[2024-01-25 18:12:20,525] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:12:20,527] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:12:20,527] [INFO] DQC Reference Directory: /var/lib/cwl/stge2d57ec6-a32d-498f-822a-04f70e3781a2/dqc_reference
[2024-01-25 18:12:21,678] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:12:21,679] [INFO] Task started: Prodigal
[2024-01-25 18:12:21,679] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d26c10d-eb07-4cfe-9895-3678d6ec0957/GCF_009755815.1_ASM975581v1_genomic.fna.gz | prodigal -d GCF_009755815.1_ASM975581v1_genomic.fna/cds.fna -a GCF_009755815.1_ASM975581v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:12:39,621] [INFO] Task succeeded: Prodigal
[2024-01-25 18:12:39,621] [INFO] Task started: HMMsearch
[2024-01-25 18:12:39,621] [INFO] Running command: hmmsearch --tblout GCF_009755815.1_ASM975581v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2d57ec6-a32d-498f-822a-04f70e3781a2/dqc_reference/reference_markers.hmm GCF_009755815.1_ASM975581v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:12:40,018] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:12:40,019] [INFO] Found 6/6 markers.
[2024-01-25 18:12:40,088] [INFO] Query marker FASTA was written to GCF_009755815.1_ASM975581v1_genomic.fna/markers.fasta
[2024-01-25 18:12:40,088] [INFO] Task started: Blastn
[2024-01-25 18:12:40,089] [INFO] Running command: blastn -query GCF_009755815.1_ASM975581v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2d57ec6-a32d-498f-822a-04f70e3781a2/dqc_reference/reference_markers.fasta -out GCF_009755815.1_ASM975581v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:41,056] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:41,059] [INFO] Selected 22 target genomes.
[2024-01-25 18:12:41,059] [INFO] Target genome list was writen to GCF_009755815.1_ASM975581v1_genomic.fna/target_genomes.txt
[2024-01-25 18:12:41,090] [INFO] Task started: fastANI
[2024-01-25 18:12:41,091] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d26c10d-eb07-4cfe-9895-3678d6ec0957/GCF_009755815.1_ASM975581v1_genomic.fna.gz --refList GCF_009755815.1_ASM975581v1_genomic.fna/target_genomes.txt --output GCF_009755815.1_ASM975581v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:13:02,032] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:02,033] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2d57ec6-a32d-498f-822a-04f70e3781a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:13:02,033] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2d57ec6-a32d-498f-822a-04f70e3781a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:13:02,045] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:13:02,046] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:13:02,046] [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
Sphingomonas formosensis	strain=CC-Nfb-2	GCA_009755815.1	861534	861534	type	True	100.0	2276	2279	95	conclusive
Sphingomonas oleivorans	strain=FW-11	GCA_003050615.1	1735121	1735121	type	True	79.5836	509	2279	95	below_threshold
Sphingomonas fennica	strain=K101	GCA_003034225.1	114404	114404	type	True	79.4749	619	2279	95	below_threshold
Rhizorhabdus dicambivorans	strain=Ndbn-20	GCA_002355275.1	1850238	1850238	type	True	79.378	572	2279	95	below_threshold
Rhizorhabdus histidinilytica	strain=UM2	GCA_900167915.1	439228	439228	type	True	79.2932	644	2279	95	below_threshold
Sphingomonas laterariae	strain=LNB2	GCA_900188165.1	861865	861865	type	True	79.1035	554	2279	95	below_threshold
Sphingomonas oligoaromativorans	strain=DSM 102246	GCA_011762195.1	575322	575322	type	True	79.0802	547	2279	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	79.0075	623	2279	95	below_threshold
Sphingomonas sanxanigenens	strain=NX02	GCA_000512205.2	397260	397260	type	True	78.9685	679	2279	95	below_threshold
Sphingomonas jatrophae	strain=S5-249	GCA_900113315.1	1166337	1166337	type	True	78.6782	565	2279	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	78.6657	548	2279	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.5689	404	2279	95	below_threshold
Sphingomonas colocasiae	strain=JCM 31229	GCA_019880585.1	1848973	1848973	type	True	78.5415	603	2279	95	below_threshold
Sphingosinicella humi	strain=QZX222	GCA_003129465.1	2068657	2068657	type	True	78.4825	351	2279	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	78.4055	403	2279	95	below_threshold
Sphingomonas crusticola	strain=MIMD3	GCA_003391115.1	1697973	1697973	type	True	78.2161	367	2279	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	78.2012	478	2279	95	below_threshold
Sphingomonas parva	strain=17J27-24	GCA_004564275.1	2555898	2555898	type	True	78.0648	457	2279	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	78.0358	453	2279	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	78.0161	400	2279	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	77.9907	412	2279	95	below_threshold
Sphingomonas xinjiangensis	strain=DSM 26736	GCA_014199255.1	643568	643568	type	True	77.9129	346	2279	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:13:02,047] [INFO] DFAST Taxonomy check result was written to GCF_009755815.1_ASM975581v1_genomic.fna/tc_result.tsv
[2024-01-25 18:13:02,048] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:13:02,048] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:13:02,048] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2d57ec6-a32d-498f-822a-04f70e3781a2/dqc_reference/checkm_data
