[2024-01-25 17:41:35,575] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:41:35,578] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:41:35,578] [INFO] DQC Reference Directory: /var/lib/cwl/stg639cb431-124c-4d25-89a2-f92179bcb960/dqc_reference
[2024-01-25 17:41:36,715] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:41:36,715] [INFO] Task started: Prodigal
[2024-01-25 17:41:36,716] [INFO] Running command: gunzip -c /var/lib/cwl/stg9c714216-8a90-4cbe-b3d4-0978fd032125/GCF_000508325.2_BAVI_1_genomic.fna.gz | prodigal -d GCF_000508325.2_BAVI_1_genomic.fna/cds.fna -a GCF_000508325.2_BAVI_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:41:46,042] [INFO] Task succeeded: Prodigal
[2024-01-25 17:41:46,042] [INFO] Task started: HMMsearch
[2024-01-25 17:41:46,042] [INFO] Running command: hmmsearch --tblout GCF_000508325.2_BAVI_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg639cb431-124c-4d25-89a2-f92179bcb960/dqc_reference/reference_markers.hmm GCF_000508325.2_BAVI_1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:41:46,342] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:41:46,343] [INFO] Found 6/6 markers.
[2024-01-25 17:41:46,384] [INFO] Query marker FASTA was written to GCF_000508325.2_BAVI_1_genomic.fna/markers.fasta
[2024-01-25 17:41:46,384] [INFO] Task started: Blastn
[2024-01-25 17:41:46,385] [INFO] Running command: blastn -query GCF_000508325.2_BAVI_1_genomic.fna/markers.fasta -db /var/lib/cwl/stg639cb431-124c-4d25-89a2-f92179bcb960/dqc_reference/reference_markers.fasta -out GCF_000508325.2_BAVI_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:46,948] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:46,950] [INFO] Selected 13 target genomes.
[2024-01-25 17:41:46,951] [INFO] Target genome list was writen to GCF_000508325.2_BAVI_1_genomic.fna/target_genomes.txt
[2024-01-25 17:41:46,990] [INFO] Task started: fastANI
[2024-01-25 17:41:46,991] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c714216-8a90-4cbe-b3d4-0978fd032125/GCF_000508325.2_BAVI_1_genomic.fna.gz --refList GCF_000508325.2_BAVI_1_genomic.fna/target_genomes.txt --output GCF_000508325.2_BAVI_1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:42:00,380] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:00,380] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg639cb431-124c-4d25-89a2-f92179bcb960/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:42:00,381] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg639cb431-124c-4d25-89a2-f92179bcb960/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:42:00,389] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:42:00,390] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:42:00,390] [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
Neobacillus vireti	strain=LMG 21834	GCA_000508325.2	220686	220686	type	True	100.0	1643	1655	95	conclusive
Neobacillus vireti	strain=DSM 15602	GCA_001026695.1	220686	220686	type	True	99.9934	1654	1655	95	conclusive
Neobacillus novalis	strain=NBRC 102450	GCA_001591805.1	220687	220687	type	True	90.3878	1226	1655	95	below_threshold
Neobacillus novalis	strain=FJAT-14227	GCA_001636395.1	220687	220687	type	True	90.3334	1272	1655	95	below_threshold
Neobacillus soli	strain=NBRC 102451	GCA_001591665.1	220688	220688	type	True	81.6203	864	1655	95	below_threshold
Neobacillus bataviensis	strain=LMG 21833	GCA_000307875.1	220685	220685	type	True	80.9237	808	1655	95	below_threshold
Neobacillus drentensis	strain=FJAT-10044	GCA_001636415.1	220684	220684	type	True	79.3948	595	1655	95	below_threshold
Neobacillus rhizophilus	strain=FJAT-49825	GCA_018343535.1	2833579	2833579	type	True	78.7677	452	1655	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	78.6879	408	1655	95	below_threshold
Neobacillus mesonae	strain=FJAT-13985	GCA_001636315.1	1193713	1193713	type	True	78.5547	446	1655	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	77.5905	195	1655	95	below_threshold
Anoxybacillus calidus	strain=DSM 25220	GCA_013760845.1	575178	575178	type	True	76.7057	71	1655	95	below_threshold
Bacillus kexueae	strain=KCTC 33881	GCA_022809095.1	2078952	2078952	type	True	76.7007	56	1655	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:42:00,391] [INFO] DFAST Taxonomy check result was written to GCF_000508325.2_BAVI_1_genomic.fna/tc_result.tsv
