[2024-01-24 14:31:28,809] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:28,811] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:28,811] [INFO] DQC Reference Directory: /var/lib/cwl/stg3fc1a87b-b4c7-460f-b98d-a818ced27002/dqc_reference
[2024-01-24 14:31:29,891] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:29,892] [INFO] Task started: Prodigal
[2024-01-24 14:31:29,892] [INFO] Running command: gunzip -c /var/lib/cwl/stg9d1ea779-d26f-4db3-ae03-5707983cbbb8/GCF_018075365.1_ASM1807536v1_genomic.fna.gz | prodigal -d GCF_018075365.1_ASM1807536v1_genomic.fna/cds.fna -a GCF_018075365.1_ASM1807536v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:38,539] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:38,540] [INFO] Task started: HMMsearch
[2024-01-24 14:31:38,540] [INFO] Running command: hmmsearch --tblout GCF_018075365.1_ASM1807536v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3fc1a87b-b4c7-460f-b98d-a818ced27002/dqc_reference/reference_markers.hmm GCF_018075365.1_ASM1807536v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:38,760] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:38,761] [INFO] Found 6/6 markers.
[2024-01-24 14:31:38,792] [INFO] Query marker FASTA was written to GCF_018075365.1_ASM1807536v1_genomic.fna/markers.fasta
[2024-01-24 14:31:38,793] [INFO] Task started: Blastn
[2024-01-24 14:31:38,793] [INFO] Running command: blastn -query GCF_018075365.1_ASM1807536v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3fc1a87b-b4c7-460f-b98d-a818ced27002/dqc_reference/reference_markers.fasta -out GCF_018075365.1_ASM1807536v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:39,333] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:39,343] [INFO] Selected 16 target genomes.
[2024-01-24 14:31:39,343] [INFO] Target genome list was writen to GCF_018075365.1_ASM1807536v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:39,453] [INFO] Task started: fastANI
[2024-01-24 14:31:39,454] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d1ea779-d26f-4db3-ae03-5707983cbbb8/GCF_018075365.1_ASM1807536v1_genomic.fna.gz --refList GCF_018075365.1_ASM1807536v1_genomic.fna/target_genomes.txt --output GCF_018075365.1_ASM1807536v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:56,343] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:56,344] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3fc1a87b-b4c7-460f-b98d-a818ced27002/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:56,344] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3fc1a87b-b4c7-460f-b98d-a818ced27002/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:56,351] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:31:56,351] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:56,351] [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
Virgibacillus pantothenticus	strain=DSM 26	GCA_018075365.1	1473	1473	type	True	100.0	1587	1587	95	conclusive
Virgibacillus pantothenticus	strain=DSM 26	GCA_900156795.1	1473	1473	type	True	99.9802	1537	1587	95	conclusive
Virgibacillus pantothenticus	strain=DSM 26	GCA_001189575.1	1473	1473	type	True	99.9789	1570	1587	95	conclusive
Virgibacillus chiguensis	strain=CGMCC 1.6496	GCA_900129865.1	411959	411959	type	True	80.3647	832	1587	95	below_threshold
Oceanobacillus zhaokaii	strain=160	GCA_003352005.1	2052660	2052660	type	True	78.0992	127	1587	95	below_threshold
Paraliobacillus zengyii	strain=X-1125	GCA_003268595.1	2213194	2213194	type	True	78.0625	66	1587	95	below_threshold
Oceanobacillus indicireducens	strain=JCM 17251	GCA_014647195.1	1004261	1004261	type	True	77.7639	82	1587	95	below_threshold
Virgibacillus massiliensis	strain=Vm-5	GCA_000723585.1	1462526	1462526	suspected-type	True	77.7287	246	1587	95	below_threshold
Oceanobacillus jordanicus	strain=GSFE11	GCA_022095695.1	2867266	2867266	type	True	77.0804	129	1587	95	below_threshold
Aquibacillus sediminis	strain=BH258	GCA_005870085.1	2574734	2574734	type	True	76.4743	95	1587	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:56,352] [INFO] DFAST Taxonomy check result was written to GCF_018075365.1_ASM1807536v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:56,353] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:56,353] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:56,353] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3fc1a87b-b4c7-460f-b98d-a818ced27002/dqc_reference/checkm_data
[2024-01-24 14:31:56,354] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:56,399] [INFO] Task started: CheckM
[2024-01-24 14:31:56,399] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018075365.1_ASM1807536v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018075365.1_ASM1807536v1_genomic.fna/checkm_input GCF_018075365.1_ASM1807536v1_genomic.fna/checkm_result
[2024-01-24 14:32:24,932] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:24,933] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.94%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:24,952] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:24,952] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:24,952] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018075365.1_ASM1807536v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:24,952] [INFO] Task started: Blastn
[2024-01-24 14:32:24,952] [INFO] Running command: blastn -query GCF_018075365.1_ASM1807536v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3fc1a87b-b4c7-460f-b98d-a818ced27002/dqc_reference/reference_markers_gtdb.fasta -out GCF_018075365.1_ASM1807536v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:25,694] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:25,696] [INFO] Selected 12 target genomes.
[2024-01-24 14:32:25,697] [INFO] Target genome list was writen to GCF_018075365.1_ASM1807536v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:25,703] [INFO] Task started: fastANI
[2024-01-24 14:32:25,703] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d1ea779-d26f-4db3-ae03-5707983cbbb8/GCF_018075365.1_ASM1807536v1_genomic.fna.gz --refList GCF_018075365.1_ASM1807536v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018075365.1_ASM1807536v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:41,229] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:41,235] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:41,235] [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_018075365.1	s__Virgibacillus pantothenticus	100.0	1584	1587	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	99.44	97.53	0.92	0.86	18	conclusive
GCF_003612345.1	s__Virgibacillus sp003612345	92.6757	1235	1587	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	100.00	100.00	1.00	0.99	4	-
GCF_900166595.1	s__Virgibacillus dokdonensis	80.961	835	1587	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.5968	98.95	98.88	0.93	0.90	3	-
GCF_900129865.1	s__Virgibacillus chiguensis	80.4122	829	1587	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.5968	98.02	97.78	0.91	0.87	3	-
GCF_018916875.1	s__Virgibacillus proomii_B	79.4847	441	1587	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352005.1	s__Oceanobacillus zhaokaii	78.1574	125	1587	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.81	99.81	1.00	1.00	2	-
GCF_016919725.1	s__Virgibacillus sp016919725	78.1409	285	1587	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	99.34	99.27	0.95	0.91	5	-
GCF_000724085.1	s__Virgibacillus manasiensis	77.8661	133	1587	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647195.1	s__Oceanobacillus indicireducens	77.7639	82	1587	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	97.29	97.29	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:41,236] [INFO] GTDB search result was written to GCF_018075365.1_ASM1807536v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:41,236] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:41,239] [INFO] DFAST_QC result json was written to GCF_018075365.1_ASM1807536v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:41,239] [INFO] DFAST_QC completed!
[2024-01-24 14:32:41,239] [INFO] Total running time: 0h1m12s