[2024-01-24 11:51:06,407] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:06,409] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:06,409] [INFO] DQC Reference Directory: /var/lib/cwl/stg783858a5-56c4-443a-b014-26cd618d985c/dqc_reference
[2024-01-24 11:51:08,674] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:08,675] [INFO] Task started: Prodigal
[2024-01-24 11:51:08,676] [INFO] Running command: gunzip -c /var/lib/cwl/stg932f9446-1954-4a51-be62-eeca00e06f89/GCF_022664435.1_ASM2266443v1_genomic.fna.gz | prodigal -d GCF_022664435.1_ASM2266443v1_genomic.fna/cds.fna -a GCF_022664435.1_ASM2266443v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:20,575] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:20,575] [INFO] Task started: HMMsearch
[2024-01-24 11:51:20,575] [INFO] Running command: hmmsearch --tblout GCF_022664435.1_ASM2266443v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg783858a5-56c4-443a-b014-26cd618d985c/dqc_reference/reference_markers.hmm GCF_022664435.1_ASM2266443v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:20,907] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:20,908] [INFO] Found 6/6 markers.
[2024-01-24 11:51:20,958] [INFO] Query marker FASTA was written to GCF_022664435.1_ASM2266443v1_genomic.fna/markers.fasta
[2024-01-24 11:51:20,958] [INFO] Task started: Blastn
[2024-01-24 11:51:20,958] [INFO] Running command: blastn -query GCF_022664435.1_ASM2266443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg783858a5-56c4-443a-b014-26cd618d985c/dqc_reference/reference_markers.fasta -out GCF_022664435.1_ASM2266443v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:21,824] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:21,829] [INFO] Selected 20 target genomes.
[2024-01-24 11:51:21,830] [INFO] Target genome list was writen to GCF_022664435.1_ASM2266443v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:21,862] [INFO] Task started: fastANI
[2024-01-24 11:51:21,862] [INFO] Running command: fastANI --query /var/lib/cwl/stg932f9446-1954-4a51-be62-eeca00e06f89/GCF_022664435.1_ASM2266443v1_genomic.fna.gz --refList GCF_022664435.1_ASM2266443v1_genomic.fna/target_genomes.txt --output GCF_022664435.1_ASM2266443v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:38,147] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:38,147] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg783858a5-56c4-443a-b014-26cd618d985c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:38,148] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg783858a5-56c4-443a-b014-26cd618d985c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:38,167] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:38,167] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:38,167] [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 panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	100.0	1369	1369	95	conclusive
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	87.6148	950	1369	95	below_threshold
Sphingomonas adhaesiva	strain=NBRC 15099	GCA_001592345.1	28212	28212	type	True	81.1504	527	1369	95	below_threshold
Sphingomonas adhaesiva	strain=DSM 7418	GCA_002374855.1	28212	28212	type	True	80.3146	612	1369	95	below_threshold
Sphingomonas pseudosanguinis	strain=DSM 19512	GCA_014196255.1	413712	413712	type	True	80.2849	622	1369	95	below_threshold
Sphingomonas ginsenosidimutans	strain=KACC 14949	GCA_002374835.1	862134	862134	type	True	80.1084	595	1369	95	below_threshold
Sphingomonas yabuuchiae	strain=DSM 14562	GCA_014199595.1	172044	172044	type	True	79.9991	613	1369	95	below_threshold
Sphingomonas yabuuchiae	strain=DSM 14562	GCA_017052455.1	172044	172044	type	True	79.9941	609	1369	95	below_threshold
Sphingomonas desiccabilis	strain=DSM 16792	GCA_014196135.1	429134	429134	type	True	79.9488	537	1369	95	below_threshold
Sphingomonas desiccabilis	strain=CP1D	GCA_004135605.1	429134	429134	type	True	79.8966	538	1369	95	below_threshold
Sphingomonas turrisvirgatae	strain=MCT13	GCA_001721295.1	1888892	1888892	type	True	79.8749	478	1369	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	79.5906	576	1369	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	79.2692	493	1369	95	below_threshold
Sphingomonas koreensis	strain=NBRC 16723	GCA_001598395.1	93064	93064	type	True	79.2636	526	1369	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	79.0373	523	1369	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	78.9479	554	1369	95	below_threshold
Sphingobium wenxiniae	strain=JZ-1	GCA_014205735.1	595605	595605	type	True	78.9213	369	1369	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	78.7944	527	1369	95	below_threshold
Sphingobium jiangsuense	strain=DSM 26189	GCA_014196495.1	870476	870476	type	True	78.5215	440	1369	95	below_threshold
Blastomonas fulva	strain=T2	GCA_003431825.1	1550728	1550728	type	True	77.7814	330	1369	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:38,170] [INFO] DFAST Taxonomy check result was written to GCF_022664435.1_ASM2266443v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:38,171] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:38,172] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:38,172] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg783858a5-56c4-443a-b014-26cd618d985c/dqc_reference/checkm_data
[2024-01-24 11:51:38,173] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:38,214] [INFO] Task started: CheckM
[2024-01-24 11:51:38,214] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022664435.1_ASM2266443v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022664435.1_ASM2266443v1_genomic.fna/checkm_input GCF_022664435.1_ASM2266443v1_genomic.fna/checkm_result
[2024-01-24 11:52:14,687] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:14,691] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:14,710] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:14,711] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:14,711] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022664435.1_ASM2266443v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:14,711] [INFO] Task started: Blastn
[2024-01-24 11:52:14,712] [INFO] Running command: blastn -query GCF_022664435.1_ASM2266443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg783858a5-56c4-443a-b014-26cd618d985c/dqc_reference/reference_markers_gtdb.fasta -out GCF_022664435.1_ASM2266443v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:16,001] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:16,004] [INFO] Selected 8 target genomes.
[2024-01-24 11:52:16,005] [INFO] Target genome list was writen to GCF_022664435.1_ASM2266443v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:16,010] [INFO] Task started: fastANI
[2024-01-24 11:52:16,011] [INFO] Running command: fastANI --query /var/lib/cwl/stg932f9446-1954-4a51-be62-eeca00e06f89/GCF_022664435.1_ASM2266443v1_genomic.fna.gz --refList GCF_022664435.1_ASM2266443v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022664435.1_ASM2266443v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:24,573] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:24,580] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:52:24,581] [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_001619955.1	s__Sphingomonas hankookensis	89.5544	975	1369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.49	99.35	0.90	0.87	3	-
GCF_001421355.1	s__Sphingomonas sp001421355	89.4464	981	1369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.29	96.58	0.97	0.94	3	-
GCF_001421765.1	s__Sphingomonas sp001421765	89.0408	993	1369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003946805.1	s__Sphingomonas sp003946805	87.6615	896	1369	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	87.1949	828	1369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421245.1	s__Sphingomonas sp001421245	86.5107	931	1369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421715.1	s__Sphingomonas sp001421715	86.3007	919	1369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.52	97.51	0.91	0.91	3	-
GCF_001421965.1	s__Sphingomonas sp001421965	86.1382	932	1369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.43	97.43	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:24,582] [INFO] GTDB search result was written to GCF_022664435.1_ASM2266443v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:24,583] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:24,586] [INFO] DFAST_QC result json was written to GCF_022664435.1_ASM2266443v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:24,587] [INFO] DFAST_QC completed!
[2024-01-24 11:52:24,587] [INFO] Total running time: 0h1m18s