[2024-01-24 13:49:55,176] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:55,177] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:55,178] [INFO] DQC Reference Directory: /var/lib/cwl/stg65e7bcc9-6c14-404f-beec-02aa173408d1/dqc_reference
[2024-01-24 13:49:56,304] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:56,305] [INFO] Task started: Prodigal
[2024-01-24 13:49:56,305] [INFO] Running command: gunzip -c /var/lib/cwl/stgc6f07d95-0357-4728-b80f-1c91d585f286/GCF_019880585.1_ASM1988058v1_genomic.fna.gz | prodigal -d GCF_019880585.1_ASM1988058v1_genomic.fna/cds.fna -a GCF_019880585.1_ASM1988058v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:13,219] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:13,220] [INFO] Task started: HMMsearch
[2024-01-24 13:50:13,220] [INFO] Running command: hmmsearch --tblout GCF_019880585.1_ASM1988058v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg65e7bcc9-6c14-404f-beec-02aa173408d1/dqc_reference/reference_markers.hmm GCF_019880585.1_ASM1988058v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:13,472] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:13,473] [INFO] Found 6/6 markers.
[2024-01-24 13:50:13,523] [INFO] Query marker FASTA was written to GCF_019880585.1_ASM1988058v1_genomic.fna/markers.fasta
[2024-01-24 13:50:13,523] [INFO] Task started: Blastn
[2024-01-24 13:50:13,523] [INFO] Running command: blastn -query GCF_019880585.1_ASM1988058v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65e7bcc9-6c14-404f-beec-02aa173408d1/dqc_reference/reference_markers.fasta -out GCF_019880585.1_ASM1988058v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:14,300] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:14,302] [INFO] Selected 24 target genomes.
[2024-01-24 13:50:14,303] [INFO] Target genome list was writen to GCF_019880585.1_ASM1988058v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:14,309] [INFO] Task started: fastANI
[2024-01-24 13:50:14,309] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6f07d95-0357-4728-b80f-1c91d585f286/GCF_019880585.1_ASM1988058v1_genomic.fna.gz --refList GCF_019880585.1_ASM1988058v1_genomic.fna/target_genomes.txt --output GCF_019880585.1_ASM1988058v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:34,572] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:34,573] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg65e7bcc9-6c14-404f-beec-02aa173408d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:34,573] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg65e7bcc9-6c14-404f-beec-02aa173408d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:34,586] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:34,586] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:34,586] [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
Sphingomonas colocasiae	strain=JCM 31229	GCA_019880585.1	1848973	1848973	type	True	100.0	2171	2178	95	conclusive
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	80.3362	658	2178	95	below_threshold
Sphingobium boeckii	strain=DSM 25079	GCA_014199215.1	1082345	1082345	type	True	79.5628	587	2178	95	below_threshold
Sphingomonas gilva	strain=ZDH117	GCA_003515075.1	2305907	2305907	type	True	79.3942	559	2178	95	below_threshold
Sphingomonas leidyi	strain=DSM 4733	GCA_011761945.1	68569	68569	type	True	79.2066	599	2178	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	79.076	507	2178	95	below_threshold
Sphingomonas oleivorans	strain=FW-11	GCA_003050615.1	1735121	1735121	type	True	79.0334	493	2178	95	below_threshold
Sphingomonas horti	strain=MAH-20	GCA_009753715.1	2682842	2682842	type	True	78.9479	510	2178	95	below_threshold
Sphingomonas trueperi	strain=DSM 7225	GCA_011927635.1	53317	53317	type	True	78.9376	543	2178	95	below_threshold
Sphingomonas koreensis	strain=NBRC 16723	GCA_001598395.1	93064	93064	type	True	78.9075	566	2178	95	below_threshold
Sphingomonas changbaiensis	strain=NBRC 104936	GCA_000974765.1	529705	529705	type	True	78.8097	463	2178	95	below_threshold
Sphingomonas desiccabilis	strain=CP1D	GCA_004135605.1	429134	429134	type	True	78.7587	443	2178	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	78.7352	556	2178	95	below_threshold
Sphingomonas pituitosa	strain=NBRC 102491	GCA_001598435.1	99597	99597	type	True	78.7269	537	2178	95	below_threshold
Sphingomonas soli	strain=NBRC 100801	GCA_001591025.1	266127	266127	type	True	78.675	496	2178	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	78.6564	520	2178	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	78.5843	597	2178	95	below_threshold
Sphingobium amiense	strain=DSM 16289	GCA_003967075.1	135719	135719	type	True	78.5555	451	2178	95	below_threshold
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	78.5384	489	2178	95	below_threshold
Sphingomonas glacialis	strain=CGMCC 1.8957	GCA_014653575.1	658225	658225	type	True	78.4067	490	2178	95	below_threshold
Sphingomonas jejuensis	strain=DSM 27651	GCA_011927695.1	904715	904715	type	True	78.2968	375	2178	95	below_threshold
Sphingomonas solaris	strain=R4DWN	GCA_007785815.1	2529389	2529389	type	True	78.2386	468	2178	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	78.0682	522	2178	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	77.9916	510	2178	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:34,587] [INFO] DFAST Taxonomy check result was written to GCF_019880585.1_ASM1988058v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:34,588] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:34,588] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:34,588] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg65e7bcc9-6c14-404f-beec-02aa173408d1/dqc_reference/checkm_data
[2024-01-24 13:50:34,589] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:34,648] [INFO] Task started: CheckM
[2024-01-24 13:50:34,648] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019880585.1_ASM1988058v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019880585.1_ASM1988058v1_genomic.fna/checkm_input GCF_019880585.1_ASM1988058v1_genomic.fna/checkm_result
[2024-01-24 13:51:36,859] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:36,860] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:36,875] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:36,875] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:36,875] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019880585.1_ASM1988058v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:36,876] [INFO] Task started: Blastn
[2024-01-24 13:51:36,876] [INFO] Running command: blastn -query GCF_019880585.1_ASM1988058v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65e7bcc9-6c14-404f-beec-02aa173408d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_019880585.1_ASM1988058v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:38,250] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:38,268] [INFO] Selected 30 target genomes.
