[2024-01-24 14:06:44,626] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:44,628] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:44,628] [INFO] DQC Reference Directory: /var/lib/cwl/stg15832d6e-10f1-425c-953d-e86fb11ca4ae/dqc_reference
[2024-01-24 14:06:45,957] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:45,958] [INFO] Task started: Prodigal
[2024-01-24 14:06:45,958] [INFO] Running command: gunzip -c /var/lib/cwl/stg976fbe7c-021a-43a1-b73c-aa7c206de665/GCF_002019635.1_ASM201963v1_genomic.fna.gz | prodigal -d GCF_002019635.1_ASM201963v1_genomic.fna/cds.fna -a GCF_002019635.1_ASM201963v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:57,502] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:57,502] [INFO] Task started: HMMsearch
[2024-01-24 14:06:57,503] [INFO] Running command: hmmsearch --tblout GCF_002019635.1_ASM201963v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15832d6e-10f1-425c-953d-e86fb11ca4ae/dqc_reference/reference_markers.hmm GCF_002019635.1_ASM201963v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:57,858] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:57,860] [INFO] Found 6/6 markers.
[2024-01-24 14:06:57,909] [INFO] Query marker FASTA was written to GCF_002019635.1_ASM201963v1_genomic.fna/markers.fasta
[2024-01-24 14:06:57,909] [INFO] Task started: Blastn
[2024-01-24 14:06:57,909] [INFO] Running command: blastn -query GCF_002019635.1_ASM201963v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15832d6e-10f1-425c-953d-e86fb11ca4ae/dqc_reference/reference_markers.fasta -out GCF_002019635.1_ASM201963v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:58,534] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:58,538] [INFO] Selected 18 target genomes.
[2024-01-24 14:06:58,538] [INFO] Target genome list was writen to GCF_002019635.1_ASM201963v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:58,555] [INFO] Task started: fastANI
[2024-01-24 14:06:58,555] [INFO] Running command: fastANI --query /var/lib/cwl/stg976fbe7c-021a-43a1-b73c-aa7c206de665/GCF_002019635.1_ASM201963v1_genomic.fna.gz --refList GCF_002019635.1_ASM201963v1_genomic.fna/target_genomes.txt --output GCF_002019635.1_ASM201963v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:15,956] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:15,956] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15832d6e-10f1-425c-953d-e86fb11ca4ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:15,957] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15832d6e-10f1-425c-953d-e86fb11ca4ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:15,972] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:07:15,972] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:15,973] [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
Metabacillus halosaccharovorans	strain=DSM 25387	GCA_002019635.1	930124	930124	type	True	100.0	1796	1798	95	conclusive
Metabacillus schmidteae	strain=Marseille-P9898	GCA_903166545.1	2730405	2730405	type	True	85.7387	1242	1798	95	below_threshold
Metabacillus endolithicus	strain=KCTC 33579	GCA_023078335.1	1535204	1535204	type	True	80.6245	703	1798	95	below_threshold
Metabacillus sediminilitoris	strain=DSL-17	GCA_009720625.1	2567941	2567941	type	True	79.6116	515	1798	95	below_threshold
Bacillus weihaiensis	strain=Alg07	GCA_001889165.1	1547283	1547283	type	True	79.2591	429	1798	95	below_threshold
Metabacillus litoralis	strain=SW-211	GCA_007994985.1	152268	152268	suspected-type	True	79.2024	556	1798	95	below_threshold
Metabacillus crassostreae	strain=DSM 24486	GCA_016908395.1	929098	929098	type	True	79.2024	546	1798	95	below_threshold
Metabacillus sediminilitoris	strain=DSL-17	GCA_004801455.1	2567941	2567941	type	True	79.1431	509	1798	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	79.1198	639	1798	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	78.6006	149	1798	95	below_threshold
Bacillus alkalisoli	strain=FJAT-45122	GCA_002797415.1	2011008	2011008	type	True	78.3642	130	1798	95	below_threshold
Niallia alba	strain=UniB3	GCA_012933555.1	2729105	2729105	type	True	78.1142	140	1798	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_025263665.1	38875	38875	type	True	77.8291	142	1798	95	below_threshold
Pseudoneobacillus rhizosphaerae	strain=CIP 111885	GCA_917563885.1	2880968	2880968	type	True	77.3188	118	1798	95	below_threshold
