[2024-01-24 11:51:50,359] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:50,364] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:50,364] [INFO] DQC Reference Directory: /var/lib/cwl/stgfdc14a87-efb9-467d-9a65-d2cdf12fba20/dqc_reference
[2024-01-24 11:51:51,607] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:51,607] [INFO] Task started: Prodigal
[2024-01-24 11:51:51,608] [INFO] Running command: gunzip -c /var/lib/cwl/stgb34740d9-3ef7-4877-9504-4874a1b25bb1/GCF_019351405.1_ASM1935140v1_genomic.fna.gz | prodigal -d GCF_019351405.1_ASM1935140v1_genomic.fna/cds.fna -a GCF_019351405.1_ASM1935140v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:52:01,561] [INFO] Task succeeded: Prodigal
[2024-01-24 11:52:01,561] [INFO] Task started: HMMsearch
[2024-01-24 11:52:01,562] [INFO] Running command: hmmsearch --tblout GCF_019351405.1_ASM1935140v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfdc14a87-efb9-467d-9a65-d2cdf12fba20/dqc_reference/reference_markers.hmm GCF_019351405.1_ASM1935140v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:52:01,815] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:52:01,817] [INFO] Found 6/6 markers.
[2024-01-24 11:52:01,846] [INFO] Query marker FASTA was written to GCF_019351405.1_ASM1935140v1_genomic.fna/markers.fasta
[2024-01-24 11:52:01,846] [INFO] Task started: Blastn
[2024-01-24 11:52:01,846] [INFO] Running command: blastn -query GCF_019351405.1_ASM1935140v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdc14a87-efb9-467d-9a65-d2cdf12fba20/dqc_reference/reference_markers.fasta -out GCF_019351405.1_ASM1935140v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:02,726] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:02,752] [INFO] Selected 17 target genomes.
[2024-01-24 11:52:02,753] [INFO] Target genome list was writen to GCF_019351405.1_ASM1935140v1_genomic.fna/target_genomes.txt
[2024-01-24 11:52:02,784] [INFO] Task started: fastANI
[2024-01-24 11:52:02,785] [INFO] Running command: fastANI --query /var/lib/cwl/stgb34740d9-3ef7-4877-9504-4874a1b25bb1/GCF_019351405.1_ASM1935140v1_genomic.fna.gz --refList GCF_019351405.1_ASM1935140v1_genomic.fna/target_genomes.txt --output GCF_019351405.1_ASM1935140v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:14,824] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:14,825] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfdc14a87-efb9-467d-9a65-d2cdf12fba20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:14,825] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfdc14a87-efb9-467d-9a65-d2cdf12fba20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:14,841] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:52:14,841] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:14,841] [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
Stakelama flava	strain=CBK3Z-3	GCA_019351405.1	2860338	2860338	type	True	100.0	1110	1113	95	conclusive
Stakelama pacifica	strain=CGMCC 1.7294	GCA_014645395.1	517720	517720	type	True	82.661	732	1113	95	below_threshold
Stakelama pacifica	strain=DSM 25059	GCA_004361835.1	517720	517720	type	True	82.6376	734	1113	95	below_threshold
Stakelama sediminis	strain=DSM 27203	GCA_014199335.1	463200	463200	type	True	79.8321	501	1113	95	below_threshold
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	79.0914	444	1113	95	below_threshold
Sphingosinithalassobacter portus	strain=FM6	GCA_003171655.1	2676234	2676234	type	True	78.9756	447	1113	95	below_threshold
Sphingomonas japonica	strain=DSM 22753	GCA_011762085.1	511662	511662	type	True	78.5276	380	1113	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	78.3725	401	1113	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	78.3475	432	1113	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	78.2988	378	1113	95	below_threshold
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	78.2163	393	1113	95	below_threshold
Sphingomonas trueperi	strain=DSM 7225	GCA_011927635.1	53317	53317	type	True	78.1297	403	1113	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	77.9465	406	1113	95	below_threshold
Sphingomonas colocasiae	strain=JCM 31229	GCA_019880585.1	1848973	1848973	type	True	77.9005	386	1113	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	77.7695	392	1113	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	77.2845	179	1113	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	77.2663	302	1113	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:14,845] [INFO] DFAST Taxonomy check result was written to GCF_019351405.1_ASM1935140v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:14,845] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:14,845] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:14,846] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfdc14a87-efb9-467d-9a65-d2cdf12fba20/dqc_reference/checkm_data