[2024-01-25 18:13:02,049] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:13:02,111] [INFO] Task started: CheckM
[2024-01-25 18:13:02,111] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009755815.1_ASM975581v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009755815.1_ASM975581v1_genomic.fna/checkm_input GCF_009755815.1_ASM975581v1_genomic.fna/checkm_result
[2024-01-25 18:13:52,582] [INFO] Task succeeded: CheckM
[2024-01-25 18:13:52,583] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:13:52,603] [INFO] ===== Completeness check finished =====
[2024-01-25 18:13:52,604] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:13:52,604] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009755815.1_ASM975581v1_genomic.fna/markers.fasta)
[2024-01-25 18:13:52,604] [INFO] Task started: Blastn
[2024-01-25 18:13:52,605] [INFO] Running command: blastn -query GCF_009755815.1_ASM975581v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2d57ec6-a32d-498f-822a-04f70e3781a2/dqc_reference/reference_markers_gtdb.fasta -out GCF_009755815.1_ASM975581v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:54,473] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:54,476] [INFO] Selected 23 target genomes.
[2024-01-25 18:13:54,476] [INFO] Target genome list was writen to GCF_009755815.1_ASM975581v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:13:54,516] [INFO] Task started: fastANI
[2024-01-25 18:13:54,516] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d26c10d-eb07-4cfe-9895-3678d6ec0957/GCF_009755815.1_ASM975581v1_genomic.fna.gz --refList GCF_009755815.1_ASM975581v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009755815.1_ASM975581v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:14:17,118] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:17,131] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:14:17,132] [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_009755815.1	s__Sphingomonas_M formosensis	100.0	2276	2279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_M	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000016765.1	s__Rhizorhabdus wittichii	79.6713	684	2279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	98.56	98.46	0.83	0.82	5	-
GCF_003050615.1	s__Sphingomonas_H oleivorans	79.5482	513	2279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_H	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034225.1	s__Sphingomonas_E fennica	79.5259	611	2279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_E	95.0	98.08	97.94	0.82	0.81	3	-
GCF_900167915.1	s__Rhizorhabdus histidinilytica	79.3419	637	2279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	99.24	99.18	0.90	0.89	3	-
GCF_018863195.1	s__XMGL2 sp018863195	79.2575	495	2279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__XMGL2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188165.1	s__Sphingomonas_E laterariae	79.1117	553	2279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009739515.1	s__Sphingomonas_G sp009739515	79.0257	620	2279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000512205.2	s__Sphingomonas_D sanxanigenens	78.9707	679	2279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724715.1	s__SCN-67-18 sp001724715	78.8626	418	2279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__SCN-67-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003240855.1	s__Sphingomonas_L sanxanigenens_A	78.8105	418	2279	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_004005865.1	s__Rhizorhabdus crocodyli	78.7196	555	2279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113315.1	s__Sphingomonas_G jatrophae	78.7146	562	2279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903644055.1	s__Sphingomonas_I sp903644055	78.6786	317	2279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003515075.1	s__Sphingomonas gilva	78.5815	494	2279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008274695.1	s__Rhizorhabdus montanisoli	78.5745	528	2279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009913435.1	s__Sphingomonas_B sp009913435	78.5393	407	2279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007995055.1	s__Allosphingosinicella ginsenosidimutans	78.4143	402	2279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114095.1	s__Sphingomonas sp900114095	78.4016	492	2279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013344685.1	s__Sphingomonas sp013344685	78.2321	522	2279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002291855.1	s__Sphingomonas_B sp002291855	78.1796	307	2279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004564275.1	s__Allosphingosinicella parva	78.0965	454	2279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003345355.1	s__Sphingomonas sp003345355	77.9997	411	2279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:14:17,133] [INFO] GTDB search result was written to GCF_009755815.1_ASM975581v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:14:17,134] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:14:17,138] [INFO] DFAST_QC result json was written to GCF_009755815.1_ASM975581v1_genomic.fna/dqc_result.json
[2024-01-25 18:14:17,138] [INFO] DFAST_QC completed!
[2024-01-25 18:14:17,138] [INFO] Total running time: 0h1m57s