[2024-01-24 14:32:30,495] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:32:30,497] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:32:30,497] [INFO] DQC Reference Directory: /var/lib/cwl/stg5847b4d0-e39d-45e0-8cd1-4c2960830a0e/dqc_reference
[2024-01-24 14:32:31,716] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:32:31,717] [INFO] Task started: Prodigal
[2024-01-24 14:32:31,717] [INFO] Running command: gunzip -c /var/lib/cwl/stgd1024c7e-687e-4271-9e21-4c32b3888d09/GCF_000935025.1_ASM93502v1_genomic.fna.gz | prodigal -d GCF_000935025.1_ASM93502v1_genomic.fna/cds.fna -a GCF_000935025.1_ASM93502v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:32:47,212] [INFO] Task succeeded: Prodigal
[2024-01-24 14:32:47,212] [INFO] Task started: HMMsearch
[2024-01-24 14:32:47,213] [INFO] Running command: hmmsearch --tblout GCF_000935025.1_ASM93502v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5847b4d0-e39d-45e0-8cd1-4c2960830a0e/dqc_reference/reference_markers.hmm GCF_000935025.1_ASM93502v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:32:47,519] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:32:47,521] [INFO] Found 6/6 markers.
[2024-01-24 14:32:47,568] [INFO] Query marker FASTA was written to GCF_000935025.1_ASM93502v1_genomic.fna/markers.fasta
[2024-01-24 14:32:47,568] [INFO] Task started: Blastn
[2024-01-24 14:32:47,568] [INFO] Running command: blastn -query GCF_000935025.1_ASM93502v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5847b4d0-e39d-45e0-8cd1-4c2960830a0e/dqc_reference/reference_markers.fasta -out GCF_000935025.1_ASM93502v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:48,554] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:48,558] [INFO] Selected 15 target genomes.
[2024-01-24 14:32:48,558] [INFO] Target genome list was writen to GCF_000935025.1_ASM93502v1_genomic.fna/target_genomes.txt
[2024-01-24 14:32:48,568] [INFO] Task started: fastANI
[2024-01-24 14:32:48,568] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1024c7e-687e-4271-9e21-4c32b3888d09/GCF_000935025.1_ASM93502v1_genomic.fna.gz --refList GCF_000935025.1_ASM93502v1_genomic.fna/target_genomes.txt --output GCF_000935025.1_ASM93502v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:33:03,748] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:03,749] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5847b4d0-e39d-45e0-8cd1-4c2960830a0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:33:03,749] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5847b4d0-e39d-45e0-8cd1-4c2960830a0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:33:03,768] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:33:03,768] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:33:03,768] [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 hengshuiensis	strain=WHSC-8	GCA_000935025.1	1609977	1609977	type	True	100.0	1741	1742	95	conclusive
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	82.2886	842	1742	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	82.1911	838	1742	95	below_threshold
Sphingomonas gei	strain=ZFGT-11	GCA_004792685.1	1395960	1395960	type	True	81.7717	827	1742	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	81.7366	867	1742	95	below_threshold
Sphingomonas pituitosa	strain=NBRC 102491	GCA_001598435.1	99597	99597	type	True	81.4842	736	1742	95	below_threshold
Sphingomonas leidyi	strain=DSM 4733	GCA_011761945.1	68569	68569	type	True	81.3141	825	1742	95	below_threshold
Sphingomonas kyeonggiensis	strain=DSM 101806	GCA_014196745.1	1268553	1268553	type	True	81.2042	842	1742	95	below_threshold
Sphingomonas azotifigens	strain=NBRC 15497	GCA_002091475.1	330920	330920	type	True	81.1381	775	1742	95	below_threshold
Sphingomonas xinjiangensis	strain=DSM 26736	GCA_014199255.1	643568	643568	type	True	80.3442	643	1742	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	80.0793	684	1742	95	below_threshold
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	79.8151	594	1742	95	below_threshold
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	79.2856	572	1742	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	79.1067	582	1742	95	below_threshold
Sphingomonas radiodurans	strain=S9-5	GCA_020866845.1	2890321	2890321	type	True	78.6478	498	1742	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:33:03,770] [INFO] DFAST Taxonomy check result was written to GCF_000935025.1_ASM93502v1_genomic.fna/tc_result.tsv
[2024-01-24 14:33:03,771] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:33:03,771] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:33:03,771] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5847b4d0-e39d-45e0-8cd1-4c2960830a0e/dqc_reference/checkm_data
[2024-01-24 14:33:03,772] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:33:03,833] [INFO] Task started: CheckM
[2024-01-24 14:33:03,834] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000935025.1_ASM93502v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000935025.1_ASM93502v1_genomic.fna/checkm_input GCF_000935025.1_ASM93502v1_genomic.fna/checkm_result
[2024-01-24 14:33:52,263] [INFO] Task succeeded: CheckM
[2024-01-24 14:33:52,265] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:33:52,287] [INFO] ===== Completeness check finished =====
[2024-01-24 14:33:52,288] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:33:52,288] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000935025.1_ASM93502v1_genomic.fna/markers.fasta)
[2024-01-24 14:33:52,289] [INFO] Task started: Blastn
[2024-01-24 14:33:52,289] [INFO] Running command: blastn -query GCF_000935025.1_ASM93502v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5847b4d0-e39d-45e0-8cd1-4c2960830a0e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000935025.1_ASM93502v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:33:54,158] [INFO] Task succeeded: Blastn
[2024-01-24 14:33:54,161] [INFO] Selected 14 target genomes.
[2024-01-24 14:33:54,161] [INFO] Target genome list was writen to GCF_000935025.1_ASM93502v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:33:54,170] [INFO] Task started: fastANI
[2024-01-24 14:33:54,171] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1024c7e-687e-4271-9e21-4c32b3888d09/GCF_000935025.1_ASM93502v1_genomic.fna.gz --refList GCF_000935025.1_ASM93502v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000935025.1_ASM93502v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:34:09,459] [INFO] Task succeeded: fastANI
[2024-01-24 14:34:09,479] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:34:09,479] [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_000935025.1	s__Sphingomonas hengshuiensis	100.0	1742	1742	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_018449795.1	s__Sphingomonas sp018449795	82.5559	784	1742	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	82.1964	837	1742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002002925.1	s__Sphingomonas sp002002925	81.9931	821	1742	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	81.9574	806	1742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428865.1	s__Sphingomonas sp001428865	81.8764	791	1742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000712135.1	s__Sphingomonas sp000712135	81.8276	793	1742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004792685.1	s__Sphingomonas gei	81.7402	831	1742	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	81.7039	753	1742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017418975.1	s__Sphingomonas sp017418975	81.5076	825	1742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002127225.1	s__Sphingomonas sp002127225	81.4864	801	1742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011761945.1	s__Sphingomonas leidyi	81.3284	823	1742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.87	98.83	0.90	0.87	3	-
GCF_005503355.1	s__Sphingomonas sp005503355	81.2982	802	1742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014196745.1	s__Sphingomonas kyeonggiensis	81.1765	846	1742	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 14:34:09,481] [INFO] GTDB search result was written to GCF_000935025.1_ASM93502v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:34:09,482] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:34:09,489] [INFO] DFAST_QC result json was written to GCF_000935025.1_ASM93502v1_genomic.fna/dqc_result.json
[2024-01-24 14:34:09,489] [INFO] DFAST_QC completed!
[2024-01-24 14:34:09,489] [INFO] Total running time: 0h1m39s