[2024-01-24 12:39:35,544] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:35,545] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:35,546] [INFO] DQC Reference Directory: /var/lib/cwl/stg41d238ad-81b7-4c2b-a91f-39182011aba4/dqc_reference
[2024-01-24 12:39:36,739] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:36,740] [INFO] Task started: Prodigal
[2024-01-24 12:39:36,740] [INFO] Running command: gunzip -c /var/lib/cwl/stg551161d8-a104-4075-aaf2-603e7fb98983/GCF_000482485.1_ASM48248v1_genomic.fna.gz | prodigal -d GCF_000482485.1_ASM48248v1_genomic.fna/cds.fna -a GCF_000482485.1_ASM48248v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:39:44,778] [INFO] Task succeeded: Prodigal
[2024-01-24 12:39:44,779] [INFO] Task started: HMMsearch
[2024-01-24 12:39:44,779] [INFO] Running command: hmmsearch --tblout GCF_000482485.1_ASM48248v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg41d238ad-81b7-4c2b-a91f-39182011aba4/dqc_reference/reference_markers.hmm GCF_000482485.1_ASM48248v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:39:45,072] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:39:45,074] [INFO] Found 6/6 markers.
[2024-01-24 12:39:45,113] [INFO] Query marker FASTA was written to GCF_000482485.1_ASM48248v1_genomic.fna/markers.fasta
[2024-01-24 12:39:45,113] [INFO] Task started: Blastn
[2024-01-24 12:39:45,114] [INFO] Running command: blastn -query GCF_000482485.1_ASM48248v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41d238ad-81b7-4c2b-a91f-39182011aba4/dqc_reference/reference_markers.fasta -out GCF_000482485.1_ASM48248v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:45,711] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:45,715] [INFO] Selected 29 target genomes.
[2024-01-24 12:39:45,715] [INFO] Target genome list was writen to GCF_000482485.1_ASM48248v1_genomic.fna/target_genomes.txt
[2024-01-24 12:39:45,724] [INFO] Task started: fastANI
[2024-01-24 12:39:45,724] [INFO] Running command: fastANI --query /var/lib/cwl/stg551161d8-a104-4075-aaf2-603e7fb98983/GCF_000482485.1_ASM48248v1_genomic.fna.gz --refList GCF_000482485.1_ASM48248v1_genomic.fna/target_genomes.txt --output GCF_000482485.1_ASM48248v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:01,546] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:01,546] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg41d238ad-81b7-4c2b-a91f-39182011aba4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:01,547] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg41d238ad-81b7-4c2b-a91f-39182011aba4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:01,565] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:40:01,565] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:40:01,565] [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
Ornithinibacillus halotolerans	strain=CGMCC 1.12408	GCA_014637405.1	1274357	1274357	type	True	78.9868	460	1394	95	below_threshold
Ornithinibacillus massiliensis	strain=Marseille-P3601	GCA_018310345.1	1944633	1944633	type	True	78.9189	423	1394	95	below_threshold
Ornithinibacillus scapharcae	strain=TW25	GCA_000190475.2	1147159	1147159	type	True	78.674	440	1394	95	below_threshold
Ornithinibacillus contaminans	strain=DSM 22953	GCA_001038425.2	694055	694055	type	True	78.5349	329	1394	95	below_threshold
Virgibacillus ndiopensis	strain=Marseille-P3835	GCA_900187325.1	2004408	2004408	type	True	77.9286	167	1394	95	below_threshold
Ornithinibacillus halophilus	strain=IBRC-M 10683	GCA_900129485.1	930117	930117	type	True	77.7093	214	1394	95	below_threshold
Aquibacillus kalidii	strain=HU2P27	GCA_014280935.1	2762597	2762597	type	True	77.6985	93	1394	95	below_threshold
Gracilibacillus suaedae	strain=LD4P30	GCA_017599345.1	2820273	2820273	type	True	77.4936	85	1394	95	below_threshold
Oceanobacillus chungangensis	strain=CAU 1051	GCA_003369565.1	1229152	1229152	type	True	77.4746	137	1394	95	below_threshold
Aquibacillus koreensis	strain=JCM 12387	GCA_025154055.1	279446	279446	type	True	77.3246	97	1394	95	below_threshold
Ornithinibacillus gellani	strain=LJ137	GCA_003730295.1	2293253	2293253	type	True	77.2312	122	1394	95	below_threshold
Oceanobacillus senegalensis	strain=Marseille-P3587	GCA_900176885.1	1936063	1936063	type	True	77.1458	131	1394	95	below_threshold
Oceanobacillus iheyensis	strain=HTE831	GCA_000011245.1	182710	182710	type	True	76.9967	114	1394	95	below_threshold
Terribacillus aidingensis	strain=CGMCC 1.8913	GCA_900215625.1	586416	586416	type	True	76.9135	52	1394	95	below_threshold
