[2024-01-24 13:40:34,974] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:34,976] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:34,977] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ebba52a-aee9-4b3d-85ed-d0e75868ed28/dqc_reference
[2024-01-24 13:40:36,318] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:36,319] [INFO] Task started: Prodigal
[2024-01-24 13:40:36,320] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f80467d-6f8c-4688-b108-8e6a353d44a2/GCF_002352765.1_ASM235276v2_genomic.fna.gz | prodigal -d GCF_002352765.1_ASM235276v2_genomic.fna/cds.fna -a GCF_002352765.1_ASM235276v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:46,549] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:46,549] [INFO] Task started: HMMsearch
[2024-01-24 13:40:46,549] [INFO] Running command: hmmsearch --tblout GCF_002352765.1_ASM235276v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ebba52a-aee9-4b3d-85ed-d0e75868ed28/dqc_reference/reference_markers.hmm GCF_002352765.1_ASM235276v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:46,939] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:46,940] [INFO] Found 6/6 markers.
[2024-01-24 13:40:46,981] [INFO] Query marker FASTA was written to GCF_002352765.1_ASM235276v2_genomic.fna/markers.fasta
[2024-01-24 13:40:46,982] [INFO] Task started: Blastn
[2024-01-24 13:40:46,982] [INFO] Running command: blastn -query GCF_002352765.1_ASM235276v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ebba52a-aee9-4b3d-85ed-d0e75868ed28/dqc_reference/reference_markers.fasta -out GCF_002352765.1_ASM235276v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:47,600] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:47,604] [INFO] Selected 25 target genomes.
[2024-01-24 13:40:47,604] [INFO] Target genome list was writen to GCF_002352765.1_ASM235276v2_genomic.fna/target_genomes.txt
[2024-01-24 13:40:47,613] [INFO] Task started: fastANI
[2024-01-24 13:40:47,614] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f80467d-6f8c-4688-b108-8e6a353d44a2/GCF_002352765.1_ASM235276v2_genomic.fna.gz --refList GCF_002352765.1_ASM235276v2_genomic.fna/target_genomes.txt --output GCF_002352765.1_ASM235276v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:06,330] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:06,331] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ebba52a-aee9-4b3d-85ed-d0e75868ed28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:06,331] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ebba52a-aee9-4b3d-85ed-d0e75868ed28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:06,343] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:06,344] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:06,344] [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
Alteribacter populi	strain=FJAT-45347	GCA_002352765.2	2011011	2011011	type	True	100.0	1481	1504	95	conclusive
Paenalkalicoccus suaedae	strain=M4U3P1	GCA_006965545.2	2592382	2592382	type	True	80.6583	60	1504	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_022221345.1	1392	1392	type	True	79.261	55	1504	95	below_threshold
Alkalihalobacterium alkalinitrilicum	strain=DSM 22532	GCA_002019605.1	427920	427920	type	True	79.1298	67	1504	95	below_threshold
Alkalihalobacillus krulwichiae	strain=AM31D	GCA_002109385.1	199441	199441	type	True	78.9111	68	1504	95	below_threshold
Alteribacter salitolerans	strain=APA H-16(1)	GCA_016901055.1	2912333	2912333	type	True	78.6497	247	1504	95	below_threshold
Alteribacter keqinensis	strain=KQ-3	GCA_003710255.1	2483800	2483800	type	True	78.5407	248	1504	95	below_threshold
Alteribacter aurantiacus	strain=DSM 18675	GCA_000429705.1	254410	254410	type	True	78.4032	255	1504	95	below_threshold
Alteribacter lacisalsi	strain=YSP-3	GCA_003226345.1	2045244	2045244	type	True	78.2033	164	1504	95	below_threshold
Alteribacter natronophilus	strain=M30	GCA_006007885.1	2583810	2583810	type	True	78.0223	140	1504	95	below_threshold
Anaerobacillus alkalidiazotrophicus	strain=DSM 22531	GCA_001866055.1	472963	472963	type	True	77.8888	63	1504	95	below_threshold
Alkalihalobacillus krulwichiae	strain=NBRC 102362	GCA_001591945.1	199441	199441	type	True	77.0592	58	1504	95	below_threshold
Alkalihalobacillus okhensis	strain=Kh10-101	GCA_000787375.1	333138	333138	type	True	76.9141	60	1504	95	below_threshold
Desertibacillus haloalkaliphilus	strain=KJ1-10-99	GCA_019039105.1	1328930	1328930	type	True	76.8802	66	1504	95	below_threshold
Alkalihalobacillus bogoriensis	strain=ATCC BAA-922	GCA_000621445.1	246272	246272	type	True	76.75	64	1504	95	below_threshold
Alkalihalobacterium elongatum	strain=MEB199	GCA_019024285.1	2675466	2675466	type	True	76.1392	63	1504	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:06,345] [INFO] DFAST Taxonomy check result was written to GCF_002352765.1_ASM235276v2_genomic.fna/tc_result.tsv
