[2024-01-24 13:37:15,349] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:15,353] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:15,353] [INFO] DQC Reference Directory: /var/lib/cwl/stg38a22295-9a4c-4b0b-bf47-c2116f993b98/dqc_reference
[2024-01-24 13:37:18,465] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:18,466] [INFO] Task started: Prodigal
[2024-01-24 13:37:18,466] [INFO] Running command: gunzip -c /var/lib/cwl/stg7f3d2c36-aa7c-4ab8-b242-7d9495d8d929/GCF_014712675.1_ASM1471267v1_genomic.fna.gz | prodigal -d GCF_014712675.1_ASM1471267v1_genomic.fna/cds.fna -a GCF_014712675.1_ASM1471267v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:27,309] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:27,309] [INFO] Task started: HMMsearch
[2024-01-24 13:37:27,309] [INFO] Running command: hmmsearch --tblout GCF_014712675.1_ASM1471267v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg38a22295-9a4c-4b0b-bf47-c2116f993b98/dqc_reference/reference_markers.hmm GCF_014712675.1_ASM1471267v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:27,621] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:27,623] [INFO] Found 6/6 markers.
[2024-01-24 13:37:27,661] [INFO] Query marker FASTA was written to GCF_014712675.1_ASM1471267v1_genomic.fna/markers.fasta
[2024-01-24 13:37:27,661] [INFO] Task started: Blastn
[2024-01-24 13:37:27,661] [INFO] Running command: blastn -query GCF_014712675.1_ASM1471267v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38a22295-9a4c-4b0b-bf47-c2116f993b98/dqc_reference/reference_markers.fasta -out GCF_014712675.1_ASM1471267v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:28,341] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:28,346] [INFO] Selected 30 target genomes.
[2024-01-24 13:37:28,346] [INFO] Target genome list was writen to GCF_014712675.1_ASM1471267v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:28,365] [INFO] Task started: fastANI
[2024-01-24 13:37:28,365] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f3d2c36-aa7c-4ab8-b242-7d9495d8d929/GCF_014712675.1_ASM1471267v1_genomic.fna.gz --refList GCF_014712675.1_ASM1471267v1_genomic.fna/target_genomes.txt --output GCF_014712675.1_ASM1471267v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:49,730] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:49,731] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg38a22295-9a4c-4b0b-bf47-c2116f993b98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:49,731] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg38a22295-9a4c-4b0b-bf47-c2116f993b98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:49,754] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:49,754] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:49,754] [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
Peribacillus faecalis	strain=AGMB 02131	GCA_014712675.1	2772559	2772559	type	True	100.0	1310	1317	95	conclusive
Bacillus massiliogorillae	strain=G2	GCA_000380245.2	1243664	1243664	type	True	78.5754	235	1317	95	below_threshold
Peribacillus alkalitolerans	strain=KCTC 33631	GCA_010882125.1	1550385	1550385	type	True	78.0433	105	1317	95	below_threshold
Priestia taiwanensis	strain=DSM 27845	GCA_016908755.1	1347902	1347902	type	True	77.8578	58	1317	95	below_threshold
Priestia taiwanensis	strain=CGMCC 1.12698	GCA_014638355.1	1347902	1347902	type	True	77.8564	59	1317	95	below_threshold
Peribacillus acanthi	strain=L28	GCA_003073175.1	2171554	2171554	type	True	77.8305	114	1317	95	below_threshold
Robertmurraya massiliosenegalensis	strain=JC6	GCA_000311725.1	1287657	1287657	type	True	77.6131	71	1317	95	below_threshold
Bacillus dafuensis	strain=FJAT-25496	GCA_007995155.1	1742359	1742359	type	True	77.4891	73	1317	95	below_threshold
Peribacillus deserti	strain=DSM 105482	GCA_016909175.1	673318	673318	type	True	77.4299	79	1317	95	below_threshold
Bacillus dakarensis	strain=Marseille-P3515	GCA_900156875.1	1926278	1926278	type	True	77.3411	76	1317	95	below_threshold
Peribacillus asahii	strain=MA001	GCA_003570725.1	228899	228899	suspected-type	True	77.3125	101	1317	95	below_threshold
Bacillus marasmi	strain=Marseille-P3556	GCA_902168435.1	1926279	1926279	type	True	77.2468	81	1317	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	77.0966	82	1317	95	below_threshold
Bacillus mycoides	strain=ATCC 6462	GCA_000832605.1	1405	1405	type	True	77.0794	78	1317	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_000003925.1	1405	1405	type	True	77.0555	75	1317	95	below_threshold
Neobacillus rhizophilus	strain=FJAT-49825	GCA_018343535.1	2833579	2833579	type	True	76.993	77	1317	95	below_threshold
Peribacillus psychrosaccharolyticus	strain=ATCC 23296	GCA_000305495.2	1407	1407	type	True	76.9926	88	1317	95	below_threshold
Bacillus gaemokensis	strain=JCM 15801	GCA_000712615.1	574375	574375	type	True	76.9011	87	1317	95	below_threshold
Bacillus gaemokensis	strain=KCTC 13318	GCA_001590835.1	574375	574375	type	True	76.8709	86	1317	95	below_threshold
Cytobacillus stercorigallinarum	strain=Sa5YUA1	GCA_014836495.1	2762240	2762240	type	True	76.6596	91	1317	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:49,756] [INFO] DFAST Taxonomy check result was written to GCF_014712675.1_ASM1471267v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:49,757] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:49,757] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:49,757] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg38a22295-9a4c-4b0b-bf47-c2116f993b98/dqc_reference/checkm_data
[2024-01-24 13:37:49,759] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:49,810] [INFO] Task started: CheckM
[2024-01-24 13:37:49,811] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014712675.1_ASM1471267v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014712675.1_ASM1471267v1_genomic.fna/checkm_input GCF_014712675.1_ASM1471267v1_genomic.fna/checkm_result
[2024-01-24 13:38:22,250] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:22,252] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:22,275] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:22,276] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:22,276] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014712675.1_ASM1471267v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:22,277] [INFO] Task started: Blastn
[2024-01-24 13:38:22,277] [INFO] Running command: blastn -query GCF_014712675.1_ASM1471267v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38a22295-9a4c-4b0b-bf47-c2116f993b98/dqc_reference/reference_markers_gtdb.fasta -out GCF_014712675.1_ASM1471267v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:23,285] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:23,290] [INFO] Selected 28 target genomes.
