[2024-01-25 17:50:50,633] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:50:50,634] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:50:50,634] [INFO] DQC Reference Directory: /var/lib/cwl/stg196c1e74-83de-4b12-a727-5234d7e793a1/dqc_reference
[2024-01-25 17:50:51,768] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:50:51,768] [INFO] Task started: Prodigal
[2024-01-25 17:50:51,769] [INFO] Running command: gunzip -c /var/lib/cwl/stge34e2026-b653-4f85-b33f-2fb01e9d920c/GCF_017874625.1_ASM1787462v1_genomic.fna.gz | prodigal -d GCF_017874625.1_ASM1787462v1_genomic.fna/cds.fna -a GCF_017874625.1_ASM1787462v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:50:58,980] [INFO] Task succeeded: Prodigal
[2024-01-25 17:50:58,981] [INFO] Task started: HMMsearch
[2024-01-25 17:50:58,981] [INFO] Running command: hmmsearch --tblout GCF_017874625.1_ASM1787462v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg196c1e74-83de-4b12-a727-5234d7e793a1/dqc_reference/reference_markers.hmm GCF_017874625.1_ASM1787462v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:50:59,226] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:50:59,227] [INFO] Found 6/6 markers.
[2024-01-25 17:50:59,255] [INFO] Query marker FASTA was written to GCF_017874625.1_ASM1787462v1_genomic.fna/markers.fasta
[2024-01-25 17:50:59,256] [INFO] Task started: Blastn
[2024-01-25 17:50:59,256] [INFO] Running command: blastn -query GCF_017874625.1_ASM1787462v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg196c1e74-83de-4b12-a727-5234d7e793a1/dqc_reference/reference_markers.fasta -out GCF_017874625.1_ASM1787462v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:59,825] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:59,829] [INFO] Selected 16 target genomes.
[2024-01-25 17:50:59,830] [INFO] Target genome list was writen to GCF_017874625.1_ASM1787462v1_genomic.fna/target_genomes.txt
[2024-01-25 17:50:59,875] [INFO] Task started: fastANI
[2024-01-25 17:50:59,875] [INFO] Running command: fastANI --query /var/lib/cwl/stge34e2026-b653-4f85-b33f-2fb01e9d920c/GCF_017874625.1_ASM1787462v1_genomic.fna.gz --refList GCF_017874625.1_ASM1787462v1_genomic.fna/target_genomes.txt --output GCF_017874625.1_ASM1787462v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:51:14,466] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:14,466] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg196c1e74-83de-4b12-a727-5234d7e793a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:51:14,467] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg196c1e74-83de-4b12-a727-5234d7e793a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:51:14,476] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:51:14,477] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:51:14,477] [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
Cytobacillus eiseniae	strain=DSM 26675	GCA_017874625.1	762947	762947	type	True	100.0	1313	1316	95	conclusive
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	80.4257	692	1316	95	below_threshold
Cytobacillus praedii	strain=FJAT-25547	GCA_001439605.1	1742358	1742358	type	True	80.0242	677	1316	95	below_threshold
Bacillus dafuensis	strain=FJAT-25496	GCA_007995155.1	1742359	1742359	type	True	78.4534	414	1316	95	below_threshold
Cytobacillus depressus	strain=BZ1	GCA_008923245.1	1602942	1602942	type	True	78.0602	338	1316	95	below_threshold
Cytobacillus horneckiae	strain=1P01SC	GCA_002835735.1	549687	549687	type	True	77.7022	225	1316	95	below_threshold
Bacillus salipaludis	strain=WN066	GCA_004358205.1	2547811	2547811	type	True	77.1893	164	1316	95	below_threshold
Sutcliffiella deserti	strain=DG-18	GCA_020037475.1	2875501	2875501	type	True	76.9885	62	1316	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	76.9375	150	1316	95	below_threshold
Bacillus methanolicus	strain=PB1	GCA_000262755.1	1471	1471	suspected-type	True	76.8489	128	1316	95	below_threshold
Pseudoneobacillus rhizosphaerae	strain=CIP 111885	GCA_917563885.1	2880968	2880968	type	True	76.8026	179	1316	95	below_threshold
Litchfieldia alkalitelluris	strain=DSM 16976	GCA_002019645.1	304268	304268	type	True	76.7752	119	1316	95	below_threshold
Bacillus suaedaesalsae	strain=RD4P76	GCA_016890225.1	2810349	2810349	type	True	76.4646	107	1316	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_022221345.1	1392	1392	type	True	76.4241	97	1316	95	below_threshold
Priestia aryabhattai	strain=B8W22	GCA_000956595.1	412384	412384	type	True	76.3527	81	1316	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:51:14,478] [INFO] DFAST Taxonomy check result was written to GCF_017874625.1_ASM1787462v1_genomic.fna/tc_result.tsv
