[2024-01-24 13:25:29,718] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:29,720] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:29,720] [INFO] DQC Reference Directory: /var/lib/cwl/stg38075200-004f-4c23-829c-90d7116026d4/dqc_reference
[2024-01-24 13:25:31,140] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:31,141] [INFO] Task started: Prodigal
[2024-01-24 13:25:31,142] [INFO] Running command: gunzip -c /var/lib/cwl/stg598e5ebc-75b0-42d4-b491-bf3a38d6ba46/GCF_008039615.1_ASM803961v1_genomic.fna.gz | prodigal -d GCF_008039615.1_ASM803961v1_genomic.fna/cds.fna -a GCF_008039615.1_ASM803961v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:58,010] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:58,010] [INFO] Task started: HMMsearch
[2024-01-24 13:25:58,010] [INFO] Running command: hmmsearch --tblout GCF_008039615.1_ASM803961v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg38075200-004f-4c23-829c-90d7116026d4/dqc_reference/reference_markers.hmm GCF_008039615.1_ASM803961v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:58,379] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:58,381] [INFO] Found 6/6 markers.
[2024-01-24 13:25:58,454] [INFO] Query marker FASTA was written to GCF_008039615.1_ASM803961v1_genomic.fna/markers.fasta
[2024-01-24 13:25:58,454] [INFO] Task started: Blastn
[2024-01-24 13:25:58,454] [INFO] Running command: blastn -query GCF_008039615.1_ASM803961v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38075200-004f-4c23-829c-90d7116026d4/dqc_reference/reference_markers.fasta -out GCF_008039615.1_ASM803961v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:59,555] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:59,560] [INFO] Selected 16 target genomes.
[2024-01-24 13:25:59,560] [INFO] Target genome list was writen to GCF_008039615.1_ASM803961v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:59,568] [INFO] Task started: fastANI
[2024-01-24 13:25:59,568] [INFO] Running command: fastANI --query /var/lib/cwl/stg598e5ebc-75b0-42d4-b491-bf3a38d6ba46/GCF_008039615.1_ASM803961v1_genomic.fna.gz --refList GCF_008039615.1_ASM803961v1_genomic.fna/target_genomes.txt --output GCF_008039615.1_ASM803961v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:22,803] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:22,804] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg38075200-004f-4c23-829c-90d7116026d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:22,805] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg38075200-004f-4c23-829c-90d7116026d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:22,822] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:26:22,822] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:22,823] [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
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	100.0	2849	2856	95	conclusive
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	79.2955	1104	2856	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	78.869	814	2856	95	below_threshold
Reyranella massiliensis	strain=521	GCA_000312425.1	445220	445220	type	True	78.5509	814	2856	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.9761	650	2856	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.9118	513	2856	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.7792	611	2856	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.7494	374	2856	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	76.6729	601	2856	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	76.5299	580	2856	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	76.4712	506	2856	95	below_threshold
Roseospira goensis	strain=JA135	GCA_014197795.1	391922	391922	type	True	76.4637	396	2856	95	below_threshold
Roseospira navarrensis	strain=DSM 15114	GCA_009601025.1	140058	140058	type	True	76.459	335	2856	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.3391	255	2856	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.1899	499	2856	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	76.0151	393	2856	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:22,824] [INFO] DFAST Taxonomy check result was written to GCF_008039615.1_ASM803961v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:22,825] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:22,825] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:22,825] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg38075200-004f-4c23-829c-90d7116026d4/dqc_reference/checkm_data
[2024-01-24 13:26:22,827] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:22,905] [INFO] Task started: CheckM
[2024-01-24 13:26:22,905] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008039615.1_ASM803961v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008039615.1_ASM803961v1_genomic.fna/checkm_input GCF_008039615.1_ASM803961v1_genomic.fna/checkm_result
[2024-01-24 13:27:52,250] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:52,252] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:52,273] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:52,273] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:52,274] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008039615.1_ASM803961v1_genomic.fna/markers.fasta)
[2024-01-24 13:27:52,274] [INFO] Task started: Blastn
[2024-01-24 13:27:52,274] [INFO] Running command: blastn -query GCF_008039615.1_ASM803961v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38075200-004f-4c23-829c-90d7116026d4/dqc_reference/reference_markers_gtdb.fasta -out GCF_008039615.1_ASM803961v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:54,418] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:54,421] [INFO] Selected 8 target genomes.
[2024-01-24 13:27:54,421] [INFO] Target genome list was writen to GCF_008039615.1_ASM803961v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:54,508] [INFO] Task started: fastANI
[2024-01-24 13:27:54,508] [INFO] Running command: fastANI --query /var/lib/cwl/stg598e5ebc-75b0-42d4-b491-bf3a38d6ba46/GCF_008039615.1_ASM803961v1_genomic.fna.gz --refList GCF_008039615.1_ASM803961v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008039615.1_ASM803961v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:28:12,553] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:12,565] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:28:12,565] [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_008039615.1	s__SYSU-D60007 sp008039615	100.0	2849	2856	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__SYSU-D60007	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007859315.1	s__SYSU-D60007 sp007859315	84.3125	1833	2856	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_003574685.1	s__SYSU-D60007 sp003574685	81.5561	1230	2856	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_016699855.1	s__GCA-016699855 sp016699855	80.8446	1147	2856	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__GCA-016699855	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869975.1	s__JAFAZJ01 sp016869975	80.3612	1003	2856	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__JAFAZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019239835.1	s__JAFAZJ01 sp019239835	79.7439	636	2856	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__JAFAZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992495.1	s__Reyranella soli	79.2695	1112	2856	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017990895.1	s__Reyranella sp017990895	78.4752	658	2856	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:28:12,567] [INFO] GTDB search result was written to GCF_008039615.1_ASM803961v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:28:12,567] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:28:12,571] [INFO] DFAST_QC result json was written to GCF_008039615.1_ASM803961v1_genomic.fna/dqc_result.json
[2024-01-24 13:28:12,571] [INFO] DFAST_QC completed!
[2024-01-24 13:28:12,571] [INFO] Total running time: 0h2m43s