[2024-01-24 13:22:11,379] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:11,381] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:11,381] [INFO] DQC Reference Directory: /var/lib/cwl/stg95ba399b-d0a9-43c4-be2f-ee4d4aed3160/dqc_reference
[2024-01-24 13:22:13,355] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:13,356] [INFO] Task started: Prodigal
[2024-01-24 13:22:13,356] [INFO] Running command: gunzip -c /var/lib/cwl/stgf84b0593-367f-4e1f-86f1-123cb693ba69/GCF_009913435.1_ASM991343v1_genomic.fna.gz | prodigal -d GCF_009913435.1_ASM991343v1_genomic.fna/cds.fna -a GCF_009913435.1_ASM991343v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:21,358] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:21,358] [INFO] Task started: HMMsearch
[2024-01-24 13:22:21,359] [INFO] Running command: hmmsearch --tblout GCF_009913435.1_ASM991343v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95ba399b-d0a9-43c4-be2f-ee4d4aed3160/dqc_reference/reference_markers.hmm GCF_009913435.1_ASM991343v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:21,609] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:21,611] [INFO] Found 6/6 markers.
[2024-01-24 13:22:21,643] [INFO] Query marker FASTA was written to GCF_009913435.1_ASM991343v1_genomic.fna/markers.fasta
[2024-01-24 13:22:21,643] [INFO] Task started: Blastn
[2024-01-24 13:22:21,643] [INFO] Running command: blastn -query GCF_009913435.1_ASM991343v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95ba399b-d0a9-43c4-be2f-ee4d4aed3160/dqc_reference/reference_markers.fasta -out GCF_009913435.1_ASM991343v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:22,518] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:22,520] [INFO] Selected 22 target genomes.
[2024-01-24 13:22:22,521] [INFO] Target genome list was writen to GCF_009913435.1_ASM991343v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:22,526] [INFO] Task started: fastANI
[2024-01-24 13:22:22,526] [INFO] Running command: fastANI --query /var/lib/cwl/stgf84b0593-367f-4e1f-86f1-123cb693ba69/GCF_009913435.1_ASM991343v1_genomic.fna.gz --refList GCF_009913435.1_ASM991343v1_genomic.fna/target_genomes.txt --output GCF_009913435.1_ASM991343v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:40,133] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:40,134] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95ba399b-d0a9-43c4-be2f-ee4d4aed3160/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:40,134] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95ba399b-d0a9-43c4-be2f-ee4d4aed3160/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:40,149] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:40,149] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:40,149] [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 changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	100.0	1000	1001	95	conclusive
Sphingomonas horti	strain=MAH-20	GCA_009753715.1	2682842	2682842	type	True	80.6046	521	1001	95	below_threshold
Sphingomonas changbaiensis	strain=NBRC 104936	GCA_000974765.1	529705	529705	type	True	80.2184	495	1001	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	79.7373	459	1001	95	below_threshold
Sphingomonas abaci	strain=DSM 15867	GCA_014199625.1	237611	237611	type	True	79.209	458	1001	95	below_threshold
Sphingobium jiangsuense	strain=DSM 26189	GCA_014196495.1	870476	870476	type	True	79.173	413	1001	95	below_threshold
Sphingomonas oleivorans	strain=FW-11	GCA_003050615.1	1735121	1735121	type	True	79.1653	393	1001	95	below_threshold
Sphingomonas pituitosa	strain=NBRC 102491	GCA_001598435.1	99597	99597	type	True	79.0918	441	1001	95	below_threshold
Sphingomonas pokkalii	strain=L3B27	GCA_003096275.1	2175090	2175090	type	True	79.0535	421	1001	95	below_threshold
Sphingomonas azotifigens	strain=NBRC 15497	GCA_002091475.1	330920	330920	type	True	79.0097	459	1001	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	79.0054	429	1001	95	below_threshold
Sphingomonas jatrophae	strain=S5-249	GCA_900113315.1	1166337	1166337	type	True	78.9769	389	1001	95	below_threshold
Sphingomonas paucimobilis	strain=NBRC 13935	GCA_000739895.2	13689	13689	type	True	78.9656	413	1001	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	78.8535	432	1001	95	below_threshold
Sphingobium indicum	strain=B90A	GCA_000264945.2	332055	332055	type	True	78.7799	380	1001	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	78.7062	445	1001	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	78.6309	412	1001	95	below_threshold
Sphingomonas oligoaromativorans	strain=DSM 102246	GCA_011762195.1	575322	575322	type	True	78.5618	383	1001	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	78.5234	421	1001	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	78.4989	442	1001	95	below_threshold
Sphingobium fuliginis	strain=CCM 7327	GCA_014636045.1	336203	336203	type	True	78.3672	385	1001	95	below_threshold
