[2024-01-25 17:40:35,556] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:40:35,557] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:40:35,558] [INFO] DQC Reference Directory: /var/lib/cwl/stg97d51822-1d8e-4f39-8464-91ab787cc4f8/dqc_reference
[2024-01-25 17:40:36,693] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:40:36,694] [INFO] Task started: Prodigal
[2024-01-25 17:40:36,694] [INFO] Running command: gunzip -c /var/lib/cwl/stgf0c2b2bb-8f62-466f-a1c3-2d87b72f1e50/GCF_015210005.1_KB22_genomic.fna.gz | prodigal -d GCF_015210005.1_KB22_genomic.fna/cds.fna -a GCF_015210005.1_KB22_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:40:51,302] [INFO] Task succeeded: Prodigal
[2024-01-25 17:40:51,303] [INFO] Task started: HMMsearch
[2024-01-25 17:40:51,303] [INFO] Running command: hmmsearch --tblout GCF_015210005.1_KB22_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97d51822-1d8e-4f39-8464-91ab787cc4f8/dqc_reference/reference_markers.hmm GCF_015210005.1_KB22_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:40:51,554] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:40:51,555] [INFO] Found 6/6 markers.
[2024-01-25 17:40:51,587] [INFO] Query marker FASTA was written to GCF_015210005.1_KB22_genomic.fna/markers.fasta
[2024-01-25 17:40:51,587] [INFO] Task started: Blastn
[2024-01-25 17:40:51,587] [INFO] Running command: blastn -query GCF_015210005.1_KB22_genomic.fna/markers.fasta -db /var/lib/cwl/stg97d51822-1d8e-4f39-8464-91ab787cc4f8/dqc_reference/reference_markers.fasta -out GCF_015210005.1_KB22_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:52,183] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:52,186] [INFO] Selected 22 target genomes.
[2024-01-25 17:40:52,186] [INFO] Target genome list was writen to GCF_015210005.1_KB22_genomic.fna/target_genomes.txt
[2024-01-25 17:40:52,208] [INFO] Task started: fastANI
[2024-01-25 17:40:52,208] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0c2b2bb-8f62-466f-a1c3-2d87b72f1e50/GCF_015210005.1_KB22_genomic.fna.gz --refList GCF_015210005.1_KB22_genomic.fna/target_genomes.txt --output GCF_015210005.1_KB22_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:41:08,706] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:08,706] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97d51822-1d8e-4f39-8464-91ab787cc4f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:41:08,706] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97d51822-1d8e-4f39-8464-91ab787cc4f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:41:08,718] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:41:08,718] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:41:08,719] [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 hungaricum	strain=KB22	GCA_015210005.1	2082723	2082723	type	True	99.9984	1349	1352	95	conclusive
Sphingobacterium cavernae	strain=5.0403-2	GCA_008520265.1	2592657	2592657	type	True	78.3666	152	1352	95	below_threshold
Sphingobacterium bovisgrunnientis	strain=KCTC 52685	GCA_009829085.1	1874697	1874697	type	True	78.2883	147	1352	95	below_threshold
Sphingobacterium alimentarium	strain=DSM 22362	GCA_004342685.1	797292	797292	type	True	78.0718	147	1352	95	below_threshold
Sphingobacterium olei	strain=HAL-9	GCA_005048855.1	2571155	2571155	type	True	78.0564	164	1352	95	below_threshold
Sphingobacterium psychroaquaticum	strain=DSM 22418	GCA_900177625.1	561061	561061	type	True	78.0057	122	1352	95	below_threshold
Sphingobacterium athyrii	strain=M46	GCA_003071065.1	2152717	2152717	type	True	77.8271	145	1352	95	below_threshold
Sphingobacterium spiritivorum	strain=FDAARGOS_1144	GCA_016725645.1	258	258	suspected-type	True	77.7807	138	1352	95	below_threshold
Sphingobacterium mizutaii	strain=NBRC 14946	GCA_007990895.1	1010	1010	type	True	77.752	137	1352	95	below_threshold
Sphingobacterium composti Ten et al. 2007 non Yoo et al. 2007	strain=KCTC 12578	GCA_009829075.1	363260	363260	type	True	77.6967	161	1352	95	below_threshold
Sphingobacterium spiritivorum	strain=ATCC 33861	GCA_000143765.1	258	258	suspected-type	True	77.689	133	1352	95	below_threshold
Sphingobacterium prati	strain=arapr2	GCA_013167215.1	2737006	2737006	type	True	77.6249	122	1352	95	below_threshold
Sphingobacterium faecium	strain=DSM 11690	GCA_003054045.1	34087	34087	type	True	77.603	162	1352	95	below_threshold
Sphingobacterium alkalisoli	strain=CGMCC 1.15782	GCA_014643675.1	1874115	1874115	type	True	77.5249	153	1352	95	below_threshold
Sphingobacterium wenxiniae	strain=DSM 22789	GCA_900116225.1	683125	683125	type	True	77.513	130	1352	95	below_threshold
Sphingobacterium alkalisoli	strain=Y3L14	GCA_005049105.1	1874115	1874115	type	True	77.5032	152	1352	95	below_threshold
Sphingobacterium endophyticum	strain=NYYP31	GCA_009733535.1	2546448	2546448	type	True	77.491	144	1352	95	below_threshold
Sphingobacterium faecium	strain=NBRC 15299	GCA_007990875.1	34087	34087	type	True	77.4859	163	1352	95	below_threshold
Sphingobacterium chungjuense	strain=IMCC25678	GCA_011316935.1	2675553	2675553	type	True	77.4712	110	1352	95	below_threshold
Sphingobacterium corticibacter	strain=2c-3	GCA_003076635.1	2171749	2171749	type	True	77.17	125	1352	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:41:08,720] [INFO] DFAST Taxonomy check result was written to GCF_015210005.1_KB22_genomic.fna/tc_result.tsv
