[2024-01-24 13:41:20,349] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:20,353] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:20,353] [INFO] DQC Reference Directory: /var/lib/cwl/stg73494614-9eb2-420d-949d-a72f907955e9/dqc_reference
[2024-01-24 13:41:21,865] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:21,866] [INFO] Task started: Prodigal
[2024-01-24 13:41:21,866] [INFO] Running command: gunzip -c /var/lib/cwl/stg1326410f-e3bf-4b75-bcac-631632920a77/GCF_030814995.1_ASM3081499v1_genomic.fna.gz | prodigal -d GCF_030814995.1_ASM3081499v1_genomic.fna/cds.fna -a GCF_030814995.1_ASM3081499v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:46,667] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:46,668] [INFO] Task started: HMMsearch
[2024-01-24 13:41:46,668] [INFO] Running command: hmmsearch --tblout GCF_030814995.1_ASM3081499v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg73494614-9eb2-420d-949d-a72f907955e9/dqc_reference/reference_markers.hmm GCF_030814995.1_ASM3081499v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:47,090] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:47,091] [INFO] Found 6/6 markers.
[2024-01-24 13:41:47,160] [INFO] Query marker FASTA was written to GCF_030814995.1_ASM3081499v1_genomic.fna/markers.fasta
[2024-01-24 13:41:47,161] [INFO] Task started: Blastn
[2024-01-24 13:41:47,161] [INFO] Running command: blastn -query GCF_030814995.1_ASM3081499v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg73494614-9eb2-420d-949d-a72f907955e9/dqc_reference/reference_markers.fasta -out GCF_030814995.1_ASM3081499v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:48,300] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:48,304] [INFO] Selected 28 target genomes.
[2024-01-24 13:41:48,304] [INFO] Target genome list was writen to GCF_030814995.1_ASM3081499v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:48,309] [INFO] Task started: fastANI
[2024-01-24 13:41:48,310] [INFO] Running command: fastANI --query /var/lib/cwl/stg1326410f-e3bf-4b75-bcac-631632920a77/GCF_030814995.1_ASM3081499v1_genomic.fna.gz --refList GCF_030814995.1_ASM3081499v1_genomic.fna/target_genomes.txt --output GCF_030814995.1_ASM3081499v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:42:21,713] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:21,713] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg73494614-9eb2-420d-949d-a72f907955e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:42:21,714] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg73494614-9eb2-420d-949d-a72f907955e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:42:21,740] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:42:21,740] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:42:21,741] [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
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	78.3569	738	2946	95	below_threshold
Ancylobacter sonchi	strain=VKM B-3145	GCA_018390695.1	1937790	1937790	type	True	78.1969	778	2946	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	78.1084	556	2946	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	78.0558	643	2946	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	78.013	739	2946	95	below_threshold
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	78.0072	608	2946	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_014201415.1	1743235	1743235	type	True	77.949	511	2946	95	below_threshold
Chelatococcus composti	strain=CGMCC 1.15283	GCA_014641535.1	1743235	1743235	type	True	77.9269	511	2946	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	77.8977	834	2946	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	77.8817	524	2946	95	below_threshold
Bosea thiooxidans	strain=DSM 9653	GCA_900168195.1	53254	53254	type	True	77.8587	695	2946	95	below_threshold
Phreatobacter cathodiphilus	strain=S-12	GCA_003008515.1	1868589	1868589	type	True	77.826	677	2946	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	77.8172	672	2946	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	77.7095	725	2946	95	below_threshold
Microvirga thermotolerans	strain=HR1	GCA_009363855.1	2651334	2651334	type	True	77.6439	469	2946	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	77.4663	812	2946	95	below_threshold
Methylobacterium platani	strain=JCM 14648	GCA_001043885.1	427683	427683	type	True	77.3855	803	2946	95	below_threshold
Methylobacterium jeotgali	strain=LMG 23639	GCA_022179345.1	381630	381630	type	True	77.3651	551	2946	95	below_threshold
Alsobacter metallidurans	strain=CGMCC 1.12214	GCA_014636935.1	340221	340221	type	True	77.3557	569	2946	95	below_threshold
Methylobacterium platani	strain=PMB02	GCA_001653715.1	427683	427683	type	True	77.3552	874	2946	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	77.3482	891	2946	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	77.3194	683	2946	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	77.2816	824	2946	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	77.2177	628	2946	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	77.2075	786	2946	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	77.1339	838	2946	95	below_threshold
Methylobacterium soli	strain=KCTC 22810	GCA_022179555.1	553447	553447	type	True	77.0451	501	2946	95	below_threshold