[2024-01-24 11:52:14,847] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:14,885] [INFO] Task started: CheckM
[2024-01-24 11:52:14,885] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019351405.1_ASM1935140v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019351405.1_ASM1935140v1_genomic.fna/checkm_input GCF_019351405.1_ASM1935140v1_genomic.fna/checkm_result
[2024-01-24 11:52:47,338] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:47,339] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:47,362] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:47,362] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:47,363] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019351405.1_ASM1935140v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:47,363] [INFO] Task started: Blastn
[2024-01-24 11:52:47,363] [INFO] Running command: blastn -query GCF_019351405.1_ASM1935140v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdc14a87-efb9-467d-9a65-d2cdf12fba20/dqc_reference/reference_markers_gtdb.fasta -out GCF_019351405.1_ASM1935140v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:48,909] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:48,915] [INFO] Selected 19 target genomes.
[2024-01-24 11:52:48,916] [INFO] Target genome list was writen to GCF_019351405.1_ASM1935140v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:48,946] [INFO] Task started: fastANI
[2024-01-24 11:52:48,946] [INFO] Running command: fastANI --query /var/lib/cwl/stgb34740d9-3ef7-4877-9504-4874a1b25bb1/GCF_019351405.1_ASM1935140v1_genomic.fna.gz --refList GCF_019351405.1_ASM1935140v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019351405.1_ASM1935140v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:01,519] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:01,539] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:53:01,540] [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_004361835.1	s__Sphingomonas pacifica	82.6265	735	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.75	97.51	0.88	0.77	3	-
GCA_018122655.1	s__Sphingomonas sp018122655	79.9441	522	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199335.1	s__Sphingomonas sediminis	79.8444	499	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003171655.1	s__Sphingomonas portus	78.9705	447	1113	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	78.7868	419	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.33	97.92	0.88	0.78	8	-
GCF_014334115.1	s__Sphingomonas sp014334115	78.49	411	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826325.1	s__Sphingomonas sp902826325	78.4791	346	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.74	97.74	0.84	0.84	2	-
GCA_003240755.1	s__Sphingomonas hengshuiensis_A	78.4424	390	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006346325.1	s__Sphingomonas japonica	78.4128	386	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013409985.1	s__Sphingomonas melonis_A	78.1814	364	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002127225.1	s__Sphingomonas sp002127225	78.107	393	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240825.1	s__Sphingomonas sp018240825	78.0485	218	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011761945.1	s__Sphingomonas leidyi	77.9714	399	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.87	98.83	0.90	0.87	3	-
GCF_002197685.1	s__Sphingomonas dokdonensis	77.8941	297	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002002925.1	s__Sphingomonas sp002002925	77.856	379	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103265.1	s__Sphingomonas sp900103265	77.8494	356	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003345355.1	s__Sphingomonas sp003345355	77.7821	348	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004173185.1	s__Sphingomonas sp004173185	77.4247	325	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004564275.1	s__Allosphingosinicella parva	77.0924	231	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:01,542] [INFO] GTDB search result was written to GCF_019351405.1_ASM1935140v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:01,543] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:01,550] [INFO] DFAST_QC result json was written to GCF_019351405.1_ASM1935140v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:01,550] [INFO] DFAST_QC completed!
[2024-01-24 11:53:01,550] [INFO] Total running time: 0h1m11s