[2024-01-24 11:27:19,113] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:27:19,114] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:27:19,115] [INFO] DQC Reference Directory: /var/lib/cwl/stgc0b30613-6b49-47be-b829-57ed0533a622/dqc_reference
[2024-01-24 11:27:20,318] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:27:20,319] [INFO] Task started: Prodigal
[2024-01-24 11:27:20,319] [INFO] Running command: gunzip -c /var/lib/cwl/stgf61c9fae-6a36-4c30-a3f3-c27bc1f806aa/GCF_030409225.1_ASM3040922v1_genomic.fna.gz | prodigal -d GCF_030409225.1_ASM3040922v1_genomic.fna/cds.fna -a GCF_030409225.1_ASM3040922v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:32,927] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:32,928] [INFO] Task started: HMMsearch
[2024-01-24 11:27:32,928] [INFO] Running command: hmmsearch --tblout GCF_030409225.1_ASM3040922v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc0b30613-6b49-47be-b829-57ed0533a622/dqc_reference/reference_markers.hmm GCF_030409225.1_ASM3040922v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:33,190] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:33,191] [INFO] Found 6/6 markers.
[2024-01-24 11:27:33,230] [INFO] Query marker FASTA was written to GCF_030409225.1_ASM3040922v1_genomic.fna/markers.fasta
[2024-01-24 11:27:33,231] [INFO] Task started: Blastn
[2024-01-24 11:27:33,231] [INFO] Running command: blastn -query GCF_030409225.1_ASM3040922v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0b30613-6b49-47be-b829-57ed0533a622/dqc_reference/reference_markers.fasta -out GCF_030409225.1_ASM3040922v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:34,179] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:34,181] [INFO] Selected 19 target genomes.
[2024-01-24 11:27:34,182] [INFO] Target genome list was writen to GCF_030409225.1_ASM3040922v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:34,189] [INFO] Task started: fastANI
[2024-01-24 11:27:34,189] [INFO] Running command: fastANI --query /var/lib/cwl/stgf61c9fae-6a36-4c30-a3f3-c27bc1f806aa/GCF_030409225.1_ASM3040922v1_genomic.fna.gz --refList GCF_030409225.1_ASM3040922v1_genomic.fna/target_genomes.txt --output GCF_030409225.1_ASM3040922v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:45,751] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:45,752] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc0b30613-6b49-47be-b829-57ed0533a622/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:45,752] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc0b30613-6b49-47be-b829-57ed0533a622/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:45,772] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:27:45,772] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:27:45,772] [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
Aquisalimonas asiatica	strain=CGMCC 1.6291	GCA_900110585.1	406100	406100	type	True	80.9929	635	1392	95	below_threshold
Methylonatrum kenyense	strain=AMT 1	GCA_023195885.1	455253	455253	type	True	78.086	233	1392	95	below_threshold
Arhodomonas aquaeolei	strain=DSM 8974	GCA_000374645.1	2369	2369	type	True	78.0381	400	1392	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	77.5825	264	1392	95	below_threshold
Natronocella acetinitrilica	strain=ANL 6-2	GCA_024170285.1	414046	414046	type	True	77.5754	281	1392	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	77.5494	205	1392	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	77.4822	255	1392	95	below_threshold
Thiohalospira halophila	strain=HL 3	GCA_900112605.1	381300	381300	type	True	77.4109	225	1392	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	77.1764	267	1392	95	below_threshold
Spiribacter aquaticus	strain=SP30	GCA_007625215.1	1935996	1935996	type	True	77.1719	184	1392	95	below_threshold
Halomonas heilongjiangensis	strain=9-2	GCA_003202165.1	1387883	1387883	type	True	77.0365	277	1392	95	below_threshold
Halomonas heilongjiangensis	strain=DSM 26881	GCA_002879645.1	1387883	1387883	type	True	76.9566	276	1392	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	76.8338	244	1392	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	76.7403	179	1392	95	below_threshold
Pseudomonas carbonaria	strain=CIP 111764	GCA_904061905.1	2762745	2762745	type	True	76.5557	235	1392	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	76.2578	181	1392	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	75.9625	171	1392	95	below_threshold
Pseudomonas ullengensis	strain=UL070	GCA_014174475.1	2759166	2759166	type	True	75.9516	170	1392	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	75.8689	169	1392	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:45,774] [INFO] DFAST Taxonomy check result was written to GCF_030409225.1_ASM3040922v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:45,774] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:45,774] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:45,774] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc0b30613-6b49-47be-b829-57ed0533a622/dqc_reference/checkm_data
