[2024-01-25 20:26:35,841] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:26:35,843] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:26:35,843] [INFO] DQC Reference Directory: /var/lib/cwl/stg8641b660-2c10-41b5-9b4b-c5e994eae867/dqc_reference
[2024-01-25 20:26:37,009] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:26:37,009] [INFO] Task started: Prodigal
[2024-01-25 20:26:37,010] [INFO] Running command: gunzip -c /var/lib/cwl/stgbbb60f7a-1030-440c-97ee-3b85142f93c3/GCF_020519665.1_ASM2051966v1_genomic.fna.gz | prodigal -d GCF_020519665.1_ASM2051966v1_genomic.fna/cds.fna -a GCF_020519665.1_ASM2051966v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:26:45,145] [INFO] Task succeeded: Prodigal
[2024-01-25 20:26:45,146] [INFO] Task started: HMMsearch
[2024-01-25 20:26:45,146] [INFO] Running command: hmmsearch --tblout GCF_020519665.1_ASM2051966v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8641b660-2c10-41b5-9b4b-c5e994eae867/dqc_reference/reference_markers.hmm GCF_020519665.1_ASM2051966v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:26:45,417] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:26:45,418] [INFO] Found 6/6 markers.
[2024-01-25 20:26:45,451] [INFO] Query marker FASTA was written to GCF_020519665.1_ASM2051966v1_genomic.fna/markers.fasta
[2024-01-25 20:26:45,451] [INFO] Task started: Blastn
[2024-01-25 20:26:45,451] [INFO] Running command: blastn -query GCF_020519665.1_ASM2051966v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8641b660-2c10-41b5-9b4b-c5e994eae867/dqc_reference/reference_markers.fasta -out GCF_020519665.1_ASM2051966v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:26:46,003] [INFO] Task succeeded: Blastn
[2024-01-25 20:26:46,005] [INFO] Selected 27 target genomes.
[2024-01-25 20:26:46,006] [INFO] Target genome list was writen to GCF_020519665.1_ASM2051966v1_genomic.fna/target_genomes.txt
[2024-01-25 20:26:46,045] [INFO] Task started: fastANI
[2024-01-25 20:26:46,045] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbb60f7a-1030-440c-97ee-3b85142f93c3/GCF_020519665.1_ASM2051966v1_genomic.fna.gz --refList GCF_020519665.1_ASM2051966v1_genomic.fna/target_genomes.txt --output GCF_020519665.1_ASM2051966v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:27:07,004] [INFO] Task succeeded: fastANI
[2024-01-25 20:27:07,004] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8641b660-2c10-41b5-9b4b-c5e994eae867/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:27:07,004] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8641b660-2c10-41b5-9b4b-c5e994eae867/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:27:07,015] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:27:07,015] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:27:07,015] [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
Bacillus shivajii	strain=JCM 32183	GCA_020519665.1	1983719	1983719	type	True	100.0	1478	1480	95	conclusive
Evansella clarkii	strain=DSM 8720	GCA_002019695.1	79879	79879	type	True	79.0552	131	1480	95	below_threshold
Evansella cellulosilytica	strain=DSM 2522	GCA_000177235.2	1413	1413	type	True	78.9826	159	1480	95	below_threshold
Bacillus alkalisoli	strain=FJAT-45122	GCA_002797415.1	2011008	2011008	type	True	78.4938	73	1480	95	below_threshold
Salipaludibacillus neizhouensis	strain=DSM 19794	GCA_002886185.1	885475	885475	type	True	77.7574	133	1480	95	below_threshold
Anaerobacillus alkalidiazotrophicus	strain=DSM 22531	GCA_001866055.1	472963	472963	type	True	77.5861	93	1480	95	below_threshold
Salipaludibacillus keqinensis	strain=KQ-12	GCA_003226325.1	2045207	2045207	type	True	77.2984	139	1480	95	below_threshold
Anaerobacillus alkalilacustris	strain=DSM 18345	GCA_001866005.1	393763	393763	type	True	77.2852	94	1480	95	below_threshold
Evansella caseinilytica	strain=SP	GCA_900107275.1	1503961	1503961	type	True	77.229	99	1480	95	below_threshold
Alteribacter aurantiacus	strain=DSM 18675	GCA_000429705.1	254410	254410	type	True	77.1355	106	1480	95	below_threshold
Evansella tamaricis	strain=CGMCC 1.15917	GCA_019042215.1	2069301	2069301	type	True	76.7707	161	1480	95	below_threshold
Bacillus mesophilus	strain=DSM 101000	GCA_016908955.1	1808955	1808955	type	True	76.7454	59	1480	95	below_threshold
Bacillus mesophilus	strain=SA4	GCA_011008845.1	1808955	1808955	type	True	76.7324	58	1480	95	below_threshold
Cytobacillus luteolus	strain=DSM 22388	GCA_017873715.1	682179	682179	type	True	76.6575	57	1480	95	below_threshold
Salipaludibacillus neizhouensis	strain=KCTC 13187	GCA_003615245.1	885475	885475	type	True	76.5079	129	1480	95	below_threshold
Alkalihalobacillus akibai	strain=JCM 9157	GCA_001315085.1	1411	1411	type	True	76.4951	91	1480	95	below_threshold
Alkalihalobacillus akibai	strain=JCM 9157	GCA_000513135.1	1411	1411	type	True	76.4951	91	1480	95	below_threshold
Cytobacillus stercorigallinarum	strain=Sa5YUA1	GCA_014836495.1	2762240	2762240	type	True	76.0481	54	1480	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:27:07,017] [INFO] DFAST Taxonomy check result was written to GCF_020519665.1_ASM2051966v1_genomic.fna/tc_result.tsv
[2024-01-25 20:27:07,017] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:27:07,017] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:27:07,017] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8641b660-2c10-41b5-9b4b-c5e994eae867/dqc_reference/checkm_data
