[2024-01-24 11:20:19,503] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:19,505] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:19,505] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e3f6118-901f-4b43-8e4c-9a413b660f39/dqc_reference
[2024-01-24 11:20:20,707] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:20,708] [INFO] Task started: Prodigal
[2024-01-24 11:20:20,708] [INFO] Running command: gunzip -c /var/lib/cwl/stg2b319c35-5e25-42e7-a272-44eaa4ac6e02/GCF_016908375.1_ASM1690837v1_genomic.fna.gz | prodigal -d GCF_016908375.1_ASM1690837v1_genomic.fna/cds.fna -a GCF_016908375.1_ASM1690837v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:28,062] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:28,063] [INFO] Task started: HMMsearch
[2024-01-24 11:20:28,063] [INFO] Running command: hmmsearch --tblout GCF_016908375.1_ASM1690837v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e3f6118-901f-4b43-8e4c-9a413b660f39/dqc_reference/reference_markers.hmm GCF_016908375.1_ASM1690837v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:28,358] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:28,359] [INFO] Found 6/6 markers.
[2024-01-24 11:20:28,390] [INFO] Query marker FASTA was written to GCF_016908375.1_ASM1690837v1_genomic.fna/markers.fasta
[2024-01-24 11:20:28,390] [INFO] Task started: Blastn
[2024-01-24 11:20:28,390] [INFO] Running command: blastn -query GCF_016908375.1_ASM1690837v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e3f6118-901f-4b43-8e4c-9a413b660f39/dqc_reference/reference_markers.fasta -out GCF_016908375.1_ASM1690837v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:28,982] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:28,987] [INFO] Selected 18 target genomes.
[2024-01-24 11:20:28,987] [INFO] Target genome list was writen to GCF_016908375.1_ASM1690837v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:29,032] [INFO] Task started: fastANI
[2024-01-24 11:20:29,032] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b319c35-5e25-42e7-a272-44eaa4ac6e02/GCF_016908375.1_ASM1690837v1_genomic.fna.gz --refList GCF_016908375.1_ASM1690837v1_genomic.fna/target_genomes.txt --output GCF_016908375.1_ASM1690837v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:40,257] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:40,258] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e3f6118-901f-4b43-8e4c-9a413b660f39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:40,259] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e3f6118-901f-4b43-8e4c-9a413b660f39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:40,279] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:20:40,279] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:40,280] [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
Amphibacillus cookii	strain=DSM 23721	GCA_016908375.1	767787	767787	type	True	100.0	1255	1256	95	conclusive
Amphibacillus jilinensis	strain=Y1	GCA_000306965.1	1216008	1216008	type	True	91.1265	1062	1256	95	below_threshold
Amphibacillus sediminis	strain=NBRC 103570	GCA_001552275.1	360185	360185	type	True	78.0954	220	1256	95	below_threshold
Amphibacillus marinus	strain=CGMCC 1.10434	GCA_900110345.1	872970	872970	type	True	77.833	210	1256	95	below_threshold
Paraliobacillus ryukyuensis	strain=DSM 15140	GCA_003315295.1	200904	200904	type	True	77.5911	107	1256	95	below_threshold
Halolactibacillus alkaliphilus	strain=NBRC 103919	GCA_007991355.1	442899	442899	type	True	77.575	105	1256	95	below_threshold
Halolactibacillus alkaliphilus	strain=CGMCC 1.6843	GCA_014645215.1	442899	442899	type	True	77.5162	108	1256	95	below_threshold
Paraliobacillus salinarum	strain=G6-18	GCA_014083865.1	1158996	1158996	type	True	77.5038	102	1256	95	below_threshold
Paraliobacillus zengyii	strain=X-1125	GCA_003268595.1	2213194	2213194	type	True	77.2148	126	1256	95	below_threshold
Amphibacillus xylanus	strain=NBRC 15112	GCA_000307165.1	1449	1449	type	True	77.0692	106	1256	95	below_threshold
Aquibacillus saliphilus	strain=KHM2	GCA_020404745.1	1909422	1909422	type	True	76.5824	77	1256	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:40,282] [INFO] DFAST Taxonomy check result was written to GCF_016908375.1_ASM1690837v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:40,282] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:40,282] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:40,283] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e3f6118-901f-4b43-8e4c-9a413b660f39/dqc_reference/checkm_data
[2024-01-24 11:20:40,284] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:40,325] [INFO] Task started: CheckM
[2024-01-24 11:20:40,325] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016908375.1_ASM1690837v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016908375.1_ASM1690837v1_genomic.fna/checkm_input GCF_016908375.1_ASM1690837v1_genomic.fna/checkm_result
[2024-01-24 11:21:09,160] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:09,161] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:09,183] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:09,184] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:09,184] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016908375.1_ASM1690837v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:09,185] [INFO] Task started: Blastn
[2024-01-24 11:21:09,185] [INFO] Running command: blastn -query GCF_016908375.1_ASM1690837v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e3f6118-901f-4b43-8e4c-9a413b660f39/dqc_reference/reference_markers_gtdb.fasta -out GCF_016908375.1_ASM1690837v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:09,957] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:09,961] [INFO] Selected 14 target genomes.
[2024-01-24 11:21:09,961] [INFO] Target genome list was writen to GCF_016908375.1_ASM1690837v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:09,970] [INFO] Task started: fastANI
[2024-01-24 11:21:09,970] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b319c35-5e25-42e7-a272-44eaa4ac6e02/GCF_016908375.1_ASM1690837v1_genomic.fna.gz --refList GCF_016908375.1_ASM1690837v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016908375.1_ASM1690837v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:19,385] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:19,397] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:19,397] [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_016908375.1	s__Amphibacillus_C cookii	100.0	1255	1256	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000306965.1	s__Amphibacillus_C jilinensis	91.1317	1062	1256	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552275.1	s__Amphibacillus_B sediminis	78.1019	219	1256	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116255.1	s__Halolactibacillus miurensis	77.9252	99	1256	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Halolactibacillus	95.0	99.76	99.51	0.98	0.95	3	-
GCF_900110345.1	s__Amphibacillus_D marinus	77.8292	209	1256	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003426025.1	s__Paraliobacillus_A quinghaiensis	77.5509	101	1256	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus_A	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900115465.1	s__Halolactibacillus alkaliphilus	77.547	110	1256	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Halolactibacillus	95.0	99.99	99.98	0.99	0.99	3	-
GCF_014083865.1	s__Paraliobacillus salinarum	77.5104	101	1256	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018919165.1	s__Amphibacillus sp018919165	77.4159	136	1256	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000307165.1	s__Amphibacillus xylanus	77.0708	107	1256	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus	95.0	97.98	97.98	0.94	0.94	2	-
GCF_000724085.1	s__Virgibacillus manasiensis	76.8589	51	1256	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:19,399] [INFO] GTDB search result was written to GCF_016908375.1_ASM1690837v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:19,400] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:19,403] [INFO] DFAST_QC result json was written to GCF_016908375.1_ASM1690837v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:19,403] [INFO] DFAST_QC completed!
[2024-01-24 11:21:19,403] [INFO] Total running time: 0h0m60s