[2024-01-24 14:05:35,469] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:35,471] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:35,471] [INFO] DQC Reference Directory: /var/lib/cwl/stga17ea525-7105-4700-9430-3435adf92067/dqc_reference
[2024-01-24 14:05:36,826] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:36,827] [INFO] Task started: Prodigal
[2024-01-24 14:05:36,828] [INFO] Running command: gunzip -c /var/lib/cwl/stg6dd2f1d5-7a11-4f01-9d67-766b34ef0a87/GCF_006385875.1_ASM638587v1_genomic.fna.gz | prodigal -d GCF_006385875.1_ASM638587v1_genomic.fna/cds.fna -a GCF_006385875.1_ASM638587v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:48,567] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:48,567] [INFO] Task started: HMMsearch
[2024-01-24 14:05:48,567] [INFO] Running command: hmmsearch --tblout GCF_006385875.1_ASM638587v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga17ea525-7105-4700-9430-3435adf92067/dqc_reference/reference_markers.hmm GCF_006385875.1_ASM638587v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:48,838] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:48,840] [INFO] Found 6/6 markers.
[2024-01-24 14:05:48,872] [INFO] Query marker FASTA was written to GCF_006385875.1_ASM638587v1_genomic.fna/markers.fasta
[2024-01-24 14:05:48,872] [INFO] Task started: Blastn
[2024-01-24 14:05:48,872] [INFO] Running command: blastn -query GCF_006385875.1_ASM638587v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga17ea525-7105-4700-9430-3435adf92067/dqc_reference/reference_markers.fasta -out GCF_006385875.1_ASM638587v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:49,778] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:49,782] [INFO] Selected 32 target genomes.
[2024-01-24 14:05:49,782] [INFO] Target genome list was writen to GCF_006385875.1_ASM638587v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:49,794] [INFO] Task started: fastANI
[2024-01-24 14:05:49,794] [INFO] Running command: fastANI --query /var/lib/cwl/stg6dd2f1d5-7a11-4f01-9d67-766b34ef0a87/GCF_006385875.1_ASM638587v1_genomic.fna.gz --refList GCF_006385875.1_ASM638587v1_genomic.fna/target_genomes.txt --output GCF_006385875.1_ASM638587v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:11,117] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:11,118] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga17ea525-7105-4700-9430-3435adf92067/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:11,118] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga17ea525-7105-4700-9430-3435adf92067/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:11,146] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:06:11,147] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:06:11,147] [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
Sphingosinicella soli	strain=DSM 17328	GCA_014199685.1	333708	333708	type	True	77.7131	229	1200	95	below_threshold
Tardibacter chloracetimidivorans	strain=JJ-A5	GCA_001890385.1	1921510	1921510	type	True	77.5938	175	1200	95	below_threshold
Sphingobium cloacae	strain=JCM 10874	GCA_002355855.1	120107	120107	type	True	77.5662	258	1200	95	below_threshold
Sphingobium chlorophenolicum	strain=NBRC 16172	GCA_000722875.1	46429	46429	type	True	77.5186	257	1200	95	below_threshold
Sphingobium indicum	strain=B90A	GCA_000264945.2	332055	332055	type	True	77.4634	235	1200	95	below_threshold
Rhizorhabdus dicambivorans	strain=Ndbn-20	GCA_002355275.1	1850238	1850238	type	True	77.4033	270	1200	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	77.3778	263	1200	95	below_threshold
Sandarakinorhabdus cyanobacteriorum	strain=TH057	GCA_002251755.1	1981098	1981098	type	True	77.3713	298	1200	95	below_threshold
Sphingomonas sinipercae	strain=HDW15C	GCA_011302055.1	2714944	2714944	type	True	77.3628	114	1200	95	below_threshold
Sphingosinicella microcystinivorans	strain=DSM 19791	GCA_003634215.1	335406	335406	type	True	77.3548	202	1200	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	77.1863	278	1200	95	below_threshold
Polymorphobacter multimanifer	strain=DSM 102189	GCA_014205635.1	1070431	1070431	type	True	77.0979	224	1200	95	below_threshold
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	77.059	206	1200	95	below_threshold
Hankyongella ginsenosidimutans	strain=W1-2-3	GCA_005144965.1	1763828	1763828	type	True	77.0239	168	1200	95	below_threshold
Rhizorhabdus histidinilytica	strain=UM2	GCA_900167915.1	439228	439228	type	True	76.9935	245	1200	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	76.9932	179	1200	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	76.9538	209	1200	95	below_threshold
Sphingobium fontiphilum	strain=DSM 29348	GCA_014196635.1	944425	944425	type	True	76.9496	219	1200	95	below_threshold
Sphingomonas jinjuensis	strain=YC6723	GCA_014197105.1	535907	535907	type	True	76.8419	187	1200	95	below_threshold
Sphingosinicella humi	strain=QZX222	GCA_003129465.1	2068657	2068657	type	True	76.8071	164	1200	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	76.7888	198	1200	95	below_threshold
Croceibacterium ferulae	strain=SX2RGS8	GCA_003660445.1	1854641	1854641	type	True	76.5365	209	1200	95	below_threshold
Novosphingobium rosa	strain=NBRC 15208	GCA_001598555.1	76978	76978	type	True	76.472	241	1200	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	76.4399	237	1200	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.2273	147	1200	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.1812	143	1200	95	below_threshold
