[2024-01-24 11:59:05,235] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:05,237] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:05,237] [INFO] DQC Reference Directory: /var/lib/cwl/stgba901b6d-5aff-4647-8464-ff4845dd4424/dqc_reference
[2024-01-24 11:59:06,436] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:06,437] [INFO] Task started: Prodigal
[2024-01-24 11:59:06,437] [INFO] Running command: gunzip -c /var/lib/cwl/stg2f1fbe24-f25f-4ea5-8516-4a289fd09565/GCF_029094545.1_ASM2909454v1_genomic.fna.gz | prodigal -d GCF_029094545.1_ASM2909454v1_genomic.fna/cds.fna -a GCF_029094545.1_ASM2909454v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:15,266] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:15,266] [INFO] Task started: HMMsearch
[2024-01-24 11:59:15,266] [INFO] Running command: hmmsearch --tblout GCF_029094545.1_ASM2909454v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba901b6d-5aff-4647-8464-ff4845dd4424/dqc_reference/reference_markers.hmm GCF_029094545.1_ASM2909454v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:15,529] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:15,530] [INFO] Found 6/6 markers.
[2024-01-24 11:59:15,566] [INFO] Query marker FASTA was written to GCF_029094545.1_ASM2909454v1_genomic.fna/markers.fasta
[2024-01-24 11:59:15,566] [INFO] Task started: Blastn
[2024-01-24 11:59:15,566] [INFO] Running command: blastn -query GCF_029094545.1_ASM2909454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba901b6d-5aff-4647-8464-ff4845dd4424/dqc_reference/reference_markers.fasta -out GCF_029094545.1_ASM2909454v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:16,161] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:16,166] [INFO] Selected 20 target genomes.
[2024-01-24 11:59:16,166] [INFO] Target genome list was writen to GCF_029094545.1_ASM2909454v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:16,191] [INFO] Task started: fastANI
[2024-01-24 11:59:16,191] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f1fbe24-f25f-4ea5-8516-4a289fd09565/GCF_029094545.1_ASM2909454v1_genomic.fna.gz --refList GCF_029094545.1_ASM2909454v1_genomic.fna/target_genomes.txt --output GCF_029094545.1_ASM2909454v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:29,782] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:29,783] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba901b6d-5aff-4647-8464-ff4845dd4424/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:29,784] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba901b6d-5aff-4647-8464-ff4845dd4424/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:29,808] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:29,808] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:29,808] [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
Alkalihalophilus marmarensis	strain=DSM 21297	GCA_000474275.2	521377	521377	type	True	95.7969	1155	1412	95	conclusive
Neobacillus drentensis	strain=FJAT-10044	GCA_001636415.1	220684	220684	type	True	80.2416	58	1412	95	below_threshold
Peribacillus frigoritolerans	strain=FJAT-2396	GCA_001636405.1	450367	450367	type	True	80.184	55	1412	95	below_threshold
Peribacillus frigoritolerans	strain=DSM 8801	GCA_024169475.1	450367	450367	type	True	80.1365	66	1412	95	below_threshold
Alkalihalobacillus nanhaiisediminis	strain=CGMCC 1.10116	GCA_007830185.1	688079	688079	type	True	78.1749	186	1412	95	below_threshold
Alkalihalobacillus akibai	strain=JCM 9157	GCA_000513135.1	1411	1411	type	True	77.9574	181	1412	95	below_threshold
Alkalihalobacillus akibai	strain=JCM 9157	GCA_001315085.1	1411	1411	type	True	77.935	181	1412	95	below_threshold
Alkalihalobacillus wakoensis	strain=JCM 9140	GCA_001315045.1	127891	127891	type	True	77.7666	186	1412	95	below_threshold
Bacillus suaedae	strain=YZJH907-2	GCA_017939705.1	2822140	2822140	type	True	77.7553	167	1412	95	below_threshold
Alkalihalobacillus wakoensis	strain=JCM 9140	GCA_000513095.1	127891	127891	type	True	77.7146	187	1412	95	below_threshold
Alkalihalobacillus okhensis	strain=Kh10-101	GCA_000787375.1	333138	333138	type	True	77.6251	205	1412	95	below_threshold
Halalkalibacterium ligniniphilum	strain=L1	GCA_000334155.1	1134413	1134413	type	True	77.4504	129	1412	95	below_threshold
Pseudoneobacillus rhizosphaerae	strain=CIP 111885	GCA_917563885.1	2880968	2880968	type	True	77.2546	52	1412	95	below_threshold
Desertibacillus haloalkaliphilus	strain=KJ1-10-99	GCA_019039105.1	1328930	1328930	type	True	77.1037	106	1412	95	below_threshold
