[2024-01-25 18:53:50,598] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:53:50,600] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:53:50,600] [INFO] DQC Reference Directory: /var/lib/cwl/stg8cd9c31a-3263-45e5-8e83-1090b1d90764/dqc_reference
[2024-01-25 18:53:51,728] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:53:51,729] [INFO] Task started: Prodigal
[2024-01-25 18:53:51,729] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ac6852c-4d9d-4c9e-a50b-751f3bc099d3/GCF_018122655.1_ASM1812265v1_genomic.fna.gz | prodigal -d GCF_018122655.1_ASM1812265v1_genomic.fna/cds.fna -a GCF_018122655.1_ASM1812265v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:54:00,354] [INFO] Task succeeded: Prodigal
[2024-01-25 18:54:00,354] [INFO] Task started: HMMsearch
[2024-01-25 18:54:00,354] [INFO] Running command: hmmsearch --tblout GCF_018122655.1_ASM1812265v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8cd9c31a-3263-45e5-8e83-1090b1d90764/dqc_reference/reference_markers.hmm GCF_018122655.1_ASM1812265v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:54:00,579] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:54:00,580] [INFO] Found 6/6 markers.
[2024-01-25 18:54:00,607] [INFO] Query marker FASTA was written to GCF_018122655.1_ASM1812265v1_genomic.fna/markers.fasta
[2024-01-25 18:54:00,607] [INFO] Task started: Blastn
[2024-01-25 18:54:00,608] [INFO] Running command: blastn -query GCF_018122655.1_ASM1812265v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8cd9c31a-3263-45e5-8e83-1090b1d90764/dqc_reference/reference_markers.fasta -out GCF_018122655.1_ASM1812265v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:01,510] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:01,513] [INFO] Selected 21 target genomes.
[2024-01-25 18:54:01,513] [INFO] Target genome list was writen to GCF_018122655.1_ASM1812265v1_genomic.fna/target_genomes.txt
[2024-01-25 18:54:01,539] [INFO] Task started: fastANI
[2024-01-25 18:54:01,539] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ac6852c-4d9d-4c9e-a50b-751f3bc099d3/GCF_018122655.1_ASM1812265v1_genomic.fna.gz --refList GCF_018122655.1_ASM1812265v1_genomic.fna/target_genomes.txt --output GCF_018122655.1_ASM1812265v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:54:17,968] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:17,968] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8cd9c31a-3263-45e5-8e83-1090b1d90764/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:54:17,968] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8cd9c31a-3263-45e5-8e83-1090b1d90764/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:54:17,980] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:54:17,981] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:54:17,981] [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	80.5508	573	1101	95	below_threshold
Stakelama pacifica	strain=CGMCC 1.7294	GCA_014645395.1	517720	517720	type	True	80.4877	576	1101	95	below_threshold
Stakelama flava	strain=CBK3Z-3	GCA_019351405.1	2860338	2860338	type	True	79.9266	514	1101	95	below_threshold
Stakelama sediminis	strain=DSM 27203	GCA_014199335.1	463200	463200	type	True	79.8415	543	1101	95	below_threshold
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	79.6941	540	1101	95	below_threshold
Sphingosinithalassobacter portus	strain=FM6	GCA_003171655.1	2676234	2676234	type	True	79.6711	518	1101	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	79.6211	539	1101	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	79.5876	545	1101	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	79.5368	476	1101	95	below_threshold
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	79.3388	507	1101	95	below_threshold
Sphingomonas desiccabilis	strain=CP1D	GCA_004135605.1	429134	429134	type	True	79.2807	428	1101	95	below_threshold
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	79.1492	477	1101	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	79.0382	506	1101	95	below_threshold
Sphingomonas glacialis	strain=CGMCC 1.8957	GCA_014653575.1	658225	658225	type	True	78.982	488	1101	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	78.9695	482	1101	95	below_threshold
Sphingomonas rubra	strain=CGMCC 1.9113	GCA_900115745.1	634430	634430	type	True	78.8574	393	1101	95	below_threshold
Sphingomonas asaccharolytica	strain=NBRC 15499	GCA_001598355.1	40681	40681	type	True	78.8479	425	1101	95	below_threshold
Sphingomonas dokdonensis	strain=DSM 21029	GCA_002197685.1	344880	344880	type	True	78.8473	366	1101	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	78.6105	408	1101	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	78.539	434	1101	95	below_threshold
Sphingomonas parva	strain=17J27-24	GCA_004564275.1	2555898	2555898	type	True	77.9372	338	1101	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:54:17,982] [INFO] DFAST Taxonomy check result was written to GCF_018122655.1_ASM1812265v1_genomic.fna/tc_result.tsv
