[2024-01-24 14:14:00,837] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:00,840] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:00,841] [INFO] DQC Reference Directory: /var/lib/cwl/stgfbb3d5fc-807a-425a-9329-67a0ef8b13c6/dqc_reference
[2024-01-24 14:14:02,082] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:02,083] [INFO] Task started: Prodigal
[2024-01-24 14:14:02,083] [INFO] Running command: gunzip -c /var/lib/cwl/stgb9ac6fd5-c378-4295-a25e-a04cfb735fd6/GCF_004361835.1_ASM436183v1_genomic.fna.gz | prodigal -d GCF_004361835.1_ASM436183v1_genomic.fna/cds.fna -a GCF_004361835.1_ASM436183v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:15,956] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:15,956] [INFO] Task started: HMMsearch
[2024-01-24 14:14:15,956] [INFO] Running command: hmmsearch --tblout GCF_004361835.1_ASM436183v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfbb3d5fc-807a-425a-9329-67a0ef8b13c6/dqc_reference/reference_markers.hmm GCF_004361835.1_ASM436183v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:16,384] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:16,385] [INFO] Found 6/6 markers.
[2024-01-24 14:14:16,465] [INFO] Query marker FASTA was written to GCF_004361835.1_ASM436183v1_genomic.fna/markers.fasta
[2024-01-24 14:14:16,466] [INFO] Task started: Blastn
[2024-01-24 14:14:16,466] [INFO] Running command: blastn -query GCF_004361835.1_ASM436183v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbb3d5fc-807a-425a-9329-67a0ef8b13c6/dqc_reference/reference_markers.fasta -out GCF_004361835.1_ASM436183v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:17,532] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:17,535] [INFO] Selected 21 target genomes.
[2024-01-24 14:14:17,535] [INFO] Target genome list was writen to GCF_004361835.1_ASM436183v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:17,544] [INFO] Task started: fastANI
[2024-01-24 14:14:17,544] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9ac6fd5-c378-4295-a25e-a04cfb735fd6/GCF_004361835.1_ASM436183v1_genomic.fna.gz --refList GCF_004361835.1_ASM436183v1_genomic.fna/target_genomes.txt --output GCF_004361835.1_ASM436183v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:36,848] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:36,849] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfbb3d5fc-807a-425a-9329-67a0ef8b13c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:36,849] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfbb3d5fc-807a-425a-9329-67a0ef8b13c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:36,866] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:14:36,866] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:36,866] [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 pacifica	strain=DSM 25059	GCA_004361835.1	517720	517720	type	True	100.0	1310	1311	95	conclusive
Stakelama pacifica	strain=CGMCC 1.7294	GCA_014645395.1	517720	517720	type	True	99.9982	1306	1311	95	conclusive
Stakelama flava	strain=CBK3Z-3	GCA_019351405.1	2860338	2860338	type	True	82.5923	727	1311	95	below_threshold
Sphingosinithalassobacter portus	strain=FM6	GCA_003171655.1	2676234	2676234	type	True	79.8836	516	1311	95	below_threshold
Stakelama sediminis	strain=DSM 27203	GCA_014199335.1	463200	463200	type	True	79.8512	527	1311	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	78.6143	461	1311	95	below_threshold
Sphingomonas paucimobilis	strain=NBRC 13935	GCA_000739895.2	13689	13689	type	True	78.3821	427	1311	95	below_threshold
Sphingomonas turrisvirgatae	strain=MCT13	GCA_001721295.1	1888892	1888892	type	True	78.3805	403	1311	95	below_threshold
Sphingomonas pseudosanguinis	strain=DSM 19512	GCA_017052355.1	413712	413712	type	True	78.3735	453	1311	95	below_threshold
Sphingomonas paucimobilis	strain=FDAARGOS_908	GCA_016027095.1	13689	13689	type	True	78.3591	448	1311	95	below_threshold
Sphingomonas pseudosanguinis	strain=DSM 19512	GCA_014196255.1	413712	413712	type	True	78.3257	452	1311	95	below_threshold
Sphingomonas zeae	strain=DSM 100049	GCA_013359795.1	1646122	1646122	type	True	78.3224	422	1311	95	below_threshold
Sphingomonas zeae	strain=DSM 100049	GCA_014197135.1	1646122	1646122	type	True	78.3179	419	1311	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	78.2378	385	1311	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	78.1073	401	1311	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	78.0409	419	1311	95	below_threshold
Sphingomonas desiccabilis	strain=CP1D	GCA_004135605.1	429134	429134	type	True	77.9475	381	1311	95	below_threshold
Sphingomonas desiccabilis	strain=DSM 16792	GCA_014196135.1	429134	429134	type	True	77.937	384	1311	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	77.7813	415	1311	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	77.3824	334	1311	95	below_threshold
Alteraurantiacibacter aestuarii	strain=JCM 16339	GCA_009827405.1	650004	650004	type	True	77.2569	125	1311	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:36,868] [INFO] DFAST Taxonomy check result was written to GCF_004361835.1_ASM436183v1_genomic.fna/tc_result.tsv
