[2024-01-24 14:30:31,171] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:31,173] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:31,174] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ab4e713-5e32-41a5-b785-60883529d1d0/dqc_reference
[2024-01-24 14:30:32,409] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:32,410] [INFO] Task started: Prodigal
[2024-01-24 14:30:32,410] [INFO] Running command: gunzip -c /var/lib/cwl/stg90e28f59-1366-4f1f-9fe5-c4a67516bcef/GCF_001721295.1_ASM172129v1_genomic.fna.gz | prodigal -d GCF_001721295.1_ASM172129v1_genomic.fna/cds.fna -a GCF_001721295.1_ASM172129v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:44,638] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:44,639] [INFO] Task started: HMMsearch
[2024-01-24 14:30:44,639] [INFO] Running command: hmmsearch --tblout GCF_001721295.1_ASM172129v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ab4e713-5e32-41a5-b785-60883529d1d0/dqc_reference/reference_markers.hmm GCF_001721295.1_ASM172129v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:44,999] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:45,001] [INFO] Found 6/6 markers.
[2024-01-24 14:30:45,046] [INFO] Query marker FASTA was written to GCF_001721295.1_ASM172129v1_genomic.fna/markers.fasta
[2024-01-24 14:30:45,047] [INFO] Task started: Blastn
[2024-01-24 14:30:45,047] [INFO] Running command: blastn -query GCF_001721295.1_ASM172129v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ab4e713-5e32-41a5-b785-60883529d1d0/dqc_reference/reference_markers.fasta -out GCF_001721295.1_ASM172129v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:46,039] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:46,043] [INFO] Selected 15 target genomes.
[2024-01-24 14:30:46,044] [INFO] Target genome list was writen to GCF_001721295.1_ASM172129v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:46,053] [INFO] Task started: fastANI
[2024-01-24 14:30:46,053] [INFO] Running command: fastANI --query /var/lib/cwl/stg90e28f59-1366-4f1f-9fe5-c4a67516bcef/GCF_001721295.1_ASM172129v1_genomic.fna.gz --refList GCF_001721295.1_ASM172129v1_genomic.fna/target_genomes.txt --output GCF_001721295.1_ASM172129v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:00,820] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:00,820] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ab4e713-5e32-41a5-b785-60883529d1d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:00,821] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ab4e713-5e32-41a5-b785-60883529d1d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:00,840] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:00,840] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:00,840] [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 turrisvirgatae	strain=MCT13	GCA_001721295.1	1888892	1888892	type	True	100.0	1330	1330	95	conclusive
Sphingomonas koreensis	strain=JSS26	GCA_002797435.1	93064	93064	type	True	82.0294	685	1330	95	below_threshold
Sphingomonas koreensis	strain=KCTC 2882	GCA_003953035.1	93064	93064	type	True	81.9794	693	1330	95	below_threshold
Sphingomonas koreensis	strain=NBRC 16723	GCA_001598395.1	93064	93064	type	True	81.9603	692	1330	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	81.5543	689	1330	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	80.3162	504	1330	95	below_threshold
Sphingomonas trueperi	strain=DSM 7225	GCA_011927635.1	53317	53317	type	True	80.0616	540	1330	95	below_threshold
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	79.8304	476	1330	95	below_threshold
Sphingomonas kyeonggiensis	strain=DSM 101806	GCA_014196745.1	1268553	1268553	type	True	79.8084	538	1330	95	below_threshold
Sphingomonas soli	strain=NBRC 100801	GCA_001591025.1	266127	266127	type	True	79.3187	471	1330	95	below_threshold
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	79.2234	479	1330	95	below_threshold
Sphingomonas japonica	strain=DSM 22753	GCA_011762085.1	511662	511662	type	True	79.1558	473	1330	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	79.1424	497	1330	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	79.1355	526	1330	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	78.7814	462	1330	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:00,842] [INFO] DFAST Taxonomy check result was written to GCF_001721295.1_ASM172129v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:00,843] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:00,843] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:00,843] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ab4e713-5e32-41a5-b785-60883529d1d0/dqc_reference/checkm_data
[2024-01-24 14:31:00,844] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:00,889] [INFO] Task started: CheckM
[2024-01-24 14:31:00,890] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001721295.1_ASM172129v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001721295.1_ASM172129v1_genomic.fna/checkm_input GCF_001721295.1_ASM172129v1_genomic.fna/checkm_result
[2024-01-24 14:31:39,136] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:39,137] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:39,159] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:39,160] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:39,160] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001721295.1_ASM172129v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:39,161] [INFO] Task started: Blastn
[2024-01-24 14:31:39,161] [INFO] Running command: blastn -query GCF_001721295.1_ASM172129v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ab4e713-5e32-41a5-b785-60883529d1d0/dqc_reference/reference_markers_gtdb.fasta -out GCF_001721295.1_ASM172129v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:41,076] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:41,080] [INFO] Selected 13 target genomes.
[2024-01-24 14:31:41,080] [INFO] Target genome list was writen to GCF_001721295.1_ASM172129v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:41,091] [INFO] Task started: fastANI
[2024-01-24 14:31:41,092] [INFO] Running command: fastANI --query /var/lib/cwl/stg90e28f59-1366-4f1f-9fe5-c4a67516bcef/GCF_001721295.1_ASM172129v1_genomic.fna.gz --refList GCF_001721295.1_ASM172129v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001721295.1_ASM172129v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:51,669] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:51,685] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:51,685] [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_001721295.1	s__Sphingomonas turrisvirgatae	100.0	1330	1330	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_002797435.1	s__Sphingomonas koreensis	82.0172	686	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.13	98.00	0.88	0.86	72	-
GCF_001557215.1	s__Sphingomonas sp001557215	81.8471	595	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.89	99.89	0.91	0.91	2	-
GCA_002280565.1	s__Sphingomonas sp002280565	81.7512	544	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.98	96.98	0.90	0.90	2	-
GCA_902826325.1	s__Sphingomonas sp902826325	81.6058	487	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.74	97.74	0.84	0.84	2	-
GCF_007833215.1	s__Sphingomonas sp007833215	81.5637	687	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927635.1	s__Sphingomonas trueperi	80.0677	539	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.33	98.84	0.92	0.91	3	-
GCF_014196745.1	s__Sphingomonas kyeonggiensis	79.7938	540	1330	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	79.7741	515	1330	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	79.7575	562	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000282895.1	s__Sphingomonas sp000282895	79.543	453	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001421355.1	s__Sphingomonas sp001421355	79.3392	469	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.29	96.58	0.97	0.94	3	-
GCF_003946805.1	s__Sphingomonas sp003946805	79.2572	494	1330	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 14:31:51,687] [INFO] GTDB search result was written to GCF_001721295.1_ASM172129v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:51,687] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:51,691] [INFO] DFAST_QC result json was written to GCF_001721295.1_ASM172129v1_genomic.fna/dqc_result.json
[2024-01-24 14:31:51,692] [INFO] DFAST_QC completed!
[2024-01-24 14:31:51,692] [INFO] Total running time: 0h1m21s