[2024-01-25 18:54:17,983] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:54:17,983] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:54:17,983] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8cd9c31a-3263-45e5-8e83-1090b1d90764/dqc_reference/checkm_data
[2024-01-25 18:54:17,984] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:54:18,018] [INFO] Task started: CheckM
[2024-01-25 18:54:18,018] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018122655.1_ASM1812265v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018122655.1_ASM1812265v1_genomic.fna/checkm_input GCF_018122655.1_ASM1812265v1_genomic.fna/checkm_result
[2024-01-25 18:54:45,432] [INFO] Task succeeded: CheckM
[2024-01-25 18:54:45,433] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:54:45,452] [INFO] ===== Completeness check finished =====
[2024-01-25 18:54:45,452] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:54:45,452] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018122655.1_ASM1812265v1_genomic.fna/markers.fasta)
[2024-01-25 18:54:45,453] [INFO] Task started: Blastn
[2024-01-25 18:54:45,453] [INFO] Running command: blastn -query GCF_018122655.1_ASM1812265v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8cd9c31a-3263-45e5-8e83-1090b1d90764/dqc_reference/reference_markers_gtdb.fasta -out GCF_018122655.1_ASM1812265v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:47,223] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:47,226] [INFO] Selected 24 target genomes.
[2024-01-25 18:54:47,226] [INFO] Target genome list was writen to GCF_018122655.1_ASM1812265v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:54:47,247] [INFO] Task started: fastANI
[2024-01-25 18:54:47,248] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ac6852c-4d9d-4c9e-a50b-751f3bc099d3/GCF_018122655.1_ASM1812265v1_genomic.fna.gz --refList GCF_018122655.1_ASM1812265v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018122655.1_ASM1812265v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:55:06,489] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:06,504] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:55:06,504] [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_018122655.1	s__Sphingomonas sp018122655	100.0	1101	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004361835.1	s__Sphingomonas pacifica	80.526	575	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.75	97.51	0.88	0.77	3	-
GCF_014199335.1	s__Sphingomonas sediminis	79.8518	542	1101	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	79.7134	538	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003550065.1	s__Sphingomonas caeni	79.6866	525	1101	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	79.6719	517	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449795.1	s__Sphingomonas sp018449795	79.6431	520	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004792695.1	s__Sphingomonas naasensis	79.5789	546	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005144715.1	s__Sphingomonas sp005144715	79.5472	475	1101	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	79.4875	482	1101	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	79.4811	514	1101	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	79.401	459	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764535.1	s__Sphingomonas taxi	79.3491	506	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.55	97.55	0.88	0.88	2	-
GCF_001421765.1	s__Sphingomonas sp001421765	79.275	466	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	3	-
GCF_004341505.2	s__Sphingomonas sp004341505	79.2723	421	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.45	95.45	0.78	0.78	2	-
GCF_004135605.1	s__Sphingomonas desiccabilis	79.2594	430	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014199325.1	s__Sphingomonas yantingensis	79.2441	475	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.75	96.75	0.89	0.89	2	-
GCF_003946805.1	s__Sphingomonas sp003946805	79.233	478	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489075.1	s__Sphingomonas sp014489075	79.2265	512	1101	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	79.1818	448	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002351485.1	s__Sphingomonas spermidinifaciens	79.1628	469	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004799495.1	s__Sphingomonas sp004799495	78.7751	455	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903884945.1	s__Sphingomonas sp903884945	78.6633	484	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241685.1	s__Sphingopyxis macrogoltabida_A	77.9721	375	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:55:06,506] [INFO] GTDB search result was written to GCF_018122655.1_ASM1812265v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:55:06,507] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:55:06,511] [INFO] DFAST_QC result json was written to GCF_018122655.1_ASM1812265v1_genomic.fna/dqc_result.json
[2024-01-25 18:55:06,511] [INFO] DFAST_QC completed!
[2024-01-25 18:55:06,511] [INFO] Total running time: 0h1m16s