[2024-01-24 13:21:43,739] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:43,741] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:43,741] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c0dd453-4c56-4b37-9256-5b40509f4bc8/dqc_reference
[2024-01-24 13:21:45,011] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:45,012] [INFO] Task started: Prodigal
[2024-01-24 13:21:45,013] [INFO] Running command: gunzip -c /var/lib/cwl/stg4cf79456-ae64-40f9-b6e7-616375a2464d/GCF_002109385.1_ASM210938v1_genomic.fna.gz | prodigal -d GCF_002109385.1_ASM210938v1_genomic.fna/cds.fna -a GCF_002109385.1_ASM210938v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:21:54,927] [INFO] Task succeeded: Prodigal
[2024-01-24 13:21:54,928] [INFO] Task started: HMMsearch
[2024-01-24 13:21:54,928] [INFO] Running command: hmmsearch --tblout GCF_002109385.1_ASM210938v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c0dd453-4c56-4b37-9256-5b40509f4bc8/dqc_reference/reference_markers.hmm GCF_002109385.1_ASM210938v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:21:55,255] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:21:55,257] [INFO] Found 6/6 markers.
[2024-01-24 13:21:55,298] [INFO] Query marker FASTA was written to GCF_002109385.1_ASM210938v1_genomic.fna/markers.fasta
[2024-01-24 13:21:55,299] [INFO] Task started: Blastn
[2024-01-24 13:21:55,299] [INFO] Running command: blastn -query GCF_002109385.1_ASM210938v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c0dd453-4c56-4b37-9256-5b40509f4bc8/dqc_reference/reference_markers.fasta -out GCF_002109385.1_ASM210938v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:55,944] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:55,948] [INFO] Selected 18 target genomes.
[2024-01-24 13:21:55,948] [INFO] Target genome list was writen to GCF_002109385.1_ASM210938v1_genomic.fna/target_genomes.txt
[2024-01-24 13:21:55,972] [INFO] Task started: fastANI
[2024-01-24 13:21:55,972] [INFO] Running command: fastANI --query /var/lib/cwl/stg4cf79456-ae64-40f9-b6e7-616375a2464d/GCF_002109385.1_ASM210938v1_genomic.fna.gz --refList GCF_002109385.1_ASM210938v1_genomic.fna/target_genomes.txt --output GCF_002109385.1_ASM210938v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:10,786] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:10,787] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c0dd453-4c56-4b37-9256-5b40509f4bc8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:10,787] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c0dd453-4c56-4b37-9256-5b40509f4bc8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:10,797] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:22:10,797] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:10,797] [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
Alkalihalobacillus krulwichiae	strain=AM31D	GCA_002109385.1	199441	199441	type	True	100.0	1536	1536	95	conclusive
Alkalihalobacillus krulwichiae	strain=NBRC 102362	GCA_001591945.1	199441	199441	type	True	99.9699	1475	1536	95	conclusive
Peribacillus frigoritolerans	strain=DSM 8801	GCA_024169475.1	450367	450367	type	True	81.2317	59	1536	95	below_threshold
Lederbergia citrisecundus	strain=FJAT-49732	GCA_018343695.1	2833583	2833583	type	True	80.3813	51	1536	95	below_threshold
Alkalihalobacillus akibai	strain=JCM 9157	GCA_000513135.1	1411	1411	type	True	79.723	468	1536	95	below_threshold
Alkalihalobacillus akibai	strain=JCM 9157	GCA_001315085.1	1411	1411	type	True	79.7185	467	1536	95	below_threshold
Alkalihalobacillus okhensis	strain=Kh10-101	GCA_000787375.1	333138	333138	type	True	79.0843	388	1536	95	below_threshold
Alkalihalobacillus wakoensis	strain=JCM 9140	GCA_001315045.1	127891	127891	type	True	78.8541	372	1536	95	below_threshold
Alkalihalobacillus wakoensis	strain=JCM 9140	GCA_000513095.1	127891	127891	type	True	78.8503	372	1536	95	below_threshold
Bacillus suaedae	strain=YZJH907-2	GCA_017939705.1	2822140	2822140	type	True	78.2545	206	1536	95	below_threshold
Alkalihalobacillus nanhaiisediminis	strain=CGMCC 1.10116	GCA_007830185.1	688079	688079	type	True	78.137	276	1536	95	below_threshold
Alkalihalophilus marmarensis	strain=DSM 21297	GCA_000474275.2	521377	521377	type	True	77.9324	194	1536	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:10,799] [INFO] DFAST Taxonomy check result was written to GCF_002109385.1_ASM210938v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:10,800] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:10,800] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:10,800] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c0dd453-4c56-4b37-9256-5b40509f4bc8/dqc_reference/checkm_data
