[2023-06-17 08:06:58,789] [INFO] DFAST_QC pipeline started.
[2023-06-17 08:06:58,792] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 08:06:58,792] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ef9176b-bcda-4ee9-8d86-f6ef2d588568/dqc_reference
[2023-06-17 08:07:00,059] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 08:07:00,060] [INFO] Task started: Prodigal
[2023-06-17 08:07:00,060] [INFO] Running command: gunzip -c /var/lib/cwl/stg4aac4422-f5fd-469d-bee1-b841cbf53017/GCA_028821005.1_ASM2882100v1_genomic.fna.gz | prodigal -d GCA_028821005.1_ASM2882100v1_genomic.fna/cds.fna -a GCA_028821005.1_ASM2882100v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 08:07:08,764] [INFO] Task succeeded: Prodigal
[2023-06-17 08:07:08,765] [INFO] Task started: HMMsearch
[2023-06-17 08:07:08,765] [INFO] Running command: hmmsearch --tblout GCA_028821005.1_ASM2882100v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ef9176b-bcda-4ee9-8d86-f6ef2d588568/dqc_reference/reference_markers.hmm GCA_028821005.1_ASM2882100v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 08:07:09,017] [INFO] Task succeeded: HMMsearch
[2023-06-17 08:07:09,019] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4aac4422-f5fd-469d-bee1-b841cbf53017/GCA_028821005.1_ASM2882100v1_genomic.fna.gz]
[2023-06-17 08:07:09,050] [INFO] Query marker FASTA was written to GCA_028821005.1_ASM2882100v1_genomic.fna/markers.fasta
[2023-06-17 08:07:09,051] [INFO] Task started: Blastn
[2023-06-17 08:07:09,051] [INFO] Running command: blastn -query GCA_028821005.1_ASM2882100v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ef9176b-bcda-4ee9-8d86-f6ef2d588568/dqc_reference/reference_markers.fasta -out GCA_028821005.1_ASM2882100v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 08:07:09,635] [INFO] Task succeeded: Blastn
[2023-06-17 08:07:09,639] [INFO] Selected 20 target genomes.
[2023-06-17 08:07:09,639] [INFO] Target genome list was writen to GCA_028821005.1_ASM2882100v1_genomic.fna/target_genomes.txt
[2023-06-17 08:07:09,643] [INFO] Task started: fastANI
[2023-06-17 08:07:09,643] [INFO] Running command: fastANI --query /var/lib/cwl/stg4aac4422-f5fd-469d-bee1-b841cbf53017/GCA_028821005.1_ASM2882100v1_genomic.fna.gz --refList GCA_028821005.1_ASM2882100v1_genomic.fna/target_genomes.txt --output GCA_028821005.1_ASM2882100v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 08:07:25,357] [INFO] Task succeeded: fastANI
[2023-06-17 08:07:25,358] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ef9176b-bcda-4ee9-8d86-f6ef2d588568/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 08:07:25,358] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ef9176b-bcda-4ee9-8d86-f6ef2d588568/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 08:07:25,368] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 08:07:25,368] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 08:07:25,368] [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
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	75.6024	60	899	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	75.5125	66	899	95	below_threshold
Caulobacter rhizosphaerae	strain=KCTC 52515	GCA_010977555.1	2010972	2010972	type	True	75.4512	52	899	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	75.4316	53	899	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	75.3387	51	899	95	below_threshold
Bradyrhizobium frederickii	strain=CNPSo 3426	GCA_004570865.1	2560054	2560054	type	True	75.3354	51	899	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	75.3268	96	899	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	75.3102	98	899	95	below_threshold
Methylobacterium phyllosphaerae	strain=CBMB27	GCA_001936175.1	418223	418223	suspected-type	True	75.1675	57	899	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	74.9893	68	899	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 08:07:25,370] [INFO] DFAST Taxonomy check result was written to GCA_028821005.1_ASM2882100v1_genomic.fna/tc_result.tsv
[2023-06-17 08:07:25,370] [INFO] ===== Taxonomy check completed =====
