[2024-01-24 13:18:27,726] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:27,730] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:27,730] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b9f3317-5414-446c-83f7-930149b9b54b/dqc_reference
[2024-01-24 13:18:29,137] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:29,138] [INFO] Task started: Prodigal
[2024-01-24 13:18:29,138] [INFO] Running command: gunzip -c /var/lib/cwl/stg472b1432-980c-40bf-a0cf-9a59450ec6e7/GCF_014196495.1_ASM1419649v1_genomic.fna.gz | prodigal -d GCF_014196495.1_ASM1419649v1_genomic.fna/cds.fna -a GCF_014196495.1_ASM1419649v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:43,128] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:43,128] [INFO] Task started: HMMsearch
[2024-01-24 13:18:43,129] [INFO] Running command: hmmsearch --tblout GCF_014196495.1_ASM1419649v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b9f3317-5414-446c-83f7-930149b9b54b/dqc_reference/reference_markers.hmm GCF_014196495.1_ASM1419649v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:43,432] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:43,434] [INFO] Found 6/6 markers.
[2024-01-24 13:18:43,484] [INFO] Query marker FASTA was written to GCF_014196495.1_ASM1419649v1_genomic.fna/markers.fasta
[2024-01-24 13:18:43,485] [INFO] Task started: Blastn
[2024-01-24 13:18:43,485] [INFO] Running command: blastn -query GCF_014196495.1_ASM1419649v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b9f3317-5414-446c-83f7-930149b9b54b/dqc_reference/reference_markers.fasta -out GCF_014196495.1_ASM1419649v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:44,391] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:44,395] [INFO] Selected 28 target genomes.
[2024-01-24 13:18:44,396] [INFO] Target genome list was writen to GCF_014196495.1_ASM1419649v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:44,408] [INFO] Task started: fastANI
[2024-01-24 13:18:44,409] [INFO] Running command: fastANI --query /var/lib/cwl/stg472b1432-980c-40bf-a0cf-9a59450ec6e7/GCF_014196495.1_ASM1419649v1_genomic.fna.gz --refList GCF_014196495.1_ASM1419649v1_genomic.fna/target_genomes.txt --output GCF_014196495.1_ASM1419649v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:07,434] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:07,435] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b9f3317-5414-446c-83f7-930149b9b54b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:07,436] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b9f3317-5414-446c-83f7-930149b9b54b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:07,474] [INFO] Found 28 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:07,475] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:07,475] [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
Sphingobium jiangsuense	strain=DSM 26189	GCA_014196495.1	870476	870476	type	True	100.0	1565	1571	95	conclusive
Sphingobium baderi	strain=LL03	GCA_001046655.1	1332080	1332080	type	True	81.8219	564	1571	95	below_threshold
Sphingobium cloacae	strain=NBRC 102517	GCA_001591285.1	120107	120107	type	True	81.6224	578	1571	95	below_threshold
Sphingobium cloacae	strain=JCM 10874	GCA_002355855.1	120107	120107	type	True	81.51	601	1571	95	below_threshold
Sphingobium amiense	strain=DSM 16289	GCA_003967075.1	135719	135719	type	True	81.031	615	1571	95	below_threshold
Sphingobium amiense	strain=NBRC 102518	GCA_001591305.1	135719	135719	type	True	80.965	601	1571	95	below_threshold
Sphingobium phenoxybenzoativorans	strain=SC_3	GCA_001757355.1	1592790	1592790	type	True	80.872	498	1571	95	below_threshold
Sphingobium ummariense	strain=RL-3	GCA_000447205.1	420994	420994	type	True	80.8291	541	1571	95	below_threshold
Sphingobium indicum	strain=B90A	GCA_000264945.2	332055	332055	type	True	80.759	555	1571	95	below_threshold
Sphingobium chlorophenolicum	strain=NBRC 16172	GCA_000722875.1	46429	46429	type	True	80.7332	603	1571	95	below_threshold
Sphingobium fuliginis	strain=DSM 18781	GCA_004152845.1	336203	336203	type	True	80.4831	576	1571	95	below_threshold
Sphingobium fuliginis	strain=CCM 7327	GCA_014636045.1	336203	336203	type	True	80.4322	576	1571	95	below_threshold
Sphingobium fluviale	strain=CHR27	GCA_004122115.1	2506423	2506423	type	True	80.418	473	1571	95	below_threshold
Sphingobium fontiphilum	strain=DSM 29348	GCA_014196635.1	944425	944425	type	True	80.3543	504	1571	95	below_threshold
Sphingobium quisquiliarum	strain=P25	GCA_000445065.1	538379	538379	type	True	80.1327	524	1571	95	below_threshold
Sphingobium scionense	strain=DSM 19371	GCA_014197035.1	1404341	1404341	type	True	80.0725	606	1571	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.9731	429	1571	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	78.643	421	1571	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	78.6289	427	1571	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	78.4689	410	1571	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	78.231	498	1571	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	78.1384	362	1571	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	78.0134	446	1571	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	77.8756	288	1571	95	below_threshold
Sphingomonas guangdongensis	strain=CGMCC 1.12672	GCA_900199185.1	1141890	1141890	type	True	77.749	370	1571	95	below_threshold
Novosphingobium fluoreni	strain=DSM 27568	GCA_014196615.1	1391222	1391222	type	True	77.5625	268	1571	95	below_threshold
Hyphomicrobium zavarzinii	strain=ZV-622	GCA_000383415.1	48292	48292	type	True	76.1143	114	1571	95	below_threshold