Methylobacterium soli	strain=YIM 48816	GCA_008806385.1	553447	553447	type	True	77.0124	624	2946	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:42:21,742] [INFO] DFAST Taxonomy check result was written to GCF_030814995.1_ASM3081499v1_genomic.fna/tc_result.tsv
[2024-01-24 13:42:21,743] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:42:21,743] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:42:21,743] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg73494614-9eb2-420d-949d-a72f907955e9/dqc_reference/checkm_data
[2024-01-24 13:42:21,744] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:21,822] [INFO] Task started: CheckM
[2024-01-24 13:42:21,822] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030814995.1_ASM3081499v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030814995.1_ASM3081499v1_genomic.fna/checkm_input GCF_030814995.1_ASM3081499v1_genomic.fna/checkm_result
[2024-01-24 13:44:24,189] [INFO] Task succeeded: CheckM
[2024-01-24 13:44:24,190] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:44:24,216] [INFO] ===== Completeness check finished =====
[2024-01-24 13:44:24,217] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:44:24,217] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030814995.1_ASM3081499v1_genomic.fna/markers.fasta)
[2024-01-24 13:44:24,218] [INFO] Task started: Blastn
[2024-01-24 13:44:24,218] [INFO] Running command: blastn -query GCF_030814995.1_ASM3081499v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg73494614-9eb2-420d-949d-a72f907955e9/dqc_reference/reference_markers_gtdb.fasta -out GCF_030814995.1_ASM3081499v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:44:26,534] [INFO] Task succeeded: Blastn
[2024-01-24 13:44:26,538] [INFO] Selected 17 target genomes.
[2024-01-24 13:44:26,539] [INFO] Target genome list was writen to GCF_030814995.1_ASM3081499v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:44:26,572] [INFO] Task started: fastANI
[2024-01-24 13:44:26,572] [INFO] Running command: fastANI --query /var/lib/cwl/stg1326410f-e3bf-4b75-bcac-631632920a77/GCF_030814995.1_ASM3081499v1_genomic.fna.gz --refList GCF_030814995.1_ASM3081499v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030814995.1_ASM3081499v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:44:47,103] [INFO] Task succeeded: fastANI
[2024-01-24 13:44:47,123] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:44:47,123] [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_002982075.1	s__Labrys okinawensis	79.8108	966	2946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Labraceae;g__Labrys	95.0	98.61	98.61	0.96	0.96	2	-
GCF_001676615.1	s__Labrys sp001676615	79.7678	1023	2946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Labraceae;g__Labrys	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008330945.1	s__Labrys sp008330945	79.6298	1008	2946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Labraceae;g__Labrys	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900466745.1	s__Bosea sp900466745	78.2762	724	2946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.99	99.98	0.99	0.99	7	-
GCF_000702305.1	s__GCF-000702305 sp000702305	78.2652	673	2946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__GCF-000702305	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018390555.1	s__Ancylobacter_B oerskovii	78.2335	773	2946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196925.1	s__Chelatococcus_A caeni	78.0257	737	2946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus_A	95.0	98.75	98.72	0.96	0.95	3	-
GCF_900168195.1	s__Bosea thiooxidans	77.8698	692	2946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.77	99.77	0.94	0.94	2	-
GCF_900112185.1	s__Bosea sp900112185	77.8417	761	2946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196455.1	s__Kaistia hirudinis	77.8349	669	2946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	96.80	96.80	0.96	0.96	2	-
GCF_015904235.1	s__L22 sp015904235	77.6898	729	2946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__L22	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363855.1	s__Microvirga thermotolerans	77.635	468	2946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716745.1	s__GCA-013693735 sp016716745	77.5649	586	2946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__GCA-013693735	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793505.1	s__GCA-013693735 sp016793505	77.5213	583	2946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__GCA-013693735	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001653715.1	s__Methylobacterium platani	77.3654	868	2946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.94	99.94	0.97	0.97	2	-
GCF_016807805.1	s__Xanthobacter sp016807805	77.3052	681	2946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008806385.1	s__Methylobacterium soli	77.0122	624	2946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:44:47,125] [INFO] GTDB search result was written to GCF_030814995.1_ASM3081499v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:44:47,125] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:44:47,130] [INFO] DFAST_QC result json was written to GCF_030814995.1_ASM3081499v1_genomic.fna/dqc_result.json
[2024-01-24 13:44:47,130] [INFO] DFAST_QC completed!
[2024-01-24 13:44:47,130] [INFO] Total running time: 0h3m27s