[2024-01-24 10:57:37,958] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:37,960] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:37,960] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f32cfd9-816b-46d2-9f04-c91698e610a1/dqc_reference
[2024-01-24 10:57:39,301] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:39,302] [INFO] Task started: Prodigal
[2024-01-24 10:57:39,302] [INFO] Running command: gunzip -c /var/lib/cwl/stg4b58d061-6849-4cf4-88a6-735c17416c9f/GCF_017908035.1_ASM1790803v1_genomic.fna.gz | prodigal -d GCF_017908035.1_ASM1790803v1_genomic.fna/cds.fna -a GCF_017908035.1_ASM1790803v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:01,802] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:01,802] [INFO] Task started: HMMsearch
[2024-01-24 10:58:01,802] [INFO] Running command: hmmsearch --tblout GCF_017908035.1_ASM1790803v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f32cfd9-816b-46d2-9f04-c91698e610a1/dqc_reference/reference_markers.hmm GCF_017908035.1_ASM1790803v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:02,140] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:02,141] [INFO] Found 6/6 markers.
[2024-01-24 10:58:02,185] [INFO] Query marker FASTA was written to GCF_017908035.1_ASM1790803v1_genomic.fna/markers.fasta
[2024-01-24 10:58:02,185] [INFO] Task started: Blastn
[2024-01-24 10:58:02,186] [INFO] Running command: blastn -query GCF_017908035.1_ASM1790803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f32cfd9-816b-46d2-9f04-c91698e610a1/dqc_reference/reference_markers.fasta -out GCF_017908035.1_ASM1790803v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:02,825] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:02,828] [INFO] Selected 14 target genomes.
[2024-01-24 10:58:02,828] [INFO] Target genome list was writen to GCF_017908035.1_ASM1790803v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:02,859] [INFO] Task started: fastANI
[2024-01-24 10:58:02,859] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b58d061-6849-4cf4-88a6-735c17416c9f/GCF_017908035.1_ASM1790803v1_genomic.fna.gz --refList GCF_017908035.1_ASM1790803v1_genomic.fna/target_genomes.txt --output GCF_017908035.1_ASM1790803v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:16,604] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:16,604] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f32cfd9-816b-46d2-9f04-c91698e610a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:16,605] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f32cfd9-816b-46d2-9f04-c91698e610a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:16,625] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:16,626] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:16,626] [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
Sphingobacterium tabacisoli	strain=h337	GCA_017908035.1	2044855	2044855	type	True	100.0	1814	1814	95	conclusive
Sphingobacterium yanglingense	strain=DSM 28353	GCA_004363245.1	1437280	1437280	type	True	87.8779	1266	1814	95	below_threshold
Sphingobacterium paucimobilis	strain=HER1398	GCA_000416985.1	1385985	1385985	type	True	86.3238	974	1814	95	below_threshold
Sphingobacterium faecale	strain=C459-1	GCA_016746095.1	2803775	2803775	type	True	86.0313	950	1814	95	below_threshold
Sphingobacterium nematocida	strain=DSM 24091	GCA_900168125.1	1513896	1513896	type	True	80.6846	678	1814	95	below_threshold
Sphingobacterium cavernae	strain=5.0403-2	GCA_008520265.1	2592657	2592657	type	True	78.8871	199	1814	95	below_threshold
Sphingobacterium composti Ten et al. 2007 non Yoo et al. 2007	strain=KCTC 12578	GCA_009829075.1	363260	363260	type	True	78.3929	198	1814	95	below_threshold
Sphingobacterium endophyticum	strain=NYYP31	GCA_009733535.1	2546448	2546448	type	True	78.0344	128	1814	95	below_threshold
Sphingobacterium paramultivorum	strain=w15	GCA_009660355.1	2886510	2886510	type	True	77.6406	134	1814	95	below_threshold
Sphingobacterium corticibacterium	strain=30C10-4-7	GCA_004208525.1	2484746	2484746	type	True	77.5773	119	1814	95	below_threshold
Sphingobacterium siyangense	strain=CGMCC 1.6855	GCA_007830445.1	459529	459529	type	True	77.5735	134	1814	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:16,628] [INFO] DFAST Taxonomy check result was written to GCF_017908035.1_ASM1790803v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:16,629] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:16,629] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:16,629] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f32cfd9-816b-46d2-9f04-c91698e610a1/dqc_reference/checkm_data
[2024-01-24 10:58:16,630] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:16,689] [INFO] Task started: CheckM
[2024-01-24 10:58:16,689] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017908035.1_ASM1790803v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017908035.1_ASM1790803v1_genomic.fna/checkm_input GCF_017908035.1_ASM1790803v1_genomic.fna/checkm_result
[2024-01-24 10:59:19,843] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:19,844] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:19,865] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:19,865] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:19,866] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017908035.1_ASM1790803v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:19,866] [INFO] Task started: Blastn
[2024-01-24 10:59:19,866] [INFO] Running command: blastn -query GCF_017908035.1_ASM1790803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f32cfd9-816b-46d2-9f04-c91698e610a1/dqc_reference/reference_markers_gtdb.fasta -out GCF_017908035.1_ASM1790803v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:20,684] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:20,691] [INFO] Selected 19 target genomes.
[2024-01-24 10:59:20,691] [INFO] Target genome list was writen to GCF_017908035.1_ASM1790803v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:20,706] [INFO] Task started: fastANI
[2024-01-24 10:59:20,706] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b58d061-6849-4cf4-88a6-735c17416c9f/GCF_017908035.1_ASM1790803v1_genomic.fna.gz --refList GCF_017908035.1_ASM1790803v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017908035.1_ASM1790803v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:37,719] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:37,735] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:37,735] [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_017908035.1	s__Sphingobacterium tabacisoli	100.0	1814	1814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004363245.1	s__Sphingobacterium yanglingense	87.876	1266	1814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000416985.1	s__Sphingobacterium paucimobilis	86.3184	975	1814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016746095.1	s__Sphingobacterium sp016746095	86.0029	952	1814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011007365.1	s__Sphingobacterium sp011007365	81.2133	619	1814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	99.58	99.33	0.95	0.93	4	-
GCF_900168125.1	s__Sphingobacterium nematocida	80.6966	676	1814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008520265.1	s__Sphingobacterium cavernae	78.9133	195	1814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	96.1642	N/A	N/A	N/A	N/A	1	-
GCF_009829075.1	s__Sphingobacterium composti	78.3957	195	1814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008274825.1	s__Sphingobacterium hotanense	78.3904	123	1814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	97.82	97.82	0.91	0.91	2	-
GCA_002245855.1	s__Sphingobacterium cellulitidis	78.1864	139	1814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.02	97.95	0.91	0.90	4	-
GCF_009733535.1	s__Sphingobacterium endophyticum	78.0932	124	1814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610355.1	s__Sphingobacterium detergens	77.9551	128	1814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002420705.1	s__Sphingobacterium sp002420705	77.915	123	1814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002500745.1	s__Sphingobacterium sp002500745	77.7057	110	1814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.61	98.61	0.89	0.89	2	-
GCF_007830445.1	s__Sphingobacterium siyangense	77.6167	133	1814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	96.51	95.59	0.80	0.78	14	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:37,737] [INFO] GTDB search result was written to GCF_017908035.1_ASM1790803v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:37,737] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:37,741] [INFO] DFAST_QC result json was written to GCF_017908035.1_ASM1790803v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:37,741] [INFO] DFAST_QC completed!
[2024-01-24 10:59:37,741] [INFO] Total running time: 0h1m60s