Bacillus kexueae	strain=KCTC 33881	GCA_022809095.1	2078952	2078952	type	True	77.047	139	1798	95	below_threshold
Peribacillus asahii	strain=MA001	GCA_003570725.1	228899	228899	suspected-type	True	76.9162	115	1798	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:15,980] [INFO] DFAST Taxonomy check result was written to GCF_002019635.1_ASM201963v1_genomic.fna/tc_result.tsv
[2024-01-24 14:07:15,981] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:15,981] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:15,981] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15832d6e-10f1-425c-953d-e86fb11ca4ae/dqc_reference/checkm_data
[2024-01-24 14:07:15,983] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:16,037] [INFO] Task started: CheckM
[2024-01-24 14:07:16,037] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002019635.1_ASM201963v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002019635.1_ASM201963v1_genomic.fna/checkm_input GCF_002019635.1_ASM201963v1_genomic.fna/checkm_result
[2024-01-24 14:07:53,304] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:53,306] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:53,327] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:53,328] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:53,328] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002019635.1_ASM201963v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:53,329] [INFO] Task started: Blastn
[2024-01-24 14:07:53,329] [INFO] Running command: blastn -query GCF_002019635.1_ASM201963v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15832d6e-10f1-425c-953d-e86fb11ca4ae/dqc_reference/reference_markers_gtdb.fasta -out GCF_002019635.1_ASM201963v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:54,088] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:54,093] [INFO] Selected 15 target genomes.
[2024-01-24 14:07:54,093] [INFO] Target genome list was writen to GCF_002019635.1_ASM201963v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:54,128] [INFO] Task started: fastANI
[2024-01-24 14:07:54,128] [INFO] Running command: fastANI --query /var/lib/cwl/stg976fbe7c-021a-43a1-b73c-aa7c206de665/GCF_002019635.1_ASM201963v1_genomic.fna.gz --refList GCF_002019635.1_ASM201963v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002019635.1_ASM201963v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:08,254] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:08,266] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:08,266] [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_002019635.1	s__Metabacillus halosaccharovorans	100.0	1797	1798	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	95.47	95.47	0.86	0.86	2	conclusive
GCF_000518865.1	s__Metabacillus sp000518865	94.7256	1496	1798	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002871465.1	s__Metabacillus sp002871465	85.739	1245	1798	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.74	98.74	0.91	0.91	2	-
GCF_003667825.1	s__Metabacillus litoralis_B	80.5116	679	1798	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.61	98.61	0.90	0.90	2	-
GCF_002577655.1	s__Metabacillus sp002577655	80.3072	658	1798	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001889165.1	s__Metabacillus weihaiensis	79.2262	432	1798	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	97.24	97.24	0.88	0.88	2	-
GCF_016908395.1	s__Metabacillus crassostreae	79.1978	547	1798	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007994985.1	s__Metabacillus litoralis	79.1939	557	1798	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017497975.1	s__Metabacillus sp017497975	79.1075	640	1798	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259415.1	s__Metabacillus sp003259415	78.8889	423	1798	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013396335.1	s__Neobacillus sp013396335	77.1575	126	1798	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 14:08:08,267] [INFO] GTDB search result was written to GCF_002019635.1_ASM201963v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:08,268] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:08,271] [INFO] DFAST_QC result json was written to GCF_002019635.1_ASM201963v1_genomic.fna/dqc_result.json
[2024-01-24 14:08:08,271] [INFO] DFAST_QC completed!
[2024-01-24 14:08:08,271] [INFO] Total running time: 0h1m24s