[2024-01-25 20:26:35,922] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:26:35,923] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:26:35,924] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e643d35-9348-4538-9b13-d3e714d9563f/dqc_reference
[2024-01-25 20:26:37,139] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:26:37,140] [INFO] Task started: Prodigal
[2024-01-25 20:26:37,140] [INFO] Running command: gunzip -c /var/lib/cwl/stg8aee5f66-1b11-4def-9d07-47ebc88a7b8a/GCF_018603885.1_ASM1860388v1_genomic.fna.gz | prodigal -d GCF_018603885.1_ASM1860388v1_genomic.fna/cds.fna -a GCF_018603885.1_ASM1860388v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:26:48,680] [INFO] Task succeeded: Prodigal
[2024-01-25 20:26:48,681] [INFO] Task started: HMMsearch
[2024-01-25 20:26:48,681] [INFO] Running command: hmmsearch --tblout GCF_018603885.1_ASM1860388v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e643d35-9348-4538-9b13-d3e714d9563f/dqc_reference/reference_markers.hmm GCF_018603885.1_ASM1860388v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:26:48,917] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:26:48,918] [INFO] Found 6/6 markers.
[2024-01-25 20:26:48,958] [INFO] Query marker FASTA was written to GCF_018603885.1_ASM1860388v1_genomic.fna/markers.fasta
[2024-01-25 20:26:48,958] [INFO] Task started: Blastn
[2024-01-25 20:26:48,958] [INFO] Running command: blastn -query GCF_018603885.1_ASM1860388v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e643d35-9348-4538-9b13-d3e714d9563f/dqc_reference/reference_markers.fasta -out GCF_018603885.1_ASM1860388v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:26:49,888] [INFO] Task succeeded: Blastn
[2024-01-25 20:26:49,898] [INFO] Selected 24 target genomes.
[2024-01-25 20:26:49,898] [INFO] Target genome list was writen to GCF_018603885.1_ASM1860388v1_genomic.fna/target_genomes.txt
[2024-01-25 20:26:49,911] [INFO] Task started: fastANI
[2024-01-25 20:26:49,912] [INFO] Running command: fastANI --query /var/lib/cwl/stg8aee5f66-1b11-4def-9d07-47ebc88a7b8a/GCF_018603885.1_ASM1860388v1_genomic.fna.gz --refList GCF_018603885.1_ASM1860388v1_genomic.fna/target_genomes.txt --output GCF_018603885.1_ASM1860388v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:27:07,628] [INFO] Task succeeded: fastANI
[2024-01-25 20:27:07,628] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e643d35-9348-4538-9b13-d3e714d9563f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:27:07,628] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e643d35-9348-4538-9b13-d3e714d9563f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:27:07,642] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:27:07,642] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:27:07,642] [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
Sphingobium xanthum	strain=NL9	GCA_019737615.1	1387165	1387165	type	True	82.6952	882	1470	95	below_threshold
Sphingobium jiangsuense	strain=DSM 26189	GCA_014196495.1	870476	870476	type	True	79.1105	481	1470	95	below_threshold
Sphingobium ummariense	strain=RL-3	GCA_000447205.1	420994	420994	type	True	79.0861	478	1470	95	below_threshold
Sphingobium amiense	strain=DSM 16289	GCA_003967075.1	135719	135719	type	True	78.9704	421	1470	95	below_threshold
Sphingobium amiense	strain=NBRC 102518	GCA_001591305.1	135719	135719	type	True	78.8717	409	1470	95	below_threshold
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	78.7866	506	1470	95	below_threshold
Sphingobium wenxiniae	strain=CGMCC 1.7748	GCA_007830065.1	595605	595605	type	True	78.7471	378	1470	95	below_threshold
Sphingobium wenxiniae	strain=JZ-1	GCA_014205735.1	595605	595605	type	True	78.7101	366	1470	95	below_threshold
Sphingomonas fennica	strain=K101	GCA_003034225.1	114404	114404	type	True	78.6367	390	1470	95	below_threshold
Sphingobium quisquiliarum	strain=P25	GCA_000445065.1	538379	538379	type	True	78.5025	367	1470	95	below_threshold
Sphingomonas oligoaromativorans	strain=DSM 102246	GCA_011762195.1	575322	575322	type	True	78.4899	403	1470	95	below_threshold
Sphingomonas chungangi	strain=CGMCC 1.13654	GCA_013778325.1	2683589	2683589	type	True	78.487	389	1470	95	below_threshold
Sphingobium sufflavum	strain=HL-25	GCA_021403115.1	1129547	1129547	type	True	78.3157	408	1470	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	78.1863	360	1470	95	below_threshold
Sphingomonas changbaiensis	strain=NBRC 104936	GCA_000974765.1	529705	529705	type	True	78.1522	335	1470	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	78.1427	344	1470	95	below_threshold
