765.1	s__Rhizorhabdus wittichii	77.5522	292	1063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	98.56	98.46	0.83	0.82	5	-
GCF_004135605.1	s__Sphingomonas desiccabilis	77.5376	233	1063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002355275.1	s__Rhizorhabdus dicambivorans	77.511	277	1063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	99.99	99.99	1.00	0.99	3	-
GCF_003050615.1	s__Sphingomonas_H oleivorans	77.4721	266	1063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_H	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009993585.1	s__Sphingorhabdus_C sp009993585	77.4529	260	1063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000935025.1	s__Sphingomonas hengshuiensis	77.391	260	1063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014230355.1	s__Novosphingobium piscinae	77.3315	220	1063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422985.1	s__Erythrobacter cryptus	77.2659	221	1063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345855.1	s__Sphingomonas sp004345855	77.1338	271	1063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822125.1	s__Erythrobacter sp013822125	77.0187	165	1063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:12:13,173] [INFO] GTDB search result was written to GCF_014334095.1_ASM1433409v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:13,174] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:13,178] [INFO] DFAST_QC result json was written to GCF_014334095.1_ASM1433409v1_genomic.fna/dqc_result.json
[2024-01-24 15:12:13,179] [INFO] DFAST_QC completed!
[2024-01-24 15:12:13,179] [INFO] Total running time: 0h1m25s