[2024-01-24 13:31:31,371] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:31,375] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:31,376] [INFO] DQC Reference Directory: /var/lib/cwl/stg22a897cb-0f05-4fcd-b7b4-4110fdadf9a4/dqc_reference
[2024-01-24 13:31:32,583] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:32,584] [INFO] Task started: Prodigal
[2024-01-24 13:31:32,584] [INFO] Running command: gunzip -c /var/lib/cwl/stgadd347bc-b4fd-432e-87c7-fbf443b1b64f/GCF_011057975.1_ASM1105797v1_genomic.fna.gz | prodigal -d GCF_011057975.1_ASM1105797v1_genomic.fna/cds.fna -a GCF_011057975.1_ASM1105797v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:44,175] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:44,175] [INFO] Task started: HMMsearch
[2024-01-24 13:31:44,175] [INFO] Running command: hmmsearch --tblout GCF_011057975.1_ASM1105797v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg22a897cb-0f05-4fcd-b7b4-4110fdadf9a4/dqc_reference/reference_markers.hmm GCF_011057975.1_ASM1105797v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:44,463] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:44,465] [INFO] Found 6/6 markers.
[2024-01-24 13:31:44,505] [INFO] Query marker FASTA was written to GCF_011057975.1_ASM1105797v1_genomic.fna/markers.fasta
[2024-01-24 13:31:44,506] [INFO] Task started: Blastn
[2024-01-24 13:31:44,506] [INFO] Running command: blastn -query GCF_011057975.1_ASM1105797v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22a897cb-0f05-4fcd-b7b4-4110fdadf9a4/dqc_reference/reference_markers.fasta -out GCF_011057975.1_ASM1105797v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:45,480] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:45,483] [INFO] Selected 17 target genomes.
[2024-01-24 13:31:45,484] [INFO] Target genome list was writen to GCF_011057975.1_ASM1105797v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:45,495] [INFO] Task started: fastANI
[2024-01-24 13:31:45,495] [INFO] Running command: fastANI --query /var/lib/cwl/stgadd347bc-b4fd-432e-87c7-fbf443b1b64f/GCF_011057975.1_ASM1105797v1_genomic.fna.gz --refList GCF_011057975.1_ASM1105797v1_genomic.fna/target_genomes.txt --output GCF_011057975.1_ASM1105797v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:00,513] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:00,514] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg22a897cb-0f05-4fcd-b7b4-4110fdadf9a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:00,514] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg22a897cb-0f05-4fcd-b7b4-4110fdadf9a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:00,528] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:00,528] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:00,528] [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
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	100.0	1286	1286	95	conclusive
Sphingosinithalassobacter portus	strain=FM6	GCA_003171655.1	2676234	2676234	type	True	84.3271	813	1286	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	80.1298	610	1286	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	80.1032	617	1286	95	below_threshold
Sphingomonas hengshuiensis	strain=WHSC-8	GCA_000935025.1	1609977	1609977	type	True	79.7092	613	1286	95	below_threshold
Sphingomonas pituitosa	strain=NBRC 102491	GCA_001598435.1	99597	99597	type	True	79.4751	536	1286	95	below_threshold
Sphingomonas soli	strain=NBRC 100801	GCA_001591025.1	266127	266127	type	True	79.3732	496	1286	95	below_threshold
Sphingomonas koreensis	strain=JSS26	GCA_002797435.1	93064	93064	type	True	79.336	543	1286	95	below_threshold
Sphingomonas koreensis	strain=KCTC 2882	GCA_003953035.1	93064	93064	type	True	79.2894	536	1286	95	below_threshold
Sphingomonas koreensis	strain=NBRC 16723	GCA_001598395.1	93064	93064	type	True	79.2625	547	1286	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	79.1296	488	1286	95	below_threshold
Stakelama sediminis	strain=DSM 27203	GCA_014199335.1	463200	463200	type	True	79.025	445	1286	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	78.9615	500	1286	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	78.7373	473	1286	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	78.2975	435	1286	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	78.2921	446	1286	95	below_threshold
Sphingomonas parva	strain=17J27-24	GCA_004564275.1	2555898	2555898	type	True	77.7887	352	1286	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:00,530] [INFO] DFAST Taxonomy check result was written to GCF_011057975.1_ASM1105797v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:00,532] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:00,532] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:00,533] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg22a897cb-0f05-4fcd-b7b4-4110fdadf9a4/dqc_reference/checkm_data
[2024-01-24 13:32:00,534] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:00,579] [INFO] Task started: CheckM
[2024-01-24 13:32:00,580] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011057975.1_ASM1105797v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011057975.1_ASM1105797v1_genomic.fna/checkm_input GCF_011057975.1_ASM1105797v1_genomic.fna/checkm_result
[2024-01-24 13:32:36,830] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:36,832] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:36,851] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:36,851] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:36,852] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011057975.1_ASM1105797v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:36,852] [INFO] Task started: Blastn
[2024-01-24 13:32:36,852] [INFO] Running command: blastn -query GCF_011057975.1_ASM1105797v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22a897cb-0f05-4fcd-b7b4-4110fdadf9a4/dqc_reference/reference_markers_gtdb.fasta -out GCF_011057975.1_ASM1105797v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:38,648] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:38,654] [INFO] Selected 13 target genomes.
[2024-01-24 13:32:38,654] [INFO] Target genome list was writen to GCF_011057975.1_ASM1105797v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:38,671] [INFO] Task started: fastANI
[2024-01-24 13:32:38,672] [INFO] Running command: fastANI --query /var/lib/cwl/stgadd347bc-b4fd-432e-87c7-fbf443b1b64f/GCF_011057975.1_ASM1105797v1_genomic.fna.gz --refList GCF_011057975.1_ASM1105797v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011057975.1_ASM1105797v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:52,075] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:52,087] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:52,088] [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_011057975.1	s__Sphingomonas sp011057975	100.0	1286	1286	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_003171655.1	s__Sphingomonas portus	84.3031	815	1286	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	83.883	764	1286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014334115.1	s__Sphingomonas sp014334115	80.7233	639	1286	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	80.088	619	1286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018122655.1	s__Sphingomonas sp018122655	79.84	521	1286	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	79.8243	585	1286	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	79.7435	593	1286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000935025.1	s__Sphingomonas hengshuiensis	79.7169	612	1286	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	79.5932	571	1286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002002925.1	s__Sphingomonas sp002002925	79.5049	589	1286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797435.1	s__Sphingomonas koreensis	79.3323	543	1286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.13	98.00	0.88	0.86	72	-
GCF_014199335.1	s__Sphingomonas sediminis	79.0252	445	1286	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 13:32:52,089] [INFO] GTDB search result was written to GCF_011057975.1_ASM1105797v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:52,090] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:52,093] [INFO] DFAST_QC result json was written to GCF_011057975.1_ASM1105797v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:52,094] [INFO] DFAST_QC completed!
[2024-01-24 13:32:52,094] [INFO] Total running time: 0h1m21s