[2024-01-24 12:22:48,840] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:48,842] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:48,843] [INFO] DQC Reference Directory: /var/lib/cwl/stge9a952e4-0ec7-4535-b9b1-298856943aae/dqc_reference
[2024-01-24 12:22:50,135] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:50,136] [INFO] Task started: Prodigal
[2024-01-24 12:22:50,136] [INFO] Running command: gunzip -c /var/lib/cwl/stg35ccc19a-a765-4a0b-9986-e74fe12e36cf/GCF_937468385.1_JJ-3_genomic.fna.gz | prodigal -d GCF_937468385.1_JJ-3_genomic.fna/cds.fna -a GCF_937468385.1_JJ-3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:01,045] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:01,045] [INFO] Task started: HMMsearch
[2024-01-24 12:23:01,045] [INFO] Running command: hmmsearch --tblout GCF_937468385.1_JJ-3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9a952e4-0ec7-4535-b9b1-298856943aae/dqc_reference/reference_markers.hmm GCF_937468385.1_JJ-3_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:01,415] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:01,416] [INFO] Found 6/6 markers.
[2024-01-24 12:23:01,470] [INFO] Query marker FASTA was written to GCF_937468385.1_JJ-3_genomic.fna/markers.fasta
[2024-01-24 12:23:01,471] [INFO] Task started: Blastn
[2024-01-24 12:23:01,471] [INFO] Running command: blastn -query GCF_937468385.1_JJ-3_genomic.fna/markers.fasta -db /var/lib/cwl/stge9a952e4-0ec7-4535-b9b1-298856943aae/dqc_reference/reference_markers.fasta -out GCF_937468385.1_JJ-3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:02,136] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:02,140] [INFO] Selected 18 target genomes.
[2024-01-24 12:23:02,140] [INFO] Target genome list was writen to GCF_937468385.1_JJ-3_genomic.fna/target_genomes.txt
[2024-01-24 12:23:02,149] [INFO] Task started: fastANI
[2024-01-24 12:23:02,149] [INFO] Running command: fastANI --query /var/lib/cwl/stg35ccc19a-a765-4a0b-9986-e74fe12e36cf/GCF_937468385.1_JJ-3_genomic.fna.gz --refList GCF_937468385.1_JJ-3_genomic.fna/target_genomes.txt --output GCF_937468385.1_JJ-3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:19,321] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:19,321] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9a952e4-0ec7-4535-b9b1-298856943aae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:19,322] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9a952e4-0ec7-4535-b9b1-298856943aae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:19,339] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:23:19,339] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:23:19,340] [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 novalis	strain=NBRC 102450	GCA_001591805.1	220687	220687	type	True	82.3467	930	1645	95	below_threshold
Neobacillus novalis	strain=FJAT-14227	GCA_001636395.1	220687	220687	type	True	82.3213	956	1645	95	below_threshold
Neobacillus vireti	strain=DSM 15602	GCA_001026695.1	220686	220686	type	True	82.0168	926	1645	95	below_threshold
Neobacillus vireti	strain=LMG 21834	GCA_000508325.2	220686	220686	type	True	81.9773	844	1645	95	below_threshold
Neobacillus soli	strain=DSM 15604	GCA_002335815.1	220688	220688	type	True	80.8213	793	1645	95	below_threshold
Neobacillus soli	strain=NBRC 102451	GCA_001591665.1	220688	220688	type	True	80.7181	774	1645	95	below_threshold
Neobacillus bataviensis	strain=LMG 21833	GCA_000307875.1	220685	220685	type	True	80.3282	711	1645	95	below_threshold
Neobacillus jeddahensis	strain=JCE	GCA_000612625.1	1461580	1461580	type	True	79.525	580	1645	95	below_threshold
Neobacillus drentensis	strain=FJAT-10044	GCA_001636415.1	220684	220684	type	True	79.5127	632	1645	95	below_threshold
Neobacillus drentensis	strain=NBRC 102427	GCA_001591445.1	220684	220684	type	True	79.4298	620	1645	95	below_threshold
Neobacillus cucumis	strain=DSM 101566	GCA_016908975.1	1740721	1740721	type	True	78.8244	461	1645	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	78.3592	432	1645	95	below_threshold
Neobacillus endophyticus	strain=BRMEA1	GCA_013248975.1	2738405	2738405	type	True	78.144	380	1645	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	77.9572	205	1645	95	below_threshold
Neobacillus fumarioli	strain=NBRC 102428	GCA_001591485.1	105229	105229	type	True	77.7962	277	1645	95	below_threshold
Peribacillus frigoritolerans	strain=FJAT-2396	GCA_001636405.1	450367	450367	type	True	77.4207	103	1645	95	below_threshold
