[2024-01-25 20:13:35,717] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:13:35,719] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:13:35,719] [INFO] DQC Reference Directory: /var/lib/cwl/stg63c18724-7ab1-4412-8c6a-dd6f8f88f72e/dqc_reference
[2024-01-25 20:13:36,829] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:13:36,829] [INFO] Task started: Prodigal
[2024-01-25 20:13:36,829] [INFO] Running command: gunzip -c /var/lib/cwl/stg4552042c-6ec1-4348-b241-8bcd7f3da0d0/GCF_001402875.1_ASM140287v1_genomic.fna.gz | prodigal -d GCF_001402875.1_ASM140287v1_genomic.fna/cds.fna -a GCF_001402875.1_ASM140287v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:13:47,900] [INFO] Task succeeded: Prodigal
[2024-01-25 20:13:47,900] [INFO] Task started: HMMsearch
[2024-01-25 20:13:47,900] [INFO] Running command: hmmsearch --tblout GCF_001402875.1_ASM140287v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63c18724-7ab1-4412-8c6a-dd6f8f88f72e/dqc_reference/reference_markers.hmm GCF_001402875.1_ASM140287v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:13:48,103] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:13:48,104] [INFO] Found 6/6 markers.
[2024-01-25 20:13:48,132] [INFO] Query marker FASTA was written to GCF_001402875.1_ASM140287v1_genomic.fna/markers.fasta
[2024-01-25 20:13:48,133] [INFO] Task started: Blastn
[2024-01-25 20:13:48,133] [INFO] Running command: blastn -query GCF_001402875.1_ASM140287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63c18724-7ab1-4412-8c6a-dd6f8f88f72e/dqc_reference/reference_markers.fasta -out GCF_001402875.1_ASM140287v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:49,166] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:49,171] [INFO] Selected 13 target genomes.
[2024-01-25 20:13:49,171] [INFO] Target genome list was writen to GCF_001402875.1_ASM140287v1_genomic.fna/target_genomes.txt
[2024-01-25 20:13:49,177] [INFO] Task started: fastANI
[2024-01-25 20:13:49,177] [INFO] Running command: fastANI --query /var/lib/cwl/stg4552042c-6ec1-4348-b241-8bcd7f3da0d0/GCF_001402875.1_ASM140287v1_genomic.fna.gz --refList GCF_001402875.1_ASM140287v1_genomic.fna/target_genomes.txt --output GCF_001402875.1_ASM140287v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:14:03,571] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:03,572] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63c18724-7ab1-4412-8c6a-dd6f8f88f72e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:14:03,572] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63c18724-7ab1-4412-8c6a-dd6f8f88f72e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:14:03,581] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:14:03,582] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:14:03,582] [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
Blastochloris viridis	strain=ATCC 19567	GCA_001402875.1	1079	1079	type	True	100.0	1238	1241	95	conclusive
Blastochloris viridis	strain=DSM 133	GCA_001548155.2	1079	1079	type	True	99.9973	1235	1241	95	conclusive
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	85.0041	846	1241	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	84.8486	847	1241	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	78.5718	473	1241	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	78.4799	514	1241	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	78.3427	438	1241	95	below_threshold
Xanthobacter tagetidis	strain=DSM 11105	GCA_014206845.1	60216	60216	type	True	78.2687	437	1241	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	78.2037	420	1241	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	78.0628	417	1241	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	77.948	400	1241	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	77.7451	490	1241	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	77.3603	438	1241	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:14:03,583] [INFO] DFAST Taxonomy check result was written to GCF_001402875.1_ASM140287v1_genomic.fna/tc_result.tsv
[2024-01-25 20:14:03,584] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:14:03,584] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:14:03,584] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63c18724-7ab1-4412-8c6a-dd6f8f88f72e/dqc_reference/checkm_data
[2024-01-25 20:14:03,585] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:14:03,624] [INFO] Task started: CheckM
[2024-01-25 20:14:03,624] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001402875.1_ASM140287v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001402875.1_ASM140287v1_genomic.fna/checkm_input GCF_001402875.1_ASM140287v1_genomic.fna/checkm_result
[2024-01-25 20:14:46,511] [INFO] Task succeeded: CheckM
[2024-01-25 20:14:46,512] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:14:46,529] [INFO] ===== Completeness check finished =====
[2024-01-25 20:14:46,530] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:14:46,530] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001402875.1_ASM140287v1_genomic.fna/markers.fasta)
[2024-01-25 20:14:46,530] [INFO] Task started: Blastn
[2024-01-25 20:14:46,530] [INFO] Running command: blastn -query GCF_001402875.1_ASM140287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63c18724-7ab1-4412-8c6a-dd6f8f88f72e/dqc_reference/reference_markers_gtdb.fasta -out GCF_001402875.1_ASM140287v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:48,705] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:48,708] [INFO] Selected 14 target genomes.
[2024-01-25 20:14:48,708] [INFO] Target genome list was writen to GCF_001402875.1_ASM140287v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:14:48,718] [INFO] Task started: fastANI
[2024-01-25 20:14:48,719] [INFO] Running command: fastANI --query /var/lib/cwl/stg4552042c-6ec1-4348-b241-8bcd7f3da0d0/GCF_001402875.1_ASM140287v1_genomic.fna.gz --refList GCF_001402875.1_ASM140287v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001402875.1_ASM140287v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:15:02,444] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:02,454] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:15:02,454] [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_001402875.1	s__Blastochloris viridis	100.0	1238	1241	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Blastochloris	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_008630065.1	s__Blastochloris sulfoviridis	84.9874	849	1241	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Blastochloris	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966715.1	s__Blastochloris tepida	84.8241	849	1241	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Blastochloris	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297465.1	s__SCUB01 sp004297465	78.9965	401	1241	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__SCUB01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016653355.1	s__Rhodoplanes elegans	78.6398	538	1241	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	99.89	99.89	0.96	0.96	2	-
GCF_003258865.1	s__Rhodoplanes roseus	78.4954	514	1241	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009223885.1	s__Ancylobacter sp009223885	78.4012	411	1241	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000092925.1	s__Starkeya novella	78.3331	438	1241	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007559435.1	s__Starkeya sp007559435	78.3148	397	1241	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	98.55	98.55	0.95	0.95	2	-
GCF_003667445.1	s__Xanthobacter tagetidis	78.2238	428	1241	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018390605.1	s__Ancylobacter_B defluvii	78.221	443	1241	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_007993935.1	s__Bradyrhizobium macuxiense_A	78.0288	445	1241	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009600605.1	s__Pseudoxanthobacter spirostomi	77.7499	347	1241	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pseudoxanthobacteraceae;g__Pseudoxanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464235.1	s__Phreatobacter sp001464235	77.7146	377	1241	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:15:02,456] [INFO] GTDB search result was written to GCF_001402875.1_ASM140287v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:15:02,456] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:15:02,460] [INFO] DFAST_QC result json was written to GCF_001402875.1_ASM140287v1_genomic.fna/dqc_result.json
[2024-01-25 20:15:02,460] [INFO] DFAST_QC completed!
[2024-01-25 20:15:02,460] [INFO] Total running time: 0h1m27s