Virgibacillus litoralis	strain=DSM 21085	GCA_017873675.1	578221	578221	type	True	76.9049	119	1394	95	below_threshold
Cerasibacillus terrae	strain=CC-CFT480	GCA_008039555.1	2498845	2498845	type	True	76.9005	106	1394	95	below_threshold
Virgibacillus natechei	strain=DSM 25609	GCA_017874115.1	1216297	1216297	type	True	76.8031	124	1394	95	below_threshold
Robertmurraya massiliosenegalensis	strain=JC6	GCA_000311725.1	1287657	1287657	type	True	76.7082	69	1394	95	below_threshold
Oceanobacillus salinisoli	strain=YIM B00359	GCA_009733865.1	2678611	2678611	type	True	76.6678	144	1394	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:01,567] [INFO] DFAST Taxonomy check result was written to GCF_000482485.1_ASM48248v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:01,569] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:01,570] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:01,570] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg41d238ad-81b7-4c2b-a91f-39182011aba4/dqc_reference/checkm_data
[2024-01-24 12:40:01,572] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:01,620] [INFO] Task started: CheckM
[2024-01-24 12:40:01,621] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000482485.1_ASM48248v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000482485.1_ASM48248v1_genomic.fna/checkm_input GCF_000482485.1_ASM48248v1_genomic.fna/checkm_result
[2024-01-24 12:40:32,302] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:32,303] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:32,327] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:32,327] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:32,327] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000482485.1_ASM48248v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:32,328] [INFO] Task started: Blastn
[2024-01-24 12:40:32,328] [INFO] Running command: blastn -query GCF_000482485.1_ASM48248v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41d238ad-81b7-4c2b-a91f-39182011aba4/dqc_reference/reference_markers_gtdb.fasta -out GCF_000482485.1_ASM48248v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:33,222] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:33,226] [INFO] Selected 13 target genomes.
[2024-01-24 12:40:33,226] [INFO] Target genome list was writen to GCF_000482485.1_ASM48248v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:33,233] [INFO] Task started: fastANI
[2024-01-24 12:40:33,233] [INFO] Running command: fastANI --query /var/lib/cwl/stg551161d8-a104-4075-aaf2-603e7fb98983/GCF_000482485.1_ASM48248v1_genomic.fna.gz --refList GCF_000482485.1_ASM48248v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000482485.1_ASM48248v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:42,440] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:42,454] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:42,455] [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_000482485.1	s__Ornithinibacillus globulus	100.0	1392	1394	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000577245.1	s__Ornithinibacillus sp000577245	82.66	863	1394	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184735.1	s__Ornithinibacillus globulus_B	81.3633	816	1394	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001038485.1	s__Ornithinibacillus californiensis	79.2145	496	1394	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014637405.1	s__Ornithinibacillus halotolerans	78.9629	469	1394	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018310345.1	s__Ornithinibacillus massiliensis	78.955	419	1394	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	99.20	99.20	0.97	0.97	2	-
GCF_000190475.1	s__Ornithinibacillus scapharcae	78.6962	437	1394	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001038425.2	s__Ornithinibacillus contaminans	78.5315	329	1394	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011245.1	s__Oceanobacillus iheyensis	77.0139	114	1394	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:40:42,457] [INFO] GTDB search result was written to GCF_000482485.1_ASM48248v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:42,458] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:42,465] [INFO] DFAST_QC result json was written to GCF_000482485.1_ASM48248v1_genomic.fna/dqc_result.json
[2024-01-24 12:40:42,466] [INFO] DFAST_QC completed!
[2024-01-24 12:40:42,466] [INFO] Total running time: 0h1m7s