[2024-01-25 19:09:35,572] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:09:35,573] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:09:35,573] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a25c217-b0a3-4831-b1cf-011ec40ccac4/dqc_reference
[2024-01-25 19:09:36,687] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:09:36,688] [INFO] Task started: Prodigal
[2024-01-25 19:09:36,688] [INFO] Running command: gunzip -c /var/lib/cwl/stgfaf46d97-3b47-40c6-9126-c52ceaab7928/GCF_017792025.1_ASM1779202v1_genomic.fna.gz | prodigal -d GCF_017792025.1_ASM1779202v1_genomic.fna/cds.fna -a GCF_017792025.1_ASM1779202v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:09:46,160] [INFO] Task succeeded: Prodigal
[2024-01-25 19:09:46,160] [INFO] Task started: HMMsearch
[2024-01-25 19:09:46,160] [INFO] Running command: hmmsearch --tblout GCF_017792025.1_ASM1779202v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a25c217-b0a3-4831-b1cf-011ec40ccac4/dqc_reference/reference_markers.hmm GCF_017792025.1_ASM1779202v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:09:46,411] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:09:46,412] [INFO] Found 6/6 markers.
[2024-01-25 19:09:46,444] [INFO] Query marker FASTA was written to GCF_017792025.1_ASM1779202v1_genomic.fna/markers.fasta
[2024-01-25 19:09:46,444] [INFO] Task started: Blastn
[2024-01-25 19:09:46,444] [INFO] Running command: blastn -query GCF_017792025.1_ASM1779202v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a25c217-b0a3-4831-b1cf-011ec40ccac4/dqc_reference/reference_markers.fasta -out GCF_017792025.1_ASM1779202v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:09:46,984] [INFO] Task succeeded: Blastn
[2024-01-25 19:09:46,986] [INFO] Selected 18 target genomes.
[2024-01-25 19:09:46,987] [INFO] Target genome list was writen to GCF_017792025.1_ASM1779202v1_genomic.fna/target_genomes.txt
[2024-01-25 19:09:46,997] [INFO] Task started: fastANI
[2024-01-25 19:09:46,997] [INFO] Running command: fastANI --query /var/lib/cwl/stgfaf46d97-3b47-40c6-9126-c52ceaab7928/GCF_017792025.1_ASM1779202v1_genomic.fna.gz --refList GCF_017792025.1_ASM1779202v1_genomic.fna/target_genomes.txt --output GCF_017792025.1_ASM1779202v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:10:03,133] [INFO] Task succeeded: fastANI
[2024-01-25 19:10:03,133] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a25c217-b0a3-4831-b1cf-011ec40ccac4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:10:03,134] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a25c217-b0a3-4831-b1cf-011ec40ccac4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:10:03,142] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:10:03,142] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:10:03,142] [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
Sediminibacillus dalangtanensis	strain=DP4-553-S	GCA_017792025.1	2729421	2729421	type	True	100.0	1364	1366	95	conclusive
Sediminibacillus halophilus	strain=CGMCC 1.6199	GCA_900103695.1	482461	482461	type	True	90.7745	1194	1366	95	below_threshold
Sediminibacillus terrae	strain=JSM 102062	GCA_009602435.1	1562106	1562106	type	True	87.6511	1158	1366	95	below_threshold
Paraliobacillus zengyii	strain=X-1125	GCA_003268595.1	2213194	2213194	type	True	80.5723	60	1366	95	below_threshold
Gracilibacillus salitolerans	strain=SCU50	GCA_009650095.1	2663022	2663022	type	True	79.674	82	1366	95	below_threshold
Sediminibacillus albus	strain=CGMCC 1.6502	GCA_900101125.1	407036	407036	type	True	78.7982	403	1366	95	below_threshold
Aquibacillus albus	strain=DSM 23711	GCA_016908325.1	1168171	1168171	type	True	77.5087	101	1366	95	below_threshold
Aquibacillus kalidii	strain=HU2P27	GCA_014280935.1	2762597	2762597	type	True	77.4444	93	1366	95	below_threshold
Halobacillus trueperi	strain=KCTC 3686	GCA_003386945.1	156205	156205	type	True	77.4105	54	1366	95	below_threshold
Lentibacillus halodurans	strain=CGMCC 1.3702	GCA_900112045.1	237679	237679	type	True	77.1436	56	1366	95	below_threshold