[2024-01-25 17:51:14,478] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:51:14,479] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:51:14,479] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg196c1e74-83de-4b12-a727-5234d7e793a1/dqc_reference/checkm_data
[2024-01-25 17:51:14,480] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:51:14,520] [INFO] Task started: CheckM
[2024-01-25 17:51:14,520] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017874625.1_ASM1787462v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017874625.1_ASM1787462v1_genomic.fna/checkm_input GCF_017874625.1_ASM1787462v1_genomic.fna/checkm_result
[2024-01-25 17:51:41,113] [INFO] Task succeeded: CheckM
[2024-01-25 17:51:41,114] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:51:41,130] [INFO] ===== Completeness check finished =====
[2024-01-25 17:51:41,130] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:51:41,130] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017874625.1_ASM1787462v1_genomic.fna/markers.fasta)
[2024-01-25 17:51:41,131] [INFO] Task started: Blastn
[2024-01-25 17:51:41,131] [INFO] Running command: blastn -query GCF_017874625.1_ASM1787462v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg196c1e74-83de-4b12-a727-5234d7e793a1/dqc_reference/reference_markers_gtdb.fasta -out GCF_017874625.1_ASM1787462v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:51:41,952] [INFO] Task succeeded: Blastn
[2024-01-25 17:51:41,955] [INFO] Selected 15 target genomes.
[2024-01-25 17:51:41,955] [INFO] Target genome list was writen to GCF_017874625.1_ASM1787462v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:51:41,967] [INFO] Task started: fastANI
[2024-01-25 17:51:41,967] [INFO] Running command: fastANI --query /var/lib/cwl/stge34e2026-b653-4f85-b33f-2fb01e9d920c/GCF_017874625.1_ASM1787462v1_genomic.fna.gz --refList GCF_017874625.1_ASM1787462v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017874625.1_ASM1787462v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:51:57,470] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:57,480] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:51:57,480] [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_017874625.1	s__Cytobacillus eiseniae	100.0	1313	1316	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	conclusive
GCF_001420595.1	s__Cytobacillus solani	80.4391	690	1316	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.54	99.49	0.95	0.94	3	-
GCF_900199725.1	s__Cytobacillus massiliigabonensis	80.1368	684	1316	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_001439605.1	s__Cytobacillus praedii	80.0097	678	1316	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.20	99.20	0.93	0.93	2	-
GCF_019039215.1	s__Cytobacillus sp019039215	78.4835	358	1316	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_007995155.1	s__Cytobacillus dafuensis	78.4503	413	1316	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_001509555.1	s__Cytobacillus sp001509555	78.2602	346	1316	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_018343665.1	s__Cytobacillus sp018343665	78.1878	393	1316	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_008923245.1	s__Cytobacillus depressus	78.078	336	1316	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_001636345.1	s__Cytobacillus gottheilii	77.7533	223	1316	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	96.50	95.11	0.87	0.87	3	-
GCF_002835735.1	s__Cytobacillus horneckiae	77.7309	223	1316	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	98.87	98.22	0.90	0.90	3	-
GCF_900166665.1	s__Cytobacillus gottheilii_A	77.7102	227	1316	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_000518885.1	s__Cytobacillus sp000518885	77.5805	230	1316	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_007273535.1	s__Niallia circulans_B	76.9299	117	1316	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Niallia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019219025.1	s__Neobacillus sp019219025	76.9172	156	1316	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 17:51:57,482] [INFO] GTDB search result was written to GCF_017874625.1_ASM1787462v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:51:57,482] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:51:57,485] [INFO] DFAST_QC result json was written to GCF_017874625.1_ASM1787462v1_genomic.fna/dqc_result.json
[2024-01-25 17:51:57,485] [INFO] DFAST_QC completed!
[2024-01-25 17:51:57,486] [INFO] Total running time: 0h1m7s