[2023-06-17 08:07:25,370] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 08:07:25,371] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ef9176b-bcda-4ee9-8d86-f6ef2d588568/dqc_reference/checkm_data
[2023-06-17 08:07:25,372] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 08:07:25,413] [INFO] Task started: CheckM
[2023-06-17 08:07:25,414] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028821005.1_ASM2882100v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028821005.1_ASM2882100v1_genomic.fna/checkm_input GCA_028821005.1_ASM2882100v1_genomic.fna/checkm_result
[2023-06-17 08:07:55,424] [INFO] Task succeeded: CheckM
[2023-06-17 08:07:55,426] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 08:07:55,456] [INFO] ===== Completeness check finished =====
[2023-06-17 08:07:55,456] [INFO] ===== Start GTDB Search =====
[2023-06-17 08:07:55,456] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028821005.1_ASM2882100v1_genomic.fna/markers.fasta)
[2023-06-17 08:07:55,457] [INFO] Task started: Blastn
[2023-06-17 08:07:55,457] [INFO] Running command: blastn -query GCA_028821005.1_ASM2882100v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ef9176b-bcda-4ee9-8d86-f6ef2d588568/dqc_reference/reference_markers_gtdb.fasta -out GCA_028821005.1_ASM2882100v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 08:07:56,231] [INFO] Task succeeded: Blastn
[2023-06-17 08:07:56,235] [INFO] Selected 17 target genomes.
[2023-06-17 08:07:56,236] [INFO] Target genome list was writen to GCA_028821005.1_ASM2882100v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 08:07:56,307] [INFO] Task started: fastANI
[2023-06-17 08:07:56,308] [INFO] Running command: fastANI --query /var/lib/cwl/stg4aac4422-f5fd-469d-bee1-b841cbf53017/GCA_028821005.1_ASM2882100v1_genomic.fna.gz --refList GCA_028821005.1_ASM2882100v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028821005.1_ASM2882100v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 08:08:09,755] [INFO] Task succeeded: fastANI
[2023-06-17 08:08:09,779] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 08:08:09,780] [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
GCA_009839325.1	s__VXPW01 sp009839325	98.6408	645	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__VXPW01;f__VXPW01;g__VXPW01	95.0	99.26	99.26	0.90	0.90	2	conclusive
GCA_900197615.1	s__Bin65 sp900197615	76.5063	51	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Bin65;f__Bin65;g__Bin65	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721365.1	s__GCA-2721365 sp002721365	75.7308	59	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2721365;f__GCA-2721365;g__GCA-2721365	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008040045.1	s__Methylobacterium sp008040045	75.3731	52	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.25	98.17	0.85	0.85	3	-
GCF_900103195.1	s__Methylobacterium sp900103195	75.3438	55	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	96.81	96.81	0.87	0.87	2	-
GCF_900177295.1	s__Tistlia consotensis	75.3238	96	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_007859315.1	s__SYSU-D60007 sp007859315	75.2902	60	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__SYSU-D60007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009720755.1	s__Rhodoplanes serenus	75.2743	55	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	97.72	97.48	0.91	0.88	4	-
GCF_003952525.1	s__Mesorhizobium sp002294945	75.194	51	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.39	99.02	0.88	0.85	8	-
GCF_016595245.1	s__Azospirillum sp016595245	75.0317	65	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001982615.1	s__Roseomonas deserti	74.996	67	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001639105.2	s__Azospirillum humicireducens	74.9181	66	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 08:08:09,782] [INFO] GTDB search result was written to GCA_028821005.1_ASM2882100v1_genomic.fna/result_gtdb.tsv
[2023-06-17 08:08:09,783] [INFO] ===== GTDB Search completed =====
[2023-06-17 08:08:09,787] [INFO] DFAST_QC result json was written to GCA_028821005.1_ASM2882100v1_genomic.fna/dqc_result.json
[2023-06-17 08:08:09,788] [INFO] DFAST_QC completed!
[2023-06-17 08:08:09,788] [INFO] Total running time: 0h1m11s