Halobacillus aidingensis	strain=CGMCC 1.3703	GCA_900104185.1	240303	240303	type	True	76.9439	59	1366	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:10:03,143] [INFO] DFAST Taxonomy check result was written to GCF_017792025.1_ASM1779202v1_genomic.fna/tc_result.tsv
[2024-01-25 19:10:03,144] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:10:03,144] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:10:03,144] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a25c217-b0a3-4831-b1cf-011ec40ccac4/dqc_reference/checkm_data
[2024-01-25 19:10:03,145] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:10:03,191] [INFO] Task started: CheckM
[2024-01-25 19:10:03,191] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017792025.1_ASM1779202v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017792025.1_ASM1779202v1_genomic.fna/checkm_input GCF_017792025.1_ASM1779202v1_genomic.fna/checkm_result
[2024-01-25 19:10:34,449] [INFO] Task succeeded: CheckM
[2024-01-25 19:10:34,450] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.26%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-25 19:10:34,473] [INFO] ===== Completeness check finished =====
[2024-01-25 19:10:34,473] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:10:34,473] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017792025.1_ASM1779202v1_genomic.fna/markers.fasta)
[2024-01-25 19:10:34,474] [INFO] Task started: Blastn
[2024-01-25 19:10:34,474] [INFO] Running command: blastn -query GCF_017792025.1_ASM1779202v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a25c217-b0a3-4831-b1cf-011ec40ccac4/dqc_reference/reference_markers_gtdb.fasta -out GCF_017792025.1_ASM1779202v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:35,220] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:35,223] [INFO] Selected 10 target genomes.
[2024-01-25 19:10:35,223] [INFO] Target genome list was writen to GCF_017792025.1_ASM1779202v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:10:35,236] [INFO] Task started: fastANI
[2024-01-25 19:10:35,236] [INFO] Running command: fastANI --query /var/lib/cwl/stgfaf46d97-3b47-40c6-9126-c52ceaab7928/GCF_017792025.1_ASM1779202v1_genomic.fna.gz --refList GCF_017792025.1_ASM1779202v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017792025.1_ASM1779202v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:10:46,454] [INFO] Task succeeded: fastANI
[2024-01-25 19:10:46,459] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:10:46,459] [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_017792025.1	s__Sediminibacillus sp017792025	100.0	1366	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Sediminibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900103695.1	s__Sediminibacillus halophilus	90.7745	1194	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Sediminibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009602435.1	s__Sediminibacillus terrae	87.659	1157	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Sediminibacillus	95.0	99.15	99.14	0.93	0.93	3	-
GCF_000821245.2	s__Sediminibacillus senegalensis	82.1514	870	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Sediminibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101125.1	s__Sediminibacillus albus	78.827	401	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Sediminibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009856355.1	s__Halobacillus litoralis_B	77.1184	54	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	98.99	98.95	0.95	0.95	3	-
GCF_015905325.1	s__Halobacillus sp015905325	77.0971	62	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:10:46,461] [INFO] GTDB search result was written to GCF_017792025.1_ASM1779202v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:10:46,461] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:10:46,463] [INFO] DFAST_QC result json was written to GCF_017792025.1_ASM1779202v1_genomic.fna/dqc_result.json
[2024-01-25 19:10:46,464] [INFO] DFAST_QC completed!
[2024-01-25 19:10:46,464] [INFO] Total running time: 0h1m11s