Peribacillus frigoritolerans	strain=DSM 8801	GCA_024169475.1	450367	450367	type	True	77.1727	96	1645	95	below_threshold
Sutcliffiella deserti	strain=DG-18	GCA_020037475.1	2875501	2875501	type	True	76.256	62	1645	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:19,341] [INFO] DFAST Taxonomy check result was written to GCF_937468385.1_JJ-3_genomic.fna/tc_result.tsv
[2024-01-24 12:23:19,342] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:19,342] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:19,342] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9a952e4-0ec7-4535-b9b1-298856943aae/dqc_reference/checkm_data
[2024-01-24 12:23:19,343] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:19,391] [INFO] Task started: CheckM
[2024-01-24 12:23:19,391] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_937468385.1_JJ-3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_937468385.1_JJ-3_genomic.fna/checkm_input GCF_937468385.1_JJ-3_genomic.fna/checkm_result
[2024-01-24 12:23:55,504] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:55,505] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:55,527] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:55,528] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:55,528] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_937468385.1_JJ-3_genomic.fna/markers.fasta)
[2024-01-24 12:23:55,528] [INFO] Task started: Blastn
[2024-01-24 12:23:55,529] [INFO] Running command: blastn -query GCF_937468385.1_JJ-3_genomic.fna/markers.fasta -db /var/lib/cwl/stge9a952e4-0ec7-4535-b9b1-298856943aae/dqc_reference/reference_markers_gtdb.fasta -out GCF_937468385.1_JJ-3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:56,318] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:56,322] [INFO] Selected 15 target genomes.
[2024-01-24 12:23:56,323] [INFO] Target genome list was writen to GCF_937468385.1_JJ-3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:56,334] [INFO] Task started: fastANI
[2024-01-24 12:23:56,335] [INFO] Running command: fastANI --query /var/lib/cwl/stg35ccc19a-a765-4a0b-9986-e74fe12e36cf/GCF_937468385.1_JJ-3_genomic.fna.gz --refList GCF_937468385.1_JJ-3_genomic.fna/target_genomes_gtdb.txt --output GCF_937468385.1_JJ-3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:12,079] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:12,097] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:24:12,097] [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_001591805.1	s__Neobacillus novalis	82.3354	931	1645	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_001026695.1	s__Neobacillus vireti	82.0296	923	1645	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	-
GCF_001591665.1	s__Neobacillus soli	80.7201	775	1645	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	80.3412	709	1645	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_900177675.1	s__Neobacillus sp900177675	80.069	702	1645	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_018613065.1	s__Neobacillus sp018613065	80.0497	653	1645	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_005154805.1	s__Neobacillus sp005154805	79.9548	748	1645	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	79.8513	662	1645	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	-
GCA_019219025.1	s__Neobacillus sp019219025	79.6548	672	1645	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_000686805.1	s__Neobacillus sp000686805	79.5761	635	1645	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_000612625.1	s__Neobacillus jeddahensis	79.5298	579	1645	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	99.99	99.99	0.99	0.99	3	-
GCF_002585305.1	s__Neobacillus sp002585305	79.0454	543	1645	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	97.64	95.53	0.90	0.84	3	-
GCF_013248975.1	s__Neobacillus endophyticus	78.1644	381	1645	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_001591485.1	s__Neobacillus fumarioli	77.8009	275	1645	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_001591465.1	s__Cytobacillus firmus	76.9699	129	1645	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.21	98.02	0.95	0.85	11	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:12,099] [INFO] GTDB search result was written to GCF_937468385.1_JJ-3_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:12,100] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:12,105] [INFO] DFAST_QC result json was written to GCF_937468385.1_JJ-3_genomic.fna/dqc_result.json
[2024-01-24 12:24:12,105] [INFO] DFAST_QC completed!
[2024-01-24 12:24:12,105] [INFO] Total running time: 0h1m23s