[2024-01-24 13:38:23,290] [INFO] Target genome list was writen to GCF_014712675.1_ASM1471267v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:23,316] [INFO] Task started: fastANI
[2024-01-24 13:38:23,317] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f3d2c36-aa7c-4ab8-b242-7d9495d8d929/GCF_014712675.1_ASM1471267v1_genomic.fna.gz --refList GCF_014712675.1_ASM1471267v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014712675.1_ASM1471267v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:48,780] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:48,801] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:48,802] [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_014712675.1	s__Bacillus_AD faecalis	100.0	1310	1317	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_AD	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000380245.2	s__Bacillus_AD massiliogorillae	78.5916	234	1317	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_AD	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908835.1	s__Bacillus_AD endoradicis	78.4882	202	1317	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_AD	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010882125.1	s__Bacillus_BN alkalitolerans	78.0605	103	1317	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_BN	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003073175.1	s__Bacillus_BN acanthi	77.8423	112	1317	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_BN	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004006295.1	s__Peribacillus asahii_A	77.671	117	1317	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_001645685.2	s__Peribacillus muralis_A	77.5898	80	1317	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_001877785.1	s__Rossellomorea aquimaris_A	77.5879	52	1317	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Rossellomorea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007995155.1	s__Cytobacillus dafuensis	77.4694	74	1317	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_900156875.1	s__Robertmurraya dakarensis	77.4272	71	1317	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003570725.1	s__Peribacillus asahii	77.3288	101	1317	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_902168435.1	s__Bacillus_BU marasmi	77.1774	79	1317	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BU	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002561295.1	s__Bacillus_A cereus_S	77.1746	79	1317	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.16	96.34	0.94	0.87	9	-
GCF_000612665.1	s__Neobacillus dielmonensis	77.0934	62	1317	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018343535.1	s__Neobacillus sp018343535	77.0928	77	1317	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	99.05	99.05	0.95	0.95	2	-
GCF_016820555.1	s__FJAT-46582 sp016820555	77.0219	74	1317	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__FJAT-46582	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000305495.1	s__Peribacillus psychrosaccharolyticus	77.0205	87	1317	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	99.97	99.97	1.00	1.00	2	-
GCF_002559665.1	s__Bacillus_A cereus_AV	76.9855	72	1317	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015071065.1	s__Bacillus_A cereus_BA	76.9763	83	1317	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.35	97.35	0.87	0.87	2	-
GCF_002584535.1	s__Bacillus_A cereus_AW	76.9737	82	1317	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.12	98.24	0.93	0.90	5	-
GCF_001590835.1	s__Bacillus_A gaemokensis	76.8692	86	1317	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002571225.1	s__Bacillus_A sp002571225	76.8426	95	1317	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008180415.1	s__Bacillus_BM vietnamensis_B	76.7873	59	1317	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Bacillus_BM	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836495.1	s__Cytobacillus sp014836495	76.6584	91	1317	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001076885.1	s__Niallia sp001076885	76.6238	82	1317	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Niallia	95.0	99.59	99.45	0.92	0.91	4	-
GCF_009928415.1	s__Neobacillus sp009928415	76.5997	85	1317	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:48,804] [INFO] GTDB search result was written to GCF_014712675.1_ASM1471267v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:48,805] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:48,810] [INFO] DFAST_QC result json was written to GCF_014712675.1_ASM1471267v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:48,811] [INFO] DFAST_QC completed!
[2024-01-24 13:38:48,811] [INFO] Total running time: 0h1m33s