[2024-01-24 13:22:10,802] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:10,852] [INFO] Task started: CheckM
[2024-01-24 13:22:10,852] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002109385.1_ASM210938v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002109385.1_ASM210938v1_genomic.fna/checkm_input GCF_002109385.1_ASM210938v1_genomic.fna/checkm_result
[2024-01-24 13:22:46,395] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:46,396] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:46,416] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:46,416] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:46,416] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002109385.1_ASM210938v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:46,417] [INFO] Task started: Blastn
[2024-01-24 13:22:46,417] [INFO] Running command: blastn -query GCF_002109385.1_ASM210938v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c0dd453-4c56-4b37-9256-5b40509f4bc8/dqc_reference/reference_markers_gtdb.fasta -out GCF_002109385.1_ASM210938v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:47,275] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:47,279] [INFO] Selected 19 target genomes.
[2024-01-24 13:22:47,279] [INFO] Target genome list was writen to GCF_002109385.1_ASM210938v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:47,302] [INFO] Task started: fastANI
[2024-01-24 13:22:47,302] [INFO] Running command: fastANI --query /var/lib/cwl/stg4cf79456-ae64-40f9-b6e7-616375a2464d/GCF_002109385.1_ASM210938v1_genomic.fna.gz --refList GCF_002109385.1_ASM210938v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002109385.1_ASM210938v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:03,110] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:03,123] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:03,123] [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_002109385.1	s__Bacillus_L krulwichiae	100.0	1536	1536	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_018343695.1	s__FJAT-49711 sp018343695	80.0136	51	1536	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__FJAT-49711	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513135.1	s__Bacillus_L akibai	79.7062	469	1536	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000787375.1	s__Bacillus_L okhensis	79.0784	388	1536	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000005825.2	s__Bacillus_S pseudofirmus	78.9372	198	1536	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_S	95.9507	97.22	97.22	0.89	0.89	2	-
GCF_002797395.1	s__45385 sp002797395	78.9189	186	1536	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__45385	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513095.1	s__Bacillus_L wakoensis	78.8381	372	1536	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002156385.1	s__45385 sp002156385	78.7447	185	1536	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__45385	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001865995.1	s__Anaerobacillus arseniciselenatis	78.2533	84	1536	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Anaerobacillaceae;g__Anaerobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017939705.1	s__Bacillus_L sp017939705	78.2528	206	1536	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830185.1	s__Bacillus_L nanhaiisediminis	78.1426	275	1536	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000474275.2	s__Bacillus_S marmarensis	77.9524	193	1536	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_S	95.9507	N/A	N/A	N/A	N/A	1	-
GCF_000513115.1	s__Bacillus_L hemicellulosilyticus	77.8938	175	1536	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000292245.2	s__Alkalihalobacillus alcalophilus	77.6727	160	1536	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Alkalihalobacillus	95.0	99.90	99.82	0.98	0.98	3	-
GCF_002734285.1	s__Fredinandcohnia onubensis_A	77.5117	74	1536	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:03,125] [INFO] GTDB search result was written to GCF_002109385.1_ASM210938v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:03,125] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:03,129] [INFO] DFAST_QC result json was written to GCF_002109385.1_ASM210938v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:03,129] [INFO] DFAST_QC completed!
[2024-01-24 13:23:03,129] [INFO] Total running time: 0h1m19s