[2024-01-24 14:30:59,440] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:59,442] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:59,442] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a96d054-c2b5-421f-b621-48d62a3ae2b3/dqc_reference
[2024-01-24 14:31:00,737] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:00,738] [INFO] Task started: Prodigal
[2024-01-24 14:31:00,739] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f67095c-9ff3-4b84-a062-b89f7c28af8e/GCF_003953035.1_ASM395303v1_genomic.fna.gz | prodigal -d GCF_003953035.1_ASM395303v1_genomic.fna/cds.fna -a GCF_003953035.1_ASM395303v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:14,152] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:14,153] [INFO] Task started: HMMsearch
[2024-01-24 14:31:14,153] [INFO] Running command: hmmsearch --tblout GCF_003953035.1_ASM395303v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a96d054-c2b5-421f-b621-48d62a3ae2b3/dqc_reference/reference_markers.hmm GCF_003953035.1_ASM395303v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:14,483] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:14,484] [INFO] Found 6/6 markers.
[2024-01-24 14:31:14,530] [INFO] Query marker FASTA was written to GCF_003953035.1_ASM395303v1_genomic.fna/markers.fasta
[2024-01-24 14:31:14,531] [INFO] Task started: Blastn
[2024-01-24 14:31:14,531] [INFO] Running command: blastn -query GCF_003953035.1_ASM395303v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a96d054-c2b5-421f-b621-48d62a3ae2b3/dqc_reference/reference_markers.fasta -out GCF_003953035.1_ASM395303v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:15,644] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:15,647] [INFO] Selected 13 target genomes.
[2024-01-24 14:31:15,648] [INFO] Target genome list was writen to GCF_003953035.1_ASM395303v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:15,655] [INFO] Task started: fastANI
[2024-01-24 14:31:15,655] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f67095c-9ff3-4b84-a062-b89f7c28af8e/GCF_003953035.1_ASM395303v1_genomic.fna.gz --refList GCF_003953035.1_ASM395303v1_genomic.fna/target_genomes.txt --output GCF_003953035.1_ASM395303v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:28,544] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:28,545] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a96d054-c2b5-421f-b621-48d62a3ae2b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:28,545] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a96d054-c2b5-421f-b621-48d62a3ae2b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:28,557] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:31:28,558] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:28,558] [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 koreensis	strain=KCTC 2882	GCA_003953035.1	93064	93064	type	True	100.0	1415	1417	95	conclusive
Sphingomonas koreensis	strain=JSS26	GCA_002797435.1	93064	93064	type	True	99.9984	1416	1417	95	conclusive
Sphingomonas koreensis	strain=NBRC 16723	GCA_001598395.1	93064	93064	type	True	99.9852	1389	1417	95	conclusive
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	82.6277	797	1417	95	below_threshold
Sphingomonas turrisvirgatae	strain=MCT13	GCA_001721295.1	1888892	1888892	type	True	81.8255	689	1417	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	80.795	686	1417	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	80.7238	702	1417	95	below_threshold
Sphingomonas soli	strain=NBRC 100801	GCA_001591025.1	266127	266127	type	True	79.8479	549	1417	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	79.6962	681	1417	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	79.6368	546	1417	95	below_threshold
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	79.3685	531	1417	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	79.3409	539	1417	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	78.8403	553	1417	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:28,560] [INFO] DFAST Taxonomy check result was written to GCF_003953035.1_ASM395303v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:28,560] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:28,560] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:28,561] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a96d054-c2b5-421f-b621-48d62a3ae2b3/dqc_reference/checkm_data
[2024-01-24 14:31:28,571] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:28,619] [INFO] Task started: CheckM
[2024-01-24 14:31:28,620] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003953035.1_ASM395303v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003953035.1_ASM395303v1_genomic.fna/checkm_input GCF_003953035.1_ASM395303v1_genomic.fna/checkm_result
[2024-01-24 14:32:07,881] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:07,882] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:07,904] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:07,905] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:07,905] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003953035.1_ASM395303v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:07,906] [INFO] Task started: Blastn
[2024-01-24 14:32:07,906] [INFO] Running command: blastn -query GCF_003953035.1_ASM395303v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a96d054-c2b5-421f-b621-48d62a3ae2b3/dqc_reference/reference_markers_gtdb.fasta -out GCF_003953035.1_ASM395303v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:09,884] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:09,888] [INFO] Selected 12 target genomes.
[2024-01-24 14:32:09,889] [INFO] Target genome list was writen to GCF_003953035.1_ASM395303v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:09,899] [INFO] Task started: fastANI
[2024-01-24 14:32:09,899] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f67095c-9ff3-4b84-a062-b89f7c28af8e/GCF_003953035.1_ASM395303v1_genomic.fna.gz --refList GCF_003953035.1_ASM395303v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003953035.1_ASM395303v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:20,458] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:20,471] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:20,472] [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_002797435.1	s__Sphingomonas koreensis	99.9984	1416	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.13	98.00	0.88	0.86	72	conclusive
GCF_001557215.1	s__Sphingomonas sp001557215	83.5258	678	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.89	99.89	0.91	0.91	2	-
GCF_007833215.1	s__Sphingomonas sp007833215	82.6101	799	1417	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	81.8018	691	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826325.1	s__Sphingomonas sp902826325	81.7814	506	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.74	97.74	0.84	0.84	2	-
GCF_004792695.1	s__Sphingomonas naasensis	80.7973	685	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017418975.1	s__Sphingomonas sp017418975	80.6757	678	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744835.1	s__Sphingomonas sp017744835	80.5932	649	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114095.1	s__Sphingomonas sp900114095	80.329	605	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000226955.1	s__Sphingomonas elodea_A	80.22	579	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591025.1	s__Sphingomonas soli	79.8229	552	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004173185.1	s__Sphingomonas sp004173185	79.2697	560	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:20,474] [INFO] GTDB search result was written to GCF_003953035.1_ASM395303v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:20,474] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:20,480] [INFO] DFAST_QC result json was written to GCF_003953035.1_ASM395303v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:20,480] [INFO] DFAST_QC completed!
[2024-01-24 14:32:20,480] [INFO] Total running time: 0h1m21s