[2024-01-24 13:41:06,346] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:06,346] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:06,346] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ebba52a-aee9-4b3d-85ed-d0e75868ed28/dqc_reference/checkm_data
[2024-01-24 13:41:06,347] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:06,399] [INFO] Task started: CheckM
[2024-01-24 13:41:06,399] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002352765.1_ASM235276v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002352765.1_ASM235276v2_genomic.fna/checkm_input GCF_002352765.1_ASM235276v2_genomic.fna/checkm_result
[2024-01-24 13:41:42,634] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:42,635] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:42,663] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:42,663] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:42,663] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002352765.1_ASM235276v2_genomic.fna/markers.fasta)
[2024-01-24 13:41:42,664] [INFO] Task started: Blastn
[2024-01-24 13:41:42,664] [INFO] Running command: blastn -query GCF_002352765.1_ASM235276v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ebba52a-aee9-4b3d-85ed-d0e75868ed28/dqc_reference/reference_markers_gtdb.fasta -out GCF_002352765.1_ASM235276v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:43,507] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:43,510] [INFO] Selected 27 target genomes.
[2024-01-24 13:41:43,511] [INFO] Target genome list was writen to GCF_002352765.1_ASM235276v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:43,533] [INFO] Task started: fastANI
[2024-01-24 13:41:43,534] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f80467d-6f8c-4688-b108-8e6a353d44a2/GCF_002352765.1_ASM235276v2_genomic.fna.gz --refList GCF_002352765.1_ASM235276v2_genomic.fna/target_genomes_gtdb.txt --output GCF_002352765.1_ASM235276v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:04,682] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:04,699] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:04,699] [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_002352765.1	s__Alteribacter populi	99.9985	1481	1504	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alteribacter	95.0	99.66	99.66	0.95	0.95	2	conclusive
GCF_006965545.2	s__Alkalicoccus sp006965545	80.5827	60	1504	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900240995.1	s__OESV01 sp900240995	80.0167	50	1504	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_C;f__Bacillaceae_J;g__OESV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003710255.1	s__Alteribacter sp003710255	78.5275	250	1504	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alteribacter	95.0	98.04	98.04	0.95	0.95	2	-
GCF_000429705.1	s__Alteribacter aurantiacus	78.4096	254	1504	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alteribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003226345.1	s__Alteribacter lacisalsi	78.2033	164	1504	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alteribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002153425.1	s__Evansella alkalicola	78.0697	99	1504	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Evansella	95.0	99.98	99.98	0.99	0.99	2	-
GCF_006007885.1	s__Alteribacter natronophilus	77.9998	141	1504	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alteribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001866055.1	s__Anaerobacillus alkalidiazotrophicus	77.9411	62	1504	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Anaerobacillaceae;g__Anaerobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002335745.1	s__FJAT-44876 sp002335745	77.6676	194	1504	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__FJAT-44876	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000299035.1	s__Bacillus_A bingmayongensis	77.2865	52	1504	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.40	97.40	0.86	0.86	2	-
GCF_003184905.1	s__Priestia sp003184905	77.1132	56	1504	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019039105.1	s__Desertibacillus haloalkaliphilus	76.8802	66	1504	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__KJ1-10-99;g__Desertibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000621445.1	s__Bacillus_AO bogoriensis	76.6395	63	1504	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_AO	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116295.1	s__Bacillus_A sp900116295	76.2601	51	1504	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_019024285.1	s__Bacillus_BH sp019024285	76.1392	63	1504	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	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:04,701] [INFO] GTDB search result was written to GCF_002352765.1_ASM235276v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:04,701] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:04,705] [INFO] DFAST_QC result json was written to GCF_002352765.1_ASM235276v2_genomic.fna/dqc_result.json
[2024-01-24 13:42:04,706] [INFO] DFAST_QC completed!
[2024-01-24 13:42:04,706] [INFO] Total running time: 0h1m30s