[2024-01-24 13:51:38,268] [INFO] Target genome list was writen to GCF_019880585.1_ASM1988058v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:38,643] [INFO] Task started: fastANI
[2024-01-24 13:51:38,643] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6f07d95-0357-4728-b80f-1c91d585f286/GCF_019880585.1_ASM1988058v1_genomic.fna.gz --refList GCF_019880585.1_ASM1988058v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019880585.1_ASM1988058v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:52:01,364] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:01,380] [INFO] Found 30 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:52:01,381] [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_003590775.1	s__Sphingobium_A sp003590775	80.3361	657	2178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199215.1	s__Sphingobium_A boeckii	79.5543	588	2178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003240855.1	s__Sphingomonas_L sanxanigenens_A	79.4977	480	2178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_L	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724715.1	s__SCN-67-18 sp001724715	79.2472	523	2178	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_011761945.1	s__Sphingomonas leidyi	79.1679	604	2178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.87	98.83	0.90	0.87	3	-
GCF_000016765.1	s__Rhizorhabdus wittichii	79.1034	682	2178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	98.56	98.46	0.83	0.82	5	-
GCA_017418975.1	s__Sphingomonas sp017418975	79.0934	620	2178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188165.1	s__Sphingomonas_E laterariae	79.0399	578	2178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177405.1	s__Allosphingosinicella indica	78.9576	467	2178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009753715.1	s__Sphingomonas_B horti	78.9471	509	2178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002127225.1	s__Sphingomonas sp002127225	78.8908	616	2178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013416555.1	s__Sphingomonas sp013416555	78.8866	556	2178	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	78.8504	485	2178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.33	97.92	0.88	0.78	8	-
GCF_008274695.1	s__Rhizorhabdus montanisoli	78.8292	463	2178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341505.2	s__Sphingomonas sp004341505	78.7164	446	2178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.45	95.45	0.78	0.78	2	-
GCF_004796535.1	s__Sphingomonas_L sp004796535	78.6947	516	2178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014334115.1	s__Sphingomonas sp014334115	78.6296	498	2178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019239915.1	s__Sphingomonas_N sp019239915	78.6023	424	2178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011057975.1	s__Sphingomonas sp011057975	78.539	489	2178	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	78.5334	495	2178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.05	96.05	0.80	0.80	2	-
GCF_001421505.1	s__Sphingomonas sp001421505	78.4586	435	2178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006439055.1	s__Sphingomonas glacialis_A	78.4187	521	2178	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	78.341	370	2178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000241485.1	s__Sphingomonas sp000241485	78.2862	512	2178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899715.1	s__Sphingobium sp001899715	78.042	403	2178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193845.1	s__Sphingomonas sp014193845	77.9656	504	2178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.90	98.90	0.87	0.87	2	-
GCF_014194975.1	s__Sphingomonas sp014194975	77.9434	505	2178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900117425.1	s__Novosphingobium sp900117425	77.6033	352	2178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.26	96.76	0.88	0.87	3	-
GCA_017643325.1	s__JABJAG01 sp017643325	75.7794	105	2178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABJAG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793165.1	s__CAIOSQ01 sp016793165	75.2051	342	2178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__CAIOSQ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:52:01,382] [INFO] GTDB search result was written to GCF_019880585.1_ASM1988058v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:52:01,383] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:52:01,386] [INFO] DFAST_QC result json was written to GCF_019880585.1_ASM1988058v1_genomic.fna/dqc_result.json
[2024-01-24 13:52:01,386] [INFO] DFAST_QC completed!
[2024-01-24 13:52:01,387] [INFO] Total running time: 0h2m6s