[2024-01-24 14:14:36,869] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:36,869] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:36,869] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfbb3d5fc-807a-425a-9329-67a0ef8b13c6/dqc_reference/checkm_data
[2024-01-24 14:14:36,871] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:36,912] [INFO] Task started: CheckM
[2024-01-24 14:14:36,912] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004361835.1_ASM436183v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004361835.1_ASM436183v1_genomic.fna/checkm_input GCF_004361835.1_ASM436183v1_genomic.fna/checkm_result
[2024-01-24 14:15:13,706] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:13,707] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:13,725] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:13,725] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:13,726] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004361835.1_ASM436183v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:13,726] [INFO] Task started: Blastn
[2024-01-24 14:15:13,726] [INFO] Running command: blastn -query GCF_004361835.1_ASM436183v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbb3d5fc-807a-425a-9329-67a0ef8b13c6/dqc_reference/reference_markers_gtdb.fasta -out GCF_004361835.1_ASM436183v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:15,007] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:15,011] [INFO] Selected 25 target genomes.
[2024-01-24 14:15:15,011] [INFO] Target genome list was writen to GCF_004361835.1_ASM436183v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:15,034] [INFO] Task started: fastANI
[2024-01-24 14:15:15,034] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9ac6fd5-c378-4295-a25e-a04cfb735fd6/GCF_004361835.1_ASM436183v1_genomic.fna.gz --refList GCF_004361835.1_ASM436183v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004361835.1_ASM436183v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:32,764] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:32,800] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:32,801] [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	100.0	1310	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.75	97.51	0.88	0.77	3	conclusive
GCA_018122655.1	s__Sphingomonas sp018122655	80.5829	573	1311	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	79.8924	523	1311	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	79.8369	521	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011057975.1	s__Sphingomonas sp011057975	79.2073	508	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707985.1	s__Sphingomonas sp002707985	79.0617	462	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001557215.1	s__Sphingomonas sp001557215	78.736	423	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.89	99.89	0.91	0.91	2	-
GCA_902826325.1	s__Sphingomonas sp902826325	78.7306	369	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.74	97.74	0.84	0.84	2	-
GCA_016937575.1	s__Sphingomonas aeriglobus	78.5933	380	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000786205.1	s__Sphingomonas sp000786205	78.4992	424	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003240755.1	s__Sphingomonas hengshuiensis_A	78.4816	423	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001721295.1	s__Sphingomonas turrisvirgatae	78.3764	402	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001476905.1	s__Sphingomonas sanguinis_B	78.3555	391	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.13	96.11	0.83	0.82	3	-
GCF_014196495.1	s__Sphingobium jiangsuense	78.3532	361	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196255.1	s__Sphingomonas pseudosanguinis	78.3368	450	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014641735.1	s__Sphingomonas metalli	78.1352	399	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199325.1	s__Sphingomonas yantingensis	78.1076	394	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.75	96.75	0.89	0.89	2	-
GCF_000712135.1	s__Sphingomonas sp000712135	78.0327	422	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001476895.1	s__Sphingomonas endophytica_A	77.9818	369	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897375.1	s__Sphingomonas sp001897375	77.966	377	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.01	98.04	0.97	0.96	3	-
GCF_016107325.1	s__Sphingomonas sp016107325	77.8479	419	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017418975.1	s__Sphingomonas sp017418975	77.7108	443	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193845.1	s__Sphingomonas sp014193845	77.2395	344	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.90	98.90	0.87	0.87	2	-
GCF_014641655.1	s__Alteriqipengyuania_A marina	77.2139	194	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania_A	95.0	98.02	98.02	0.89	0.89	2	-
GCA_001464915.1	s__Erythrobacter sp001464915	76.5936	148	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:32,802] [INFO] GTDB search result was written to GCF_004361835.1_ASM436183v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:32,803] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:32,808] [INFO] DFAST_QC result json was written to GCF_004361835.1_ASM436183v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:32,808] [INFO] DFAST_QC completed!
[2024-01-24 14:15:32,808] [INFO] Total running time: 0h1m32s