Pannonibacter indicus	strain=DSM 23407	GCA_001517385.1	466044	466044	type	True	76.1399	93	1200	95	below_threshold
Pannonibacter indicus	strain=DSM 23407	GCA_001418225.1	466044	466044	type	True	76.1215	94	1200	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	75.9814	94	1200	95	below_threshold
Nioella ostreopsis	strain=Z7-4	GCA_004000255.1	2448479	2448479	type	True	75.952	65	1200	95	below_threshold
Amaricoccus macauensis	strain=DSM 101730	GCA_014201905.1	57001	57001	type	True	75.8457	102	1200	95	below_threshold
Xanthobacter tagetidis	strain=DSM 11105	GCA_014206845.1	60216	60216	type	True	75.7691	155	1200	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:11,149] [INFO] DFAST Taxonomy check result was written to GCF_006385875.1_ASM638587v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:11,150] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:11,150] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:11,151] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga17ea525-7105-4700-9430-3435adf92067/dqc_reference/checkm_data
[2024-01-24 14:06:11,152] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:11,190] [INFO] Task started: CheckM
[2024-01-24 14:06:11,191] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006385875.1_ASM638587v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006385875.1_ASM638587v1_genomic.fna/checkm_input GCF_006385875.1_ASM638587v1_genomic.fna/checkm_result
[2024-01-24 14:06:51,861] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:51,862] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:51,884] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:51,885] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:51,886] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006385875.1_ASM638587v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:51,886] [INFO] Task started: Blastn
[2024-01-24 14:06:51,886] [INFO] Running command: blastn -query GCF_006385875.1_ASM638587v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga17ea525-7105-4700-9430-3435adf92067/dqc_reference/reference_markers_gtdb.fasta -out GCF_006385875.1_ASM638587v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:53,385] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:53,388] [INFO] Selected 16 target genomes.
[2024-01-24 14:06:53,388] [INFO] Target genome list was writen to GCF_006385875.1_ASM638587v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:53,403] [INFO] Task started: fastANI
[2024-01-24 14:06:53,403] [INFO] Running command: fastANI --query /var/lib/cwl/stg6dd2f1d5-7a11-4f01-9d67-766b34ef0a87/GCF_006385875.1_ASM638587v1_genomic.fna.gz --refList GCF_006385875.1_ASM638587v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006385875.1_ASM638587v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:07,258] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:07,275] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:07,275] [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_006385875.1	s__Sandaracinobacter neustonicus	100.0	1197	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandaracinobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003248865.1	s__Sandaracinobacter sp003248865	85.9609	859	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandaracinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016464365.1	s__Sandaracinobacter sp016464365	80.8089	645	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandaracinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014117445.1	s__GCA-014117445 sp014117445	77.8947	352	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__GCA-014117445	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199685.1	s__Sphingosinicella soli	77.7042	228	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308255.1	s__Croceibacterium sp001897135	77.5307	183	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	99.96	99.96	0.98	0.98	2	-
GCF_003634215.1	s__Sphingosinicella microcystinivorans	77.3257	204	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingosinicella	95.0	99.98	99.98	0.98	0.98	2	-
GCF_000016765.1	s__Rhizorhabdus wittichii	77.3098	269	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	98.56	98.46	0.83	0.82	5	-
GCA_002707985.1	s__Sphingomonas sp002707985	77.1615	195	1200	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	77.1047	271	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167915.1	s__Rhizorhabdus histidinilytica	76.9729	247	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	99.24	99.18	0.90	0.89	3	-
GCF_003129465.1	s__Allosphingosinicella humi	76.7942	165	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197105.1	s__Sphingomonas jinjuensis	76.7918	191	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248515.1	s__Sphingomonas_I sp003248515	76.6922	235	1200	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_001449105.1	s__Caulobacter vibrioides_C	76.0208	150	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903837135.1	s__CAIOYC01 sp903837135	75.7919	138	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAIOYC01	95.0	99.97	99.97	0.97	0.97	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:07,278] [INFO] GTDB search result was written to GCF_006385875.1_ASM638587v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:07,279] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:07,287] [INFO] DFAST_QC result json was written to GCF_006385875.1_ASM638587v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:07,287] [INFO] DFAST_QC completed!
[2024-01-24 14:07:07,287] [INFO] Total running time: 0h1m32s