[2024-01-24 11:12:36,236] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:36,241] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:36,241] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ebd99ac-cf53-46bb-9aba-a09e3ff4dc54/dqc_reference
[2024-01-24 11:12:38,663] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:38,664] [INFO] Task started: Prodigal
[2024-01-24 11:12:38,664] [INFO] Running command: gunzip -c /var/lib/cwl/stg4b94cd9c-4cf0-450c-9d9b-9d8f5492c2f1/GCF_003515075.1_ASM351507v1_genomic.fna.gz | prodigal -d GCF_003515075.1_ASM351507v1_genomic.fna/cds.fna -a GCF_003515075.1_ASM351507v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:48,267] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:48,267] [INFO] Task started: HMMsearch
[2024-01-24 11:12:48,268] [INFO] Running command: hmmsearch --tblout GCF_003515075.1_ASM351507v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ebd99ac-cf53-46bb-9aba-a09e3ff4dc54/dqc_reference/reference_markers.hmm GCF_003515075.1_ASM351507v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:48,469] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:48,470] [INFO] Found 6/6 markers.
[2024-01-24 11:12:48,503] [INFO] Query marker FASTA was written to GCF_003515075.1_ASM351507v1_genomic.fna/markers.fasta
[2024-01-24 11:12:48,504] [INFO] Task started: Blastn
[2024-01-24 11:12:48,504] [INFO] Running command: blastn -query GCF_003515075.1_ASM351507v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ebd99ac-cf53-46bb-9aba-a09e3ff4dc54/dqc_reference/reference_markers.fasta -out GCF_003515075.1_ASM351507v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:49,484] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:49,487] [INFO] Selected 24 target genomes.
[2024-01-24 11:12:49,488] [INFO] Target genome list was writen to GCF_003515075.1_ASM351507v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:49,536] [INFO] Task started: fastANI
[2024-01-24 11:12:49,537] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b94cd9c-4cf0-450c-9d9b-9d8f5492c2f1/GCF_003515075.1_ASM351507v1_genomic.fna.gz --refList GCF_003515075.1_ASM351507v1_genomic.fna/target_genomes.txt --output GCF_003515075.1_ASM351507v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:08,545] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:08,545] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ebd99ac-cf53-46bb-9aba-a09e3ff4dc54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:08,546] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ebd99ac-cf53-46bb-9aba-a09e3ff4dc54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:08,563] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:08,563] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:08,563] [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 gilva	strain=ZDH117	GCA_003515075.1	2305907	2305907	type	True	100.0	1168	1170	95	conclusive
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	80.2282	642	1170	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	80.1178	650	1170	95	below_threshold
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	79.9229	586	1170	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	79.9161	521	1170	95	below_threshold
Sphingomonas trueperi	strain=DSM 7225	GCA_011927635.1	53317	53317	type	True	79.831	588	1170	95	below_threshold
Sphingomonas ginsenosidivorax	strain=KHI67	GCA_007995065.1	862135	862135	type	True	79.7603	560	1170	95	below_threshold
Sphingomonas desiccabilis	strain=CP1D	GCA_004135605.1	429134	429134	type	True	79.7508	479	1170	95	below_threshold
Sphingomonas desiccabilis	strain=DSM 16792	GCA_014196135.1	429134	429134	type	True	79.7286	486	1170	95	below_threshold
Sphingomonas pituitosa	strain=NBRC 102491	GCA_001598435.1	99597	99597	type	True	79.7104	557	1170	95	below_threshold
Sphingomonas rubra	strain=CGMCC 1.9113	GCA_900115745.1	634430	634430	type	True	79.693	508	1170	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	79.6448	583	1170	95	below_threshold
Sphingomonas azotifigens	strain=NBRC 15497	GCA_002091475.1	330920	330920	type	True	79.5947	569	1170	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	79.5902	462	1170	95	below_threshold
Sphingomonas carotinifaciens	strain=DSM 27347	GCA_009789535.1	1166323	1166323	type	True	79.5522	513	1170	95	below_threshold
Sphingomonas carotinifaciens	strain=DSM 27347	GCA_014197095.1	1166323	1166323	type	True	79.5485	511	1170	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	79.5029	561	1170	95	below_threshold
Sphingomonas gei	strain=ZFGT-11	GCA_004792685.1	1395960	1395960	type	True	79.478	577	1170	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	79.4197	465	1170	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	78.9448	558	1170	95	below_threshold
Sphingomonas solaris	strain=R4DWN	GCA_007785815.1	2529389	2529389	type	True	78.865	426	1170	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	78.6869	478	1170	95	below_threshold
Sphingomonas parva	strain=17J27-24	GCA_004564275.1	2555898	2555898	type	True	78.6838	465	1170	95	below_threshold
Sphingomonas jejuensis	strain=DSM 27651	GCA_011927695.1	904715	904715	type	True	78.6808	409	1170	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:08,564] [INFO] DFAST Taxonomy check result was written to GCF_003515075.1_ASM351507v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:08,565] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:08,565] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:08,565] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ebd99ac-cf53-46bb-9aba-a09e3ff4dc54/dqc_reference/checkm_data