Geminicoccus roseus	strain=DSM 18922	GCA_000427665.1	404900	404900	type	True	75.7511	187	1571	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:07,477] [INFO] DFAST Taxonomy check result was written to GCF_014196495.1_ASM1419649v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:07,477] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:07,477] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:07,478] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b9f3317-5414-446c-83f7-930149b9b54b/dqc_reference/checkm_data
[2024-01-24 13:19:07,479] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:07,525] [INFO] Task started: CheckM
[2024-01-24 13:19:07,525] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014196495.1_ASM1419649v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014196495.1_ASM1419649v1_genomic.fna/checkm_input GCF_014196495.1_ASM1419649v1_genomic.fna/checkm_result
[2024-01-24 13:19:49,227] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:49,229] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:49,251] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:49,251] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:49,252] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014196495.1_ASM1419649v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:49,252] [INFO] Task started: Blastn
[2024-01-24 13:19:49,253] [INFO] Running command: blastn -query GCF_014196495.1_ASM1419649v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b9f3317-5414-446c-83f7-930149b9b54b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014196495.1_ASM1419649v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:50,969] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:50,973] [INFO] Selected 23 target genomes.
[2024-01-24 13:19:50,973] [INFO] Target genome list was writen to GCF_014196495.1_ASM1419649v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:51,022] [INFO] Task started: fastANI
[2024-01-24 13:19:51,022] [INFO] Running command: fastANI --query /var/lib/cwl/stg472b1432-980c-40bf-a0cf-9a59450ec6e7/GCF_014196495.1_ASM1419649v1_genomic.fna.gz --refList GCF_014196495.1_ASM1419649v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014196495.1_ASM1419649v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:13,543] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:13,567] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:13,568] [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_014196495.1	s__Sphingobium jiangsuense	100.0	1565	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_006226685.1	s__Sphingobium sp006226685	81.741	602	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.90	99.90	0.86	0.86	2	-
GCF_002355855.1	s__Sphingobium cloacae	81.5435	599	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003967075.1	s__Sphingobium amiense	81.0627	613	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009720145.1	s__Sphingobium sp009720145	80.8577	655	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001757355.1	s__Sphingobium phenoxybenzoativorans	80.8474	500	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	96.17	96.17	0.74	0.74	2	-
GCF_000447205.1	s__Sphingobium ummariense	80.7874	545	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000264945.2	s__Sphingobium indicum	80.7523	556	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.64	97.75	0.82	0.64	8	-
GCF_900100475.1	s__Sphingobium faniae	80.5231	562	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002457415.1	s__Sphingobium sp002457415	80.4099	513	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196635.1	s__Sphingobium fontiphilum	80.3881	501	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013375555.1	s__Sphingobium sp013375555	80.3808	612	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001005725.1	s__Sphingobium chungbukense	80.3551	609	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.77	97.77	0.72	0.72	2	-
GCA_003248935.1	s__Sphingobium sp003248935	80.2241	476	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000445065.1	s__Sphingobium quisquiliarum	80.1541	522	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.94	97.93	0.83	0.83	3	-
GCF_014197035.1	s__Sphingobium scionense	80.0224	610	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002312805.1	s__Sphingobium sp002312805	79.9518	543	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	95.45	95.45	0.84	0.84	2	-
GCF_004796535.1	s__Sphingomonas_L sp004796535	78.5984	430	1571	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_900114095.1	s__Sphingomonas sp900114095	78.5118	464	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428605.1	s__Rhizorhabdus sp001428605	78.4141	506	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	99.98	99.98	0.99	0.99	3	-
GCF_004361835.1	s__Sphingomonas pacifica	78.0606	374	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.75	97.51	0.88	0.77	3	-
GCF_003581645.1	s__Pelagerythrobacter aerophilus	77.8758	288	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900199185.1	s__Sphingomonas guangdongensis	77.7489	370	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:13,570] [INFO] GTDB search result was written to GCF_014196495.1_ASM1419649v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:13,570] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:13,577] [INFO] DFAST_QC result json was written to GCF_014196495.1_ASM1419649v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:13,577] [INFO] DFAST_QC completed!
[2024-01-24 13:20:13,577] [INFO] Total running time: 0h1m46s