Alkalihalobacterium elongatum	strain=MEB199	GCA_019024285.1	2675466	2675466	type	True	77.0333	127	1412	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:29,810] [INFO] DFAST Taxonomy check result was written to GCF_029094545.1_ASM2909454v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:29,810] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:29,811] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:29,811] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba901b6d-5aff-4647-8464-ff4845dd4424/dqc_reference/checkm_data
[2024-01-24 11:59:29,812] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:29,856] [INFO] Task started: CheckM
[2024-01-24 11:59:29,856] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_029094545.1_ASM2909454v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_029094545.1_ASM2909454v1_genomic.fna/checkm_input GCF_029094545.1_ASM2909454v1_genomic.fna/checkm_result
[2024-01-24 12:00:01,340] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:01,341] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:01,365] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:01,365] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:01,366] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_029094545.1_ASM2909454v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:01,367] [INFO] Task started: Blastn
[2024-01-24 12:00:01,367] [INFO] Running command: blastn -query GCF_029094545.1_ASM2909454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba901b6d-5aff-4647-8464-ff4845dd4424/dqc_reference/reference_markers_gtdb.fasta -out GCF_029094545.1_ASM2909454v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:02,148] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:02,155] [INFO] Selected 15 target genomes.
[2024-01-24 12:00:02,156] [INFO] Target genome list was writen to GCF_029094545.1_ASM2909454v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:02,167] [INFO] Task started: fastANI
[2024-01-24 12:00:02,167] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f1fbe24-f25f-4ea5-8516-4a289fd09565/GCF_029094545.1_ASM2909454v1_genomic.fna.gz --refList GCF_029094545.1_ASM2909454v1_genomic.fna/target_genomes_gtdb.txt --output GCF_029094545.1_ASM2909454v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:13,865] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:13,882] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:13,882] [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_000005825.2	s__Bacillus_S pseudofirmus	97.0606	1195	1412	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_S	95.9507	97.22	97.22	0.89	0.89	2	conclusive
GCF_000474275.2	s__Bacillus_S marmarensis	95.7969	1155	1412	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_S	95.9507	N/A	N/A	N/A	N/A	1	-
GCF_002797325.1	s__Bacillus_S sp002797325	80.0231	437	1412	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_S	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797395.1	s__45385 sp002797395	78.9199	169	1412	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__45385	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002156385.1	s__45385 sp002156385	78.7909	171	1412	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__45385	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002335805.1	s__FJAT-45350 sp002335805	78.7861	139	1412	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__FJAT-45350	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830185.1	s__Bacillus_L nanhaiisediminis	78.1638	188	1412	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513135.1	s__Bacillus_L akibai	77.9935	178	1412	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017939705.1	s__Bacillus_L sp017939705	77.8083	165	1412	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513095.1	s__Bacillus_L wakoensis	77.7715	183	1412	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000787375.1	s__Bacillus_L okhensis	77.6566	201	1412	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019024285.1	s__Bacillus_BH sp019024285	77.0078	125	1412	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_BH	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013314535.1	s__Bacillus_A sp013314535	76.5329	73	1412	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.95	99.95	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:13,884] [INFO] GTDB search result was written to GCF_029094545.1_ASM2909454v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:13,884] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:13,890] [INFO] DFAST_QC result json was written to GCF_029094545.1_ASM2909454v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:13,890] [INFO] DFAST_QC completed!
[2024-01-24 12:00:13,890] [INFO] Total running time: 0h1m9s