[2024-01-24 13:46:01,488] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:01,490] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:01,490] [INFO] DQC Reference Directory: /var/lib/cwl/stgb6636ce4-b54b-4790-aa17-ae5788d46d4e/dqc_reference
[2024-01-24 13:46:02,830] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:02,831] [INFO] Task started: Prodigal
[2024-01-24 13:46:02,832] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f00e961-305c-4364-a414-2b12a8d38219/GCF_009753715.1_ASM975371v1_genomic.fna.gz | prodigal -d GCF_009753715.1_ASM975371v1_genomic.fna/cds.fna -a GCF_009753715.1_ASM975371v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:12,514] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:12,514] [INFO] Task started: HMMsearch
[2024-01-24 13:46:12,514] [INFO] Running command: hmmsearch --tblout GCF_009753715.1_ASM975371v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb6636ce4-b54b-4790-aa17-ae5788d46d4e/dqc_reference/reference_markers.hmm GCF_009753715.1_ASM975371v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:12,811] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:12,813] [INFO] Found 6/6 markers.
[2024-01-24 13:46:12,859] [INFO] Query marker FASTA was written to GCF_009753715.1_ASM975371v1_genomic.fna/markers.fasta
[2024-01-24 13:46:12,860] [INFO] Task started: Blastn
[2024-01-24 13:46:12,860] [INFO] Running command: blastn -query GCF_009753715.1_ASM975371v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6636ce4-b54b-4790-aa17-ae5788d46d4e/dqc_reference/reference_markers.fasta -out GCF_009753715.1_ASM975371v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:13,846] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:13,850] [INFO] Selected 22 target genomes.
[2024-01-24 13:46:13,851] [INFO] Target genome list was writen to GCF_009753715.1_ASM975371v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:13,866] [INFO] Task started: fastANI
[2024-01-24 13:46:13,867] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f00e961-305c-4364-a414-2b12a8d38219/GCF_009753715.1_ASM975371v1_genomic.fna.gz --refList GCF_009753715.1_ASM975371v1_genomic.fna/target_genomes.txt --output GCF_009753715.1_ASM975371v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:32,723] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:32,723] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb6636ce4-b54b-4790-aa17-ae5788d46d4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:32,724] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb6636ce4-b54b-4790-aa17-ae5788d46d4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:32,740] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:32,740] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:32,741] [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 horti	strain=MAH-20	GCA_009753715.1	2682842	2682842	type	True	100.0	1104	1106	95	conclusive
Sphingomonas changbaiensis	strain=NBRC 104936	GCA_000974765.1	529705	529705	type	True	86.1967	800	1106	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	80.5433	529	1106	95	below_threshold
Sphingomonas gilva	strain=ZDH117	GCA_003515075.1	2305907	2305907	type	True	79.6494	473	1106	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	79.5635	494	1106	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	79.0852	491	1106	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	79.075	434	1106	95	below_threshold
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	79.0315	439	1106	95	below_threshold
Sphingomonas colocasiae	strain=JCM 31229	GCA_019880585.1	1848973	1848973	type	True	79.0111	502	1106	95	below_threshold
Sphingomonas sanxanigenens	strain=NX02	GCA_000512205.2	397260	397260	type	True	78.9613	452	1106	95	below_threshold
Sphingosinicella humi	strain=QZX222	GCA_003129465.1	2068657	2068657	type	True	78.9431	410	1106	95	below_threshold
Sphingomonas jinjuensis	strain=YC6723	GCA_014197105.1	535907	535907	type	True	78.9109	435	1106	95	below_threshold
Sphingomonas parva	strain=17J27-24	GCA_004564275.1	2555898	2555898	type	True	78.8223	448	1106	95	below_threshold
Sphingomonas rubra	strain=CGMCC 1.9113	GCA_900115745.1	634430	634430	type	True	78.7684	426	1106	95	below_threshold
Sphingomonas chungangi	strain=CGMCC 1.13654	GCA_013778325.1	2683589	2683589	type	True	78.7588	411	1106	95	below_threshold
Sphingomonas pruni	strain=NBRC 15498	GCA_001598455.1	40683	40683	type	True	78.6499	420	1106	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	78.6366	448	1106	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	78.6279	446	1106	95	below_threshold
Sphingomonas formosensis	strain=CC-Nfb-2	GCA_009755815.1	861534	861534	type	True	78.6064	380	1106	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	78.5415	439	1106	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	78.5311	415	1106	95	below_threshold
Sphingomonas vulcanisoli	strain=CECT 8804	GCA_011761305.1	1658060	1658060	type	True	78.1183	326	1106	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:32,742] [INFO] DFAST Taxonomy check result was written to GCF_009753715.1_ASM975371v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:32,743] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:32,743] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:32,743] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb6636ce4-b54b-4790-aa17-ae5788d46d4e/dqc_reference/checkm_data
[2024-01-24 13:46:32,744] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:32,784] [INFO] Task started: CheckM
[2024-01-24 13:46:32,785] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009753715.1_ASM975371v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009753715.1_ASM975371v1_genomic.fna/checkm_input GCF_009753715.1_ASM975371v1_genomic.fna/checkm_result
[2024-01-24 13:47:03,909] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:03,910] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:03,926] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:03,926] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:03,927] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009753715.1_ASM975371v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:03,927] [INFO] Task started: Blastn
[2024-01-24 13:47:03,927] [INFO] Running command: blastn -query GCF_009753715.1_ASM975371v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6636ce4-b54b-4790-aa17-ae5788d46d4e/dqc_reference/reference_markers_gtdb.fasta -out GCF_009753715.1_ASM975371v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:05,706] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:05,709] [INFO] Selected 11 target genomes.
[2024-01-24 13:47:05,709] [INFO] Target genome list was writen to GCF_009753715.1_ASM975371v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:05,733] [INFO] Task started: fastANI
[2024-01-24 13:47:05,733] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f00e961-305c-4364-a414-2b12a8d38219/GCF_009753715.1_ASM975371v1_genomic.fna.gz --refList GCF_009753715.1_ASM975371v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009753715.1_ASM975371v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:14,872] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:14,884] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:14,885] [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_009753715.1	s__Sphingomonas_B horti	100.0	1104	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000974765.1	s__Sphingomonas_B changbaiensis	86.2016	800	1106	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	82.367	657	1106	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_013044515.1	s__Sphingomonas_B sp013044515	82.2177	665	1106	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_009913435.1	s__Sphingomonas_B sp009913435	80.5535	528	1106	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_002291855.1	s__Sphingomonas_B sp002291855	80.2197	380	1106	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	79.4994	500	1106	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_017744835.1	s__Sphingomonas sp017744835	79.2692	477	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003240855.1	s__Sphingomonas_L sanxanigenens_A	79.1456	419	1106	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_005882415.1	s__Allosphingosinicella sp005882415	78.4266	340	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002277025.1	s__Sphingopyxis sp002277025	78.3443	412	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:14,889] [INFO] GTDB search result was written to GCF_009753715.1_ASM975371v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:14,890] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:14,900] [INFO] DFAST_QC result json was written to GCF_009753715.1_ASM975371v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:14,901] [INFO] DFAST_QC completed!
[2024-01-24 13:47:14,901] [INFO] Total running time: 0h1m13s