[2024-01-25 18:49:50,723] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:49:50,727] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:49:50,730] [INFO] DQC Reference Directory: /var/lib/cwl/stg19aa0f41-e042-4194-928c-624167eb7c7d/dqc_reference
[2024-01-25 18:49:51,917] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:49:51,917] [INFO] Task started: Prodigal
[2024-01-25 18:49:51,918] [INFO] Running command: gunzip -c /var/lib/cwl/stg3bbd8298-8574-4d36-b3ab-677683946a90/GCF_009659515.1_ASM965951v1_genomic.fna.gz | prodigal -d GCF_009659515.1_ASM965951v1_genomic.fna/cds.fna -a GCF_009659515.1_ASM965951v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:49:59,182] [INFO] Task succeeded: Prodigal
[2024-01-25 18:49:59,182] [INFO] Task started: HMMsearch
[2024-01-25 18:49:59,182] [INFO] Running command: hmmsearch --tblout GCF_009659515.1_ASM965951v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19aa0f41-e042-4194-928c-624167eb7c7d/dqc_reference/reference_markers.hmm GCF_009659515.1_ASM965951v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:49:59,430] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:49:59,431] [INFO] Found 6/6 markers.
[2024-01-25 18:49:59,467] [INFO] Query marker FASTA was written to GCF_009659515.1_ASM965951v1_genomic.fna/markers.fasta
[2024-01-25 18:49:59,468] [INFO] Task started: Blastn
[2024-01-25 18:49:59,468] [INFO] Running command: blastn -query GCF_009659515.1_ASM965951v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19aa0f41-e042-4194-928c-624167eb7c7d/dqc_reference/reference_markers.fasta -out GCF_009659515.1_ASM965951v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:00,008] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:00,010] [INFO] Selected 14 target genomes.
[2024-01-25 18:50:00,011] [INFO] Target genome list was writen to GCF_009659515.1_ASM965951v1_genomic.fna/target_genomes.txt
[2024-01-25 18:50:00,027] [INFO] Task started: fastANI
[2024-01-25 18:50:00,027] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bbd8298-8574-4d36-b3ab-677683946a90/GCF_009659515.1_ASM965951v1_genomic.fna.gz --refList GCF_009659515.1_ASM965951v1_genomic.fna/target_genomes.txt --output GCF_009659515.1_ASM965951v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:50:12,164] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:12,164] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19aa0f41-e042-4194-928c-624167eb7c7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:50:12,165] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19aa0f41-e042-4194-928c-624167eb7c7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:50:12,172] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 18:50:12,172] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 18:50:12,172] [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 thailandensis	strain=TP2-8	GCA_009659515.1	563735	563735	type	True	100.0	1383	1388	95	inconclusive
Gracilibacillus thailandensis	strain=TP2-8	GCA_010994055.1	563735	563735	type	True	99.9668	1329	1388	95	inconclusive
Gracilibacillus lacisalsi	strain=DSM 19029	GCA_000377765.1	393087	393087	type	True	96.1393	1160	1388	95	inconclusive
Gracilibacillus saliphilus	strain=YIM 91119	GCA_010994085.1	543890	543890	type	True	95.0364	1127	1388	95	inconclusive
Gracilibacillus suaedae	strain=LD4P30	GCA_017599345.1	2820273	2820273	type	True	91.2935	1099	1388	95	below_threshold
Gracilibacillus salitolerans	strain=SCU50	GCA_009650095.1	2663022	2663022	type	True	85.5428	1025	1388	95	below_threshold
Tenuibacillus multivorans	strain=CGMCC 1.3442	GCA_900103915.1	237069	237069	type	True	76.6652	54	1388	95	below_threshold
Sutcliffiella halmapala	strain=DSM 8723	GCA_002019665.1	79882	79882	type	True	75.9833	56	1388	95	below_threshold
Gottfriedia solisilvae	strain=CGMCC 1.14993	GCA_014640495.1	1516104	1516104	type	True	75.7866	54	1388	95	below_threshold
Gottfriedia solisilvae	strain=NEAU-cbsb5	GCA_002128405.1	1516104	1516104	type	True	75.7308	53	1388	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:50:12,174] [INFO] DFAST Taxonomy check result was written to GCF_009659515.1_ASM965951v1_genomic.fna/tc_result.tsv
[2024-01-25 18:50:12,175] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:50:12,175] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:50:12,175] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19aa0f41-e042-4194-928c-624167eb7c7d/dqc_reference/checkm_data
[2024-01-25 18:50:12,176] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:50:12,220] [INFO] Task started: CheckM
[2024-01-25 18:50:12,220] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009659515.1_ASM965951v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009659515.1_ASM965951v1_genomic.fna/checkm_input GCF_009659515.1_ASM965951v1_genomic.fna/checkm_result
[2024-01-25 18:50:39,171] [INFO] Task succeeded: CheckM
[2024-01-25 18:50:39,173] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:50:39,206] [INFO] ===== Completeness check finished =====
[2024-01-25 18:50:39,206] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:50:39,207] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009659515.1_ASM965951v1_genomic.fna/markers.fasta)
[2024-01-25 18:50:39,207] [INFO] Task started: Blastn
[2024-01-25 18:50:39,207] [INFO] Running command: blastn -query GCF_009659515.1_ASM965951v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19aa0f41-e042-4194-928c-624167eb7c7d/dqc_reference/reference_markers_gtdb.fasta -out GCF_009659515.1_ASM965951v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:39,951] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:39,955] [INFO] Selected 16 target genomes.
[2024-01-25 18:50:39,956] [INFO] Target genome list was writen to GCF_009659515.1_ASM965951v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:50:39,974] [INFO] Task started: fastANI
[2024-01-25 18:50:39,974] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bbd8298-8574-4d36-b3ab-677683946a90/GCF_009659515.1_ASM965951v1_genomic.fna.gz --refList GCF_009659515.1_ASM965951v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009659515.1_ASM965951v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:50:53,535] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:53,543] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:50:53,543] [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	96.1242	1161	1388	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	91.2903	1100	1388	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	85.5764	1021	1388	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	83.9917	937	1388	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	79.2043	496	1388	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_900143085.1	s__Gracilibacillus kekensis	79.0721	478	1388	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_000521485.1	s__Gracilibacillus boraciitolerans	78.3897	367	1388	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_016909015.1	s__Gracilibacillus alcaliphilus	77.9603	228	1388	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_007301515.1	s__Radiobacillus deserti	77.359	108	1388	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Radiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002019665.1	s__Sutcliffiella_A halmapala	75.9833	56	1388	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_I;g__Sutcliffiella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002128405.1	s__Gottfriedia solisilvae	75.7318	53	1388	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	98.14	96.28	0.93	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:50:53,545] [INFO] GTDB search result was written to GCF_009659515.1_ASM965951v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:50:53,545] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:50:53,548] [INFO] DFAST_QC result json was written to GCF_009659515.1_ASM965951v1_genomic.fna/dqc_result.json
[2024-01-25 18:50:53,548] [INFO] DFAST_QC completed!
[2024-01-25 18:50:53,548] [INFO] Total running time: 0h1m3s