[2024-01-24 11:13:08,566] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:08,600] [INFO] Task started: CheckM
[2024-01-24 11:13:08,600] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003515075.1_ASM351507v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003515075.1_ASM351507v1_genomic.fna/checkm_input GCF_003515075.1_ASM351507v1_genomic.fna/checkm_result
[2024-01-24 11:13:39,072] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:39,073] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:39,098] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:39,098] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:39,098] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003515075.1_ASM351507v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:39,098] [INFO] Task started: Blastn
[2024-01-24 11:13:39,098] [INFO] Running command: blastn -query GCF_003515075.1_ASM351507v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ebd99ac-cf53-46bb-9aba-a09e3ff4dc54/dqc_reference/reference_markers_gtdb.fasta -out GCF_003515075.1_ASM351507v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:41,011] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:41,015] [INFO] Selected 26 target genomes.
[2024-01-24 11:13:41,015] [INFO] Target genome list was writen to GCF_003515075.1_ASM351507v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:41,032] [INFO] Task started: fastANI
[2024-01-24 11:13:41,032] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b94cd9c-4cf0-450c-9d9b-9d8f5492c2f1/GCF_003515075.1_ASM351507v1_genomic.fna.gz --refList GCF_003515075.1_ASM351507v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003515075.1_ASM351507v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:03,498] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:03,518] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:03,518] [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_003515075.1	s__Sphingomonas gilva	100.0	1168	1170	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018449795.1	s__Sphingomonas sp018449795	80.2401	585	1170	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	80.0944	538	1170	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764535.1	s__Sphingomonas taxi	79.9268	586	1170	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.55	97.55	0.88	0.88	2	-
GCF_003550065.1	s__Sphingomonas caeni	79.8388	587	1170	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007995065.1	s__Sphingomonas ginsenosidivorax	79.7512	560	1170	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135605.1	s__Sphingomonas desiccabilis	79.7446	480	1170	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900114095.1	s__Sphingomonas sp900114095	79.6863	581	1170	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001555965.1	s__Sphingomonas sp001555965	79.6644	532	1170	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.33	97.92	0.88	0.78	8	-
GCF_900115745.1	s__Sphingomonas rubra	79.6428	513	1170	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000226955.1	s__Sphingomonas elodea_A	79.631	552	1170	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004796535.1	s__Sphingomonas_L sp004796535	79.6127	460	1170	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_014204695.1	s__Sphingomonas sp001897045	79.5723	571	1170	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.82	96.97	0.94	0.83	6	-
GCF_004341505.2	s__Sphingomonas sp004341505	79.5476	503	1170	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.45	95.45	0.78	0.78	2	-
GCF_902498785.1	s__Sphingomonas sp902498785	79.5367	517	1170	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489075.1	s__Sphingomonas sp014489075	79.5365	637	1170	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650735.1	s__Sphingomonas sp001650735	79.4956	509	1170	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724715.1	s__SCN-67-18 sp001724715	79.4636	468	1170	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	-
GCF_014334115.1	s__Sphingomonas sp014334115	79.4481	525	1170	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009913435.1	s__Sphingomonas_B sp009913435	79.4081	466	1170	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_001477495.1	s__Sphingomonas yabuuchiae_A	79.1924	464	1170	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009755815.1	s__Sphingomonas_M formosensis	78.7553	472	1170	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_M	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013113735.1	s__Sphingomonas_I sp013113735	78.7169	450	1170	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_004564275.1	s__Allosphingosinicella parva	78.6823	465	1170	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927695.1	s__Sphingomonas_K jejuensis	78.6548	411	1170	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899715.1	s__Sphingobium sp001899715	78.5416	388	1170	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 11:14:03,520] [INFO] GTDB search result was written to GCF_003515075.1_ASM351507v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:03,520] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:03,525] [INFO] DFAST_QC result json was written to GCF_003515075.1_ASM351507v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:03,525] [INFO] DFAST_QC completed!
[2024-01-24 11:14:03,525] [INFO] Total running time: 0h1m27s