[2024-01-24 11:27:45,775] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:45,813] [INFO] Task started: CheckM
[2024-01-24 11:27:45,814] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030409225.1_ASM3040922v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030409225.1_ASM3040922v1_genomic.fna/checkm_input GCF_030409225.1_ASM3040922v1_genomic.fna/checkm_result
[2024-01-24 11:28:25,315] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:25,316] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:25,335] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:25,335] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:25,335] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030409225.1_ASM3040922v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:25,336] [INFO] Task started: Blastn
[2024-01-24 11:28:25,336] [INFO] Running command: blastn -query GCF_030409225.1_ASM3040922v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0b30613-6b49-47be-b829-57ed0533a622/dqc_reference/reference_markers_gtdb.fasta -out GCF_030409225.1_ASM3040922v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:27,178] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:27,181] [INFO] Selected 13 target genomes.
[2024-01-24 11:28:27,182] [INFO] Target genome list was writen to GCF_030409225.1_ASM3040922v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:27,191] [INFO] Task started: fastANI
[2024-01-24 11:28:27,191] [INFO] Running command: fastANI --query /var/lib/cwl/stgf61c9fae-6a36-4c30-a3f3-c27bc1f806aa/GCF_030409225.1_ASM3040922v1_genomic.fna.gz --refList GCF_030409225.1_ASM3040922v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030409225.1_ASM3040922v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:35,658] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:35,676] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:28:35,676] [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_012044895.1	s__Aquisalimonas sp012044895	81.1023	665	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Aquisalimonadaceae;g__Aquisalimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007127625.1	s__Aquisalimonas sp007127625	81.0567	454	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Aquisalimonadaceae;g__Aquisalimonas	95.0	98.40	98.40	0.79	0.79	2	-
GCF_900110585.1	s__Aquisalimonas asiatica	80.9729	637	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Aquisalimonadaceae;g__Aquisalimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007133445.1	s__Aquisalimonas sp007133445	80.7338	306	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Aquisalimonadaceae;g__Aquisalimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007126095.1	s__Aquisalimonas sp007126095	80.5633	565	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Aquisalimonadaceae;g__Aquisalimonas	95.0	99.75	99.73	0.94	0.94	3	-
GCA_007120195.1	s__Aquisalimonas sp007120195	79.072	420	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Aquisalimonadaceae;g__Aquisalimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003149435.1	s__E85 sp003149435	78.5676	376	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__E85	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374645.1	s__Arhodomonas aquaeolei	78.0322	400	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__Arhodomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007134055.1	s__SLLM01 sp007134055	77.7544	263	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Aquisalimonadaceae;g__SLLM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002356355.1	s__Thiohalobacter thiocyanaticus_A	77.4812	240	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	98.53	98.53	0.93	0.93	2	-
GCA_014762505.1	s__SpSt-1174 sp014762505	77.4758	236	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699185.1	s__Thiohalobacter sp002699185	77.1077	182	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011322575.1	s__DRMK01 sp011322575	76.6645	59	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DRMK01;f__DRMK01;g__DRMK01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:35,677] [INFO] GTDB search result was written to GCF_030409225.1_ASM3040922v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:35,678] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:35,681] [INFO] DFAST_QC result json was written to GCF_030409225.1_ASM3040922v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:35,681] [INFO] DFAST_QC completed!
[2024-01-24 11:28:35,682] [INFO] Total running time: 0h1m17s