Sphingobium fuliginis	strain=DSM 18781	GCA_004152845.1	336203	336203	type	True	78.2843	386	1001	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:40,150] [INFO] DFAST Taxonomy check result was written to GCF_009913435.1_ASM991343v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:40,151] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:40,151] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:40,151] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95ba399b-d0a9-43c4-be2f-ee4d4aed3160/dqc_reference/checkm_data
[2024-01-24 13:22:40,152] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:40,184] [INFO] Task started: CheckM
[2024-01-24 13:22:40,184] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009913435.1_ASM991343v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009913435.1_ASM991343v1_genomic.fna/checkm_input GCF_009913435.1_ASM991343v1_genomic.fna/checkm_result
[2024-01-24 13:23:20,742] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:20,743] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:20,761] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:20,762] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:20,762] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009913435.1_ASM991343v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:20,762] [INFO] Task started: Blastn
[2024-01-24 13:23:20,762] [INFO] Running command: blastn -query GCF_009913435.1_ASM991343v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95ba399b-d0a9-43c4-be2f-ee4d4aed3160/dqc_reference/reference_markers_gtdb.fasta -out GCF_009913435.1_ASM991343v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:22,455] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:22,458] [INFO] Selected 22 target genomes.
[2024-01-24 13:23:22,458] [INFO] Target genome list was writen to GCF_009913435.1_ASM991343v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:22,467] [INFO] Task started: fastANI
[2024-01-24 13:23:22,468] [INFO] Running command: fastANI --query /var/lib/cwl/stgf84b0593-367f-4e1f-86f1-123cb693ba69/GCF_009913435.1_ASM991343v1_genomic.fna.gz --refList GCF_009913435.1_ASM991343v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009913435.1_ASM991343v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:39,738] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:39,750] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:39,750] [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_009913435.1	s__Sphingomonas_B sp009913435	100.0	1000	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002291855.1	s__Sphingomonas_B sp002291855	91.63	607	1001	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_009753715.1	s__Sphingomonas_B horti	80.6109	520	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013044515.1	s__Sphingomonas_B sp013044515	80.3271	487	1001	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_000974765.1	s__Sphingomonas_B changbaiensis	80.2253	494	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240865.1	s__Sphingomonas_B sp018240865	80.1769	484	1001	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_004796535.1	s__Sphingomonas_L sp004796535	79.7532	458	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_L	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003240855.1	s__Sphingomonas_L sanxanigenens_A	79.6974	440	1001	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_003951315.1	s__Sphingomonas sp003951315	79.5707	461	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003515075.1	s__Sphingomonas gilva	79.4517	469	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034225.1	s__Sphingomonas_E fennica	79.1689	459	1001	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_001598435.1	s__Sphingomonas pituitosa	79.0715	442	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096275.1	s__Sphingomonas pokkalii	79.0316	423	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002091475.1	s__Sphingomonas azotifigens	79.0294	457	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641735.1	s__Sphingomonas metalli	79.0018	425	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113315.1	s__Sphingomonas_G jatrophae	78.9444	389	1001	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_013344685.1	s__Sphingomonas sp013344685	78.865	444	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897375.1	s__Sphingomonas sp001897375	78.6854	432	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.01	98.04	0.97	0.96	3	-
GCF_009739515.1	s__Sphingomonas_G sp009739515	78.5016	441	1001	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_013375535.1	s__Sphingobium sp013375535	78.4684	385	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282895.1	s__Sphingomonas sp000282895	78.4266	420	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_013375555.1	s__Sphingobium sp013375555	78.3156	364	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:39,752] [INFO] GTDB search result was written to GCF_009913435.1_ASM991343v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:39,752] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:39,756] [INFO] DFAST_QC result json was written to GCF_009913435.1_ASM991343v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:39,756] [INFO] DFAST_QC completed!
[2024-01-24 13:23:39,756] [INFO] Total running time: 0h1m28s