[2023-06-29 22:35:10,868] [INFO] DFAST_QC pipeline started.
[2023-06-29 22:35:10,870] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 22:35:10,870] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b7dd3f7-1ea3-4368-8436-8b9350253450/dqc_reference
[2023-06-29 22:35:12,137] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 22:35:12,139] [INFO] Task started: Prodigal
[2023-06-29 22:35:12,140] [INFO] Running command: gunzip -c /var/lib/cwl/stg8d907b49-d1f8-4e66-92df-b163e50ae6a6/GCA_016715255.1_ASM1671525v1_genomic.fna.gz | prodigal -d GCA_016715255.1_ASM1671525v1_genomic.fna/cds.fna -a GCA_016715255.1_ASM1671525v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 22:35:22,370] [INFO] Task succeeded: Prodigal
[2023-06-29 22:35:22,371] [INFO] Task started: HMMsearch
[2023-06-29 22:35:22,371] [INFO] Running command: hmmsearch --tblout GCA_016715255.1_ASM1671525v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b7dd3f7-1ea3-4368-8436-8b9350253450/dqc_reference/reference_markers.hmm GCA_016715255.1_ASM1671525v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 22:35:22,611] [INFO] Task succeeded: HMMsearch
[2023-06-29 22:35:22,613] [INFO] Found 6/6 markers.
[2023-06-29 22:35:22,653] [INFO] Query marker FASTA was written to GCA_016715255.1_ASM1671525v1_genomic.fna/markers.fasta
[2023-06-29 22:35:22,654] [INFO] Task started: Blastn
[2023-06-29 22:35:22,654] [INFO] Running command: blastn -query GCA_016715255.1_ASM1671525v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b7dd3f7-1ea3-4368-8436-8b9350253450/dqc_reference/reference_markers.fasta -out GCA_016715255.1_ASM1671525v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:35:23,408] [INFO] Task succeeded: Blastn
[2023-06-29 22:35:23,413] [INFO] Selected 23 target genomes.
[2023-06-29 22:35:23,414] [INFO] Target genome list was writen to GCA_016715255.1_ASM1671525v1_genomic.fna/target_genomes.txt
[2023-06-29 22:35:23,429] [INFO] Task started: fastANI
[2023-06-29 22:35:23,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d907b49-d1f8-4e66-92df-b163e50ae6a6/GCA_016715255.1_ASM1671525v1_genomic.fna.gz --refList GCA_016715255.1_ASM1671525v1_genomic.fna/target_genomes.txt --output GCA_016715255.1_ASM1671525v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 22:35:38,177] [INFO] Task succeeded: fastANI
[2023-06-29 22:35:38,178] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b7dd3f7-1ea3-4368-8436-8b9350253450/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 22:35:38,179] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b7dd3f7-1ea3-4368-8436-8b9350253450/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 22:35:38,199] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 22:35:38,199] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 22:35:38,200] [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
Aquisediminimonas profunda	strain=DS48-3	GCA_019443285.1	1550733	1550733	type	True	87.2796	692	1059	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	77.6235	166	1059	95	below_threshold
Sphingobium wenxiniae	strain=JZ-1	GCA_014205735.1	595605	595605	type	True	77.5306	152	1059	95	below_threshold
Sphingomonas gilva	strain=ZDH117	GCA_003515075.1	2305907	2305907	type	True	77.3817	157	1059	95	below_threshold
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	77.3358	153	1059	95	below_threshold
Sphingomonas colocasiae	strain=JCM 31229	GCA_019880585.1	1848973	1848973	type	True	77.3232	195	1059	95	below_threshold
Novosphingobium kunmingense	strain=CGMCC 1.12274	GCA_002813245.1	1211806	1211806	type	True	77.2953	117	1059	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	77.2803	134	1059	95	below_threshold
Sphingomonas pokkalii	strain=L3B27	GCA_003096275.1	2175090	2175090	type	True	77.2635	151	1059	95	below_threshold
Sphingomonas gei	strain=ZFGT-11	GCA_004792685.1	1395960	1395960	type	True	77.2492	134	1059	95	below_threshold
Tsuneonella amylolytica	strain=NS1	GCA_003626915.1	2338327	2338327	type	True	77.2095	94	1059	95	below_threshold
Sphingomonas jejuensis	strain=DSM 27651	GCA_011927695.1	904715	904715	type	True	77.1915	109	1059	95	below_threshold
Aquisediminimonas sediminicola	strain=CH68-4	GCA_019740335.1	2676787	2676787	type	True	77.152	128	1059	95	below_threshold
Sphingomonas spermidinifaciens	strain=9NM-10	GCA_002351485.1	1141889	1141889	type	True	77.1467	124	1059	95	below_threshold
Rhizorhabdus phycosphaerae	strain=MK52	GCA_011044255.1	2711156	2711156	type	True	77.0855	144	1059	95	below_threshold
Sphingosinicella humi	strain=QZX222	GCA_003129465.1	2068657	2068657	type	True	77.0516	129	1059	95	below_threshold
Sphingomonas hengshuiensis	strain=WHSC-8	GCA_000935025.1	1609977	1609977	type	True	77.0468	169	1059	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	77.0272	131	1059	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	77.0214	112	1059	95	below_threshold
Sphingobium jiangsuense	strain=DSM 26189	GCA_014196495.1	870476	870476	type	True	77.0196	174	1059	95	below_threshold
Sphingomonas pituitosa	strain=NBRC 102491	GCA_001598435.1	99597	99597	type	True	76.8879	143	1059	95	below_threshold
Sphingomonas paeninsulae	strain=YZ-8	GCA_003660165.1	2319844	2319844	type	True	76.7859	107	1059	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 22:35:38,202] [INFO] DFAST Taxonomy check result was written to GCA_016715255.1_ASM1671525v1_genomic.fna/tc_result.tsv
[2023-06-29 22:35:38,203] [INFO] ===== Taxonomy check completed =====