Sphingomonas parva	strain=17J27-24	GCA_004564275.1	2555898	2555898	type	True	78.1371	332	1470	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.1093	338	1470	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	78.0561	366	1470	95	below_threshold
Sphingomonas gei	strain=ZFGT-11	GCA_004792685.1	1395960	1395960	type	True	77.9435	398	1470	95	below_threshold
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	77.9201	347	1470	95	below_threshold
Sphingobium algorifonticola	strain=TLA-22	GCA_004005485.1	2008318	2008318	type	True	77.8795	345	1470	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	77.6589	379	1470	95	below_threshold
Sphingomonas jejuensis	strain=DSM 27651	GCA_011927695.1	904715	904715	type	True	77.575	286	1470	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:27:07,645] [INFO] DFAST Taxonomy check result was written to GCF_018603885.1_ASM1860388v1_genomic.fna/tc_result.tsv
[2024-01-25 20:27:07,646] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:27:07,646] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:27:07,646] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e643d35-9348-4538-9b13-d3e714d9563f/dqc_reference/checkm_data
[2024-01-25 20:27:07,647] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:27:07,687] [INFO] Task started: CheckM
[2024-01-25 20:27:07,687] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018603885.1_ASM1860388v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018603885.1_ASM1860388v1_genomic.fna/checkm_input GCF_018603885.1_ASM1860388v1_genomic.fna/checkm_result
[2024-01-25 20:27:43,041] [INFO] Task succeeded: CheckM
[2024-01-25 20:27:43,042] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:27:43,061] [INFO] ===== Completeness check finished =====
[2024-01-25 20:27:43,061] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:27:43,062] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018603885.1_ASM1860388v1_genomic.fna/markers.fasta)
[2024-01-25 20:27:43,062] [INFO] Task started: Blastn
[2024-01-25 20:27:43,062] [INFO] Running command: blastn -query GCF_018603885.1_ASM1860388v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e643d35-9348-4538-9b13-d3e714d9563f/dqc_reference/reference_markers_gtdb.fasta -out GCF_018603885.1_ASM1860388v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:27:44,907] [INFO] Task succeeded: Blastn
[2024-01-25 20:27:44,910] [INFO] Selected 9 target genomes.
[2024-01-25 20:27:44,910] [INFO] Target genome list was writen to GCF_018603885.1_ASM1860388v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:27:44,917] [INFO] Task started: fastANI
[2024-01-25 20:27:44,917] [INFO] Running command: fastANI --query /var/lib/cwl/stg8aee5f66-1b11-4def-9d07-47ebc88a7b8a/GCF_018603885.1_ASM1860388v1_genomic.fna.gz --refList GCF_018603885.1_ASM1860388v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018603885.1_ASM1860388v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:27:52,984] [INFO] Task succeeded: fastANI
[2024-01-25 20:27:52,991] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:27:52,991] [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_018603885.1	s__Sphingobium sp018603885	100.0	1469	1470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017304105.1	s__Sphingobium sp017304105	82.6128	667	1470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304655.1	s__Sphingobium sp017304655	81.6048	740	1470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899715.1	s__Sphingobium sp001899715	81.001	704	1470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000283515.1	s__Sphingobium sp000283515	80.7816	725	1470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	96.32	96.27	0.90	0.89	5	-
GCF_014201265.1	s__Sphingobium sp014201265	80.7533	600	1470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	100.00	100.00	1.00	1.00	3	-
GCA_017744605.1	s__Sphingobium sp017744605	80.298	560	1470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018823325.1	s__Sphingobium sp018823325	80.1146	619	1470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.99	99.99	0.97	0.94	4	-
GCA_017745115.1	s__Sphingobium sp017745115	79.9445	478	1470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:27:52,992] [INFO] GTDB search result was written to GCF_018603885.1_ASM1860388v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:27:52,993] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:27:52,996] [INFO] DFAST_QC result json was written to GCF_018603885.1_ASM1860388v1_genomic.fna/dqc_result.json
[2024-01-25 20:27:52,996] [INFO] DFAST_QC completed!
[2024-01-25 20:27:52,996] [INFO] Total running time: 0h1m17s