[2024-01-25 20:27:07,018] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:27:07,061] [INFO] Task started: CheckM
[2024-01-25 20:27:07,061] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020519665.1_ASM2051966v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020519665.1_ASM2051966v1_genomic.fna/checkm_input GCF_020519665.1_ASM2051966v1_genomic.fna/checkm_result
[2024-01-25 20:27:35,579] [INFO] Task succeeded: CheckM
[2024-01-25 20:27:35,580] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:27:35,604] [INFO] ===== Completeness check finished =====
[2024-01-25 20:27:35,604] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:27:35,605] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020519665.1_ASM2051966v1_genomic.fna/markers.fasta)
[2024-01-25 20:27:35,605] [INFO] Task started: Blastn
[2024-01-25 20:27:35,605] [INFO] Running command: blastn -query GCF_020519665.1_ASM2051966v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8641b660-2c10-41b5-9b4b-c5e994eae867/dqc_reference/reference_markers_gtdb.fasta -out GCF_020519665.1_ASM2051966v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:27:36,382] [INFO] Task succeeded: Blastn
[2024-01-25 20:27:36,387] [INFO] Selected 27 target genomes.
[2024-01-25 20:27:36,387] [INFO] Target genome list was writen to GCF_020519665.1_ASM2051966v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:27:36,417] [INFO] Task started: fastANI
[2024-01-25 20:27:36,417] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbb60f7a-1030-440c-97ee-3b85142f93c3/GCF_020519665.1_ASM2051966v1_genomic.fna.gz --refList GCF_020519665.1_ASM2051966v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020519665.1_ASM2051966v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:27:56,714] [INFO] Task succeeded: fastANI
[2024-01-25 20:27:56,727] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:27:56,727] [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_004006295.1	s__Peribacillus asahii_A	80.1692	66	1480	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797315.1	s__C254 sp002797315	79.5863	63	1480	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Marinococcaceae;g__C254	95.0	96.15	96.15	0.88	0.88	2	-
GCF_002797325.1	s__Bacillus_S sp002797325	79.4532	84	1480	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_002019695.1	s__Evansella clarkii	79.233	131	1480	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Evansella	95.0	98.30	98.30	0.93	0.93	2	-
GCF_002019635.1	s__Metabacillus halosaccharovorans	79.2151	70	1480	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	95.47	95.47	0.86	0.86	2	-
GCF_002335745.1	s__FJAT-44876 sp002335745	79.0373	492	1480	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_002335755.1	s__FJAT-45066 sp002335755	78.9611	81	1480	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_I;g__FJAT-45066	95.0	99.38	99.38	0.94	0.94	2	-
GCF_000177235.2	s__Evansella cellulosilytica	78.8929	160	1480	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Evansella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002156385.1	s__45385 sp002156385	78.0998	79	1480	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_002886185.1	s__Salipaludibacillus neizhouensis	77.7728	133	1480	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Salipaludibacillus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002352765.1	s__Alteribacter populi	77.723	155	1480	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alteribacter	95.0	99.66	99.66	0.95	0.95	2	-
GCF_002153425.1	s__Evansella alkalicola	77.442	177	1480	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_900107275.1	s__Evansella caseinilytica	77.262	101	1480	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Evansella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001866005.1	s__Anaerobacillus alkalilacustris	77.2555	95	1480	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_003226325.1	s__Salipaludibacillus keqinensis	77.2415	138	1480	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Salipaludibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429705.1	s__Alteribacter aurantiacus	77.1415	105	1480	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_011008845.1	s__Bacillus_BS mesophilus	76.7324	58	1480	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__SA4;g__Bacillus_BS	95.0	100.00	100.00	1.00	1.00	2	-
GCF_019042215.1	s__Evansella tamaricis	76.7126	162	1480	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Evansella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513135.1	s__Bacillus_L akibai	76.4985	92	1480	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_902374955.1	s__Bacillus_AD massilioanorexius	76.3821	51	1480	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_AD	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004340305.1	s__Gottfriedia sp004340305	75.9814	61	1480	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:27:56,734] [INFO] GTDB search result was written to GCF_020519665.1_ASM2051966v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:27:56,735] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:27:56,738] [INFO] DFAST_QC result json was written to GCF_020519665.1_ASM2051966v1_genomic.fna/dqc_result.json
[2024-01-25 20:27:56,738] [INFO] DFAST_QC completed!
[2024-01-25 20:27:56,738] [INFO] Total running time: 0h1m21s