[2023-06-29 22:35:38,203] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 22:35:38,203] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b7dd3f7-1ea3-4368-8436-8b9350253450/dqc_reference/checkm_data
[2023-06-29 22:35:38,205] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 22:35:38,238] [INFO] Task started: CheckM
[2023-06-29 22:35:38,238] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016715255.1_ASM1671525v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016715255.1_ASM1671525v1_genomic.fna/checkm_input GCA_016715255.1_ASM1671525v1_genomic.fna/checkm_result
[2023-06-29 22:36:12,158] [INFO] Task succeeded: CheckM
[2023-06-29 22:36:12,159] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.44%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 22:36:12,180] [INFO] ===== Completeness check finished =====
[2023-06-29 22:36:12,181] [INFO] ===== Start GTDB Search =====
[2023-06-29 22:36:12,181] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016715255.1_ASM1671525v1_genomic.fna/markers.fasta)
[2023-06-29 22:36:12,182] [INFO] Task started: Blastn
[2023-06-29 22:36:12,182] [INFO] Running command: blastn -query GCA_016715255.1_ASM1671525v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b7dd3f7-1ea3-4368-8436-8b9350253450/dqc_reference/reference_markers_gtdb.fasta -out GCA_016715255.1_ASM1671525v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:36:13,466] [INFO] Task succeeded: Blastn
[2023-06-29 22:36:13,488] [INFO] Selected 26 target genomes.
[2023-06-29 22:36:13,488] [INFO] Target genome list was writen to GCA_016715255.1_ASM1671525v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 22:36:13,505] [INFO] Task started: fastANI
[2023-06-29 22:36:13,505] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d907b49-d1f8-4e66-92df-b163e50ae6a6/GCA_016715255.1_ASM1671525v1_genomic.fna.gz --refList GCA_016715255.1_ASM1671525v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016715255.1_ASM1671525v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 22:36:29,228] [INFO] Task succeeded: fastANI
[2023-06-29 22:36:29,249] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 22:36:29,249] [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
GCA_016704425.1	s__Chakrabartia sp016704425	99.5257	994	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Chakrabartia	95.0	98.81	97.63	0.91	0.86	10	conclusive
GCA_005518185.1	s__Chakrabartia godavariana	77.9924	233	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Chakrabartia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000512205.2	s__Sphingomonas_D sanxanigenens	77.5336	172	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009753715.1	s__Sphingomonas_B horti	77.5042	159	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001724715.1	s__SCN-67-18 sp001724715	77.5033	169	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__SCN-67-18	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003355005.1	s__Sphingomonas sp003355005	77.4931	142	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000281715.1	s__Sphingobium sp000281715	77.3661	145	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003515075.1	s__Sphingomonas gilva	77.3632	158	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006438735.1	s__Sphingomonas koreensis_A	77.3593	146	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.05	96.05	0.80	0.80	2	-
GCA_002280555.1	s__Sphingomonas sp002280555	77.358	124	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.55	97.47	0.91	0.90	3	-
GCF_001468225.1	s__Sphingopyxis sp001468225	77.3555	169	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.99	99.97	0.98	0.96	8	-
GCF_011057975.1	s__Sphingomonas sp011057975	77.3358	153	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000974765.1	s__Sphingomonas_B changbaiensis	77.2718	151	1059	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_002953135.1	s__Sphingobium sp002953135	77.2569	109	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004792685.1	s__Sphingomonas gei	77.2492	134	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927695.1	s__Sphingomonas_K jejuensis	77.1915	109	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003347635.1	s__Allosphingosinicella sp003347635	77.0056	108	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421965.1	s__Sphingomonas sp001421965	76.9646	136	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.43	97.43	0.91	0.91	2	-
GCA_001464615.1	s__Sphingomonas sp001464615	76.9636	135	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.17	95.17	0.82	0.82	2	-
GCA_016742125.1	s__Sphingorhabdus_B sp016742125	76.9243	108	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003660165.1	s__UBA1936 sp003660165	76.7859	107	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__UBA1936	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002281485.1	s__Sphingomonas sp002281485	76.7426	142	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009885425.1	s__Novosphingobium sp009885425	76.7178	62	1059	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 22:36:29,252] [INFO] GTDB search result was written to GCA_016715255.1_ASM1671525v1_genomic.fna/result_gtdb.tsv
[2023-06-29 22:36:29,252] [INFO] ===== GTDB Search completed =====
[2023-06-29 22:36:29,257] [INFO] DFAST_QC result json was written to GCA_016715255.1_ASM1671525v1_genomic.fna/dqc_result.json
[2023-06-29 22:36:29,258] [INFO] DFAST_QC completed!
[2023-06-29 22:36:29,258] [INFO] Total running time: 0h1m18s