[2024-01-25 17:41:08,721] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:41:08,721] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:41:08,721] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97d51822-1d8e-4f39-8464-91ab787cc4f8/dqc_reference/checkm_data
[2024-01-25 17:41:08,722] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:41:08,765] [INFO] Task started: CheckM
[2024-01-25 17:41:08,766] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015210005.1_KB22_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015210005.1_KB22_genomic.fna/checkm_input GCF_015210005.1_KB22_genomic.fna/checkm_result
[2024-01-25 17:41:52,128] [INFO] Task succeeded: CheckM
[2024-01-25 17:41:52,129] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:41:52,146] [INFO] ===== Completeness check finished =====
[2024-01-25 17:41:52,146] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:41:52,147] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015210005.1_KB22_genomic.fna/markers.fasta)
[2024-01-25 17:41:52,147] [INFO] Task started: Blastn
[2024-01-25 17:41:52,147] [INFO] Running command: blastn -query GCF_015210005.1_KB22_genomic.fna/markers.fasta -db /var/lib/cwl/stg97d51822-1d8e-4f39-8464-91ab787cc4f8/dqc_reference/reference_markers_gtdb.fasta -out GCF_015210005.1_KB22_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:53,103] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:53,106] [INFO] Selected 25 target genomes.
[2024-01-25 17:41:53,106] [INFO] Target genome list was writen to GCF_015210005.1_KB22_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:41:53,135] [INFO] Task started: fastANI
[2024-01-25 17:41:53,135] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0c2b2bb-8f62-466f-a1c3-2d87b72f1e50/GCF_015210005.1_KB22_genomic.fna.gz --refList GCF_015210005.1_KB22_genomic.fna/target_genomes_gtdb.txt --output GCF_015210005.1_KB22_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:42:11,163] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:11,177] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:42:11,178] [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_015210005.1	s__Sphingobacterium sp015210005	99.9984	1349	1352	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_008520265.1	s__Sphingobacterium cavernae	78.3583	153	1352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	96.1642	N/A	N/A	N/A	N/A	1	-
GCF_009829085.1	s__Sphingobacterium bovisgrunnientis	78.2621	148	1352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	96.1642	N/A	N/A	N/A	N/A	1	-
GCF_005048855.1	s__Sphingobacterium olei	78.0533	163	1352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342685.1	s__Sphingobacterium alimentarium	78.0487	148	1352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177625.1	s__Sphingobacterium psychroaquaticum	78.0436	123	1352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	99.08	99.08	0.93	0.93	2	-
GCF_000747525.1	s__Sphingobacterium sp000747525	77.9638	135	1352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187125.1	s__Sphingobacterium mizutaii	77.9533	142	1352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	99.36	98.08	0.96	0.87	4	-
GCF_016724845.1	s__Sphingobacterium spiritivorum_A	77.9087	134	1352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	97.88	95.78	0.94	0.88	3	-
GCF_012030425.1	s__Sphingobacterium kitahiroshimense	77.7889	143	1352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	97.48	96.84	0.85	0.82	6	-
GCF_008274825.1	s__Sphingobacterium hotanense	77.7819	160	1352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	97.82	97.82	0.91	0.91	2	-
GCF_009829075.1	s__Sphingobacterium composti	77.6989	160	1352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000938735.2	s__Sphingobacterium sp000938735	77.5953	163	1352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.17	98.17	0.81	0.81	2	-
GCF_005049105.1	s__Sphingobacterium alkalisoli	77.5096	153	1352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900116225.1	s__Sphingobacterium wenxiniae	77.5085	131	1352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002322865.1	s__Sphingobacterium sp002322865	77.5061	146	1352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009733535.1	s__Sphingobacterium endophyticum	77.4848	145	1352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011316935.1	s__Sphingobacterium sp011316935	77.4513	112	1352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002980575.1	s__Sphingobacterium gobiense	77.4249	97	1352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002980525.1	s__Sphingobacterium haloxyli	77.4163	94	1352	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	77.4013	130	1352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	99.58	99.33	0.95	0.93	4	-
--------------------------------------------------------------------------------
[2024-01-25 17:42:11,179] [INFO] GTDB search result was written to GCF_015210005.1_KB22_genomic.fna/result_gtdb.tsv
[2024-01-25 17:42:11,180] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:42:11,184] [INFO] DFAST_QC result json was written to GCF_015210005.1_KB22_genomic.fna/dqc_result.json
[2024-01-25 17:42:11,184] [INFO] DFAST_QC completed!
[2024-01-25 17:42:11,184] [INFO] Total running time: 0h1m36s