[2024-01-25 17:42:00,392] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:42:00,392] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:42:00,392] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg639cb431-124c-4d25-89a2-f92179bcb960/dqc_reference/checkm_data
[2024-01-25 17:42:00,393] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:42:00,444] [INFO] Task started: CheckM
[2024-01-25 17:42:00,444] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000508325.2_BAVI_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000508325.2_BAVI_1_genomic.fna/checkm_input GCF_000508325.2_BAVI_1_genomic.fna/checkm_result
[2024-01-25 17:42:31,634] [INFO] Task succeeded: CheckM
[2024-01-25 17:42:31,635] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:42:31,667] [INFO] ===== Completeness check finished =====
[2024-01-25 17:42:31,667] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:42:31,668] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000508325.2_BAVI_1_genomic.fna/markers.fasta)
[2024-01-25 17:42:31,668] [INFO] Task started: Blastn
[2024-01-25 17:42:31,668] [INFO] Running command: blastn -query GCF_000508325.2_BAVI_1_genomic.fna/markers.fasta -db /var/lib/cwl/stg639cb431-124c-4d25-89a2-f92179bcb960/dqc_reference/reference_markers_gtdb.fasta -out GCF_000508325.2_BAVI_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:32,466] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:32,469] [INFO] Selected 12 target genomes.
[2024-01-25 17:42:32,469] [INFO] Target genome list was writen to GCF_000508325.2_BAVI_1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:42:32,483] [INFO] Task started: fastANI
[2024-01-25 17:42:32,483] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c714216-8a90-4cbe-b3d4-0978fd032125/GCF_000508325.2_BAVI_1_genomic.fna.gz --refList GCF_000508325.2_BAVI_1_genomic.fna/target_genomes_gtdb.txt --output GCF_000508325.2_BAVI_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:42:48,792] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:48,801] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:42:48,801] [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_001026695.1	s__Neobacillus vireti	99.9934	1654	1655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_001591805.1	s__Neobacillus novalis	90.3842	1226	1655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001591665.1	s__Neobacillus soli	81.6168	864	1655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000307875.1	s__Neobacillus bataviensis	80.9469	804	1655	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_005154805.1	s__Neobacillus sp005154805	80.5667	763	1655	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_011250555.1	s__Neobacillus sp011250555	80.1308	672	1655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	99.98	99.98	0.98	0.98	2	-
GCF_018613065.1	s__Neobacillus sp018613065	79.4426	606	1655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	95.53	95.32	0.78	0.75	6	-
GCF_002559145.1	s__Neobacillus sp002559145	79.4026	551	1655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	95.43	95.43	0.81	0.81	2	-
GCA_019219025.1	s__Neobacillus sp019219025	79.3707	572	1655	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_001591445.1	s__Neobacillus drentensis	79.366	576	1655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900177675.1	s__Neobacillus sp900177675	79.3359	636	1655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	98.52	98.52	0.84	0.84	2	-
GCF_007678255.1	s__Neobacillus sp007678255	79.2257	535	1655	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	-
--------------------------------------------------------------------------------
[2024-01-25 17:42:48,803] [INFO] GTDB search result was written to GCF_000508325.2_BAVI_1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:42:48,804] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:42:48,809] [INFO] DFAST_QC result json was written to GCF_000508325.2_BAVI_1_genomic.fna/dqc_result.json
[2024-01-25 17:42:48,809] [INFO] DFAST_QC completed!
[2024-01-25 17:42:48,809] [INFO] Total running time: 0h1m13s