[2024-01-24 13:57:45,282] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:45,284] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:45,284] [INFO] DQC Reference Directory: /var/lib/cwl/stg9577e21e-a579-4dd1-ba9f-c365a2e26a77/dqc_reference
[2024-01-24 13:57:46,675] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:46,676] [INFO] Task started: Prodigal
[2024-01-24 13:57:46,676] [INFO] Running command: gunzip -c /var/lib/cwl/stg352d1c0b-4f5d-4a48-9190-77653f90ee46/GCF_010994085.1_ASM1099408v1_genomic.fna.gz | prodigal -d GCF_010994085.1_ASM1099408v1_genomic.fna/cds.fna -a GCF_010994085.1_ASM1099408v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:55,836] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:55,837] [INFO] Task started: HMMsearch
[2024-01-24 13:57:55,837] [INFO] Running command: hmmsearch --tblout GCF_010994085.1_ASM1099408v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9577e21e-a579-4dd1-ba9f-c365a2e26a77/dqc_reference/reference_markers.hmm GCF_010994085.1_ASM1099408v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:56,162] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:56,164] [INFO] Found 6/6 markers.
[2024-01-24 13:57:56,206] [INFO] Query marker FASTA was written to GCF_010994085.1_ASM1099408v1_genomic.fna/markers.fasta
[2024-01-24 13:57:56,208] [INFO] Task started: Blastn
[2024-01-24 13:57:56,208] [INFO] Running command: blastn -query GCF_010994085.1_ASM1099408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9577e21e-a579-4dd1-ba9f-c365a2e26a77/dqc_reference/reference_markers.fasta -out GCF_010994085.1_ASM1099408v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:56,874] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:56,877] [INFO] Selected 9 target genomes.
[2024-01-24 13:57:56,878] [INFO] Target genome list was writen to GCF_010994085.1_ASM1099408v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:56,880] [INFO] Task started: fastANI
[2024-01-24 13:57:56,880] [INFO] Running command: fastANI --query /var/lib/cwl/stg352d1c0b-4f5d-4a48-9190-77653f90ee46/GCF_010994085.1_ASM1099408v1_genomic.fna.gz --refList GCF_010994085.1_ASM1099408v1_genomic.fna/target_genomes.txt --output GCF_010994085.1_ASM1099408v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:08,366] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:08,366] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9577e21e-a579-4dd1-ba9f-c365a2e26a77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:08,367] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9577e21e-a579-4dd1-ba9f-c365a2e26a77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:08,374] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:58:08,374] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:58:08,375] [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
Gracilibacillus saliphilus	strain=YIM 91119	GCA_010994085.1	543890	543890	type	True	100.0	1463	1465	95	inconclusive
Gracilibacillus lacisalsi	strain=DSM 19029	GCA_000377765.1	393087	393087	type	True	95.371	1185	1465	95	inconclusive
Gracilibacillus thailandensis	strain=TP2-8	GCA_010994055.1	563735	563735	type	True	94.9536	1124	1465	95	below_threshold
Gracilibacillus thailandensis	strain=TP2-8	GCA_009659515.1	563735	563735	type	True	94.8617	1145	1465	95	below_threshold
Gracilibacillus suaedae	strain=LD4P30	GCA_017599345.1	2820273	2820273	type	True	91.4683	1181	1465	95	below_threshold
Gracilibacillus salitolerans	strain=SCU50	GCA_009650095.1	2663022	2663022	type	True	85.4545	1076	1465	95	below_threshold
Tenuibacillus multivorans	strain=CGMCC 1.3442	GCA_900103915.1	237069	237069	type	True	76.6429	61	1465	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:08,376] [INFO] DFAST Taxonomy check result was written to GCF_010994085.1_ASM1099408v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:08,377] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:08,377] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:08,377] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9577e21e-a579-4dd1-ba9f-c365a2e26a77/dqc_reference/checkm_data
[2024-01-24 13:58:08,378] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:08,423] [INFO] Task started: CheckM
[2024-01-24 13:58:08,423] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010994085.1_ASM1099408v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010994085.1_ASM1099408v1_genomic.fna/checkm_input GCF_010994085.1_ASM1099408v1_genomic.fna/checkm_result
[2024-01-24 13:58:43,235] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:43,236] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:43,267] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:43,268] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:43,268] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010994085.1_ASM1099408v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:43,269] [INFO] Task started: Blastn
[2024-01-24 13:58:43,269] [INFO] Running command: blastn -query GCF_010994085.1_ASM1099408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9577e21e-a579-4dd1-ba9f-c365a2e26a77/dqc_reference/reference_markers_gtdb.fasta -out GCF_010994085.1_ASM1099408v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:44,085] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:44,089] [INFO] Selected 10 target genomes.
[2024-01-24 13:58:44,089] [INFO] Target genome list was writen to GCF_010994085.1_ASM1099408v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:44,095] [INFO] Task started: fastANI
[2024-01-24 13:58:44,096] [INFO] Running command: fastANI --query /var/lib/cwl/stg352d1c0b-4f5d-4a48-9190-77653f90ee46/GCF_010994085.1_ASM1099408v1_genomic.fna.gz --refList GCF_010994085.1_ASM1099408v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010994085.1_ASM1099408v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:53,941] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:53,951] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:53,951] [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_000377765.1	s__Gracilibacillus lacisalsi	95.3743	1185	1465	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	95.88	95.36	0.83	0.81	4	conclusive
GCF_017599345.1	s__Gracilibacillus sp017599345	91.4622	1182	1465	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009650095.1	s__Gracilibacillus sp002797295	85.4712	1074	1465	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	98.80	98.80	0.91	0.91	2	-
GCF_900114645.1	s__Gracilibacillus orientalis	83.8621	994	1465	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143085.1	s__Gracilibacillus kekensis	79.147	461	1465	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458115.1	s__Gracilibacillus massiliensis	79.1089	489	1465	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010993965.1	s__Gracilibacillus sp010993965	78.0546	287	1465	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:53,953] [INFO] GTDB search result was written to GCF_010994085.1_ASM1099408v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:53,954] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:53,958] [INFO] DFAST_QC result json was written to GCF_010994085.1_ASM1099408v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:53,958] [INFO] DFAST_QC completed!
[2024-01-24 13:58:53,958] [INFO] Total running time: 0h1m9s