[2024-01-24 15:02:17,335] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:17,336] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:17,336] [INFO] DQC Reference Directory: /var/lib/cwl/stg50486ab7-10a8-4ead-82b8-3881cd959b48/dqc_reference
[2024-01-24 15:02:18,714] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:18,715] [INFO] Task started: Prodigal
[2024-01-24 15:02:18,715] [INFO] Running command: gunzip -c /var/lib/cwl/stg4b7636b4-5978-47e2-8ba6-2d8441018d26/GCF_014287465.1_ASM1428746v1_genomic.fna.gz | prodigal -d GCF_014287465.1_ASM1428746v1_genomic.fna/cds.fna -a GCF_014287465.1_ASM1428746v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:25,908] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:25,909] [INFO] Task started: HMMsearch
[2024-01-24 15:02:25,909] [INFO] Running command: hmmsearch --tblout GCF_014287465.1_ASM1428746v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50486ab7-10a8-4ead-82b8-3881cd959b48/dqc_reference/reference_markers.hmm GCF_014287465.1_ASM1428746v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:26,233] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:26,235] [INFO] Found 6/6 markers.
[2024-01-24 15:02:26,277] [INFO] Query marker FASTA was written to GCF_014287465.1_ASM1428746v1_genomic.fna/markers.fasta
[2024-01-24 15:02:26,278] [INFO] Task started: Blastn
[2024-01-24 15:02:26,278] [INFO] Running command: blastn -query GCF_014287465.1_ASM1428746v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50486ab7-10a8-4ead-82b8-3881cd959b48/dqc_reference/reference_markers.fasta -out GCF_014287465.1_ASM1428746v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:26,924] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:26,928] [INFO] Selected 18 target genomes.
[2024-01-24 15:02:26,928] [INFO] Target genome list was writen to GCF_014287465.1_ASM1428746v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:26,935] [INFO] Task started: fastANI
[2024-01-24 15:02:26,935] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b7636b4-5978-47e2-8ba6-2d8441018d26/GCF_014287465.1_ASM1428746v1_genomic.fna.gz --refList GCF_014287465.1_ASM1428746v1_genomic.fna/target_genomes.txt --output GCF_014287465.1_ASM1428746v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:40,167] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:40,168] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50486ab7-10a8-4ead-82b8-3881cd959b48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:40,168] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50486ab7-10a8-4ead-82b8-3881cd959b48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:40,182] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:02:40,182] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:40,182] [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
Ornithinibacillus massiliensis	strain=Marseille-P3601	GCA_018310345.1	1944633	1944633	type	True	99.2046	1198	1237	95	conclusive
Ornithinibacillus scapharcae	strain=TW25	GCA_000190475.2	1147159	1147159	type	True	78.8075	384	1237	95	below_threshold
Ornithinibacillus contaminans	strain=DSM 22953	GCA_001038425.2	694055	694055	type	True	78.5585	338	1237	95	below_threshold
Ornithinibacillus halotolerans	strain=CGMCC 1.12408	GCA_014637405.1	1274357	1274357	type	True	78.548	363	1237	95	below_threshold
Ornithinibacillus halophilus	strain=IBRC-M 10683	GCA_900129485.1	930117	930117	type	True	78.0631	175	1237	95	below_threshold
Oceanobacillus arenosus	strain=CAU 1183	GCA_003369575.1	1229153	1229153	type	True	77.8378	110	1237	95	below_threshold
Oceanobacillus piezotolerans	strain=YLB-02	GCA_003665065.1	2448030	2448030	type	True	77.496	114	1237	95	below_threshold
Oceanobacillus bengalensis	strain=MCCC 1K00260	GCA_003628445.1	1435466	1435466	type	True	77.4215	140	1237	95	below_threshold
Ornithinibacillus gellani	strain=LJ137	GCA_003730295.1	2293253	2293253	type	True	77.2141	112	1237	95	below_threshold
Virgibacillus profundi	strain=P3-H5	GCA_002287375.1	2024555	2024555	type	True	77.0638	135	1237	95	below_threshold
Virgibacillus natechei	strain=DSM 25609	GCA_017874115.1	1216297	1216297	type	True	76.8225	96	1237	95	below_threshold
Paraliobacillus sediminis	strain=126C4	GCA_003426055.1	1885916	1885916	type	True	76.3697	50	1237	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:40,184] [INFO] DFAST Taxonomy check result was written to GCF_014287465.1_ASM1428746v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:40,184] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:40,184] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:40,185] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50486ab7-10a8-4ead-82b8-3881cd959b48/dqc_reference/checkm_data
[2024-01-24 15:02:40,185] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:40,222] [INFO] Task started: CheckM
[2024-01-24 15:02:40,222] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014287465.1_ASM1428746v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014287465.1_ASM1428746v1_genomic.fna/checkm_input GCF_014287465.1_ASM1428746v1_genomic.fna/checkm_result
[2024-01-24 15:03:08,249] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:08,250] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:08,273] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:08,274] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:08,274] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014287465.1_ASM1428746v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:08,275] [INFO] Task started: Blastn
[2024-01-24 15:03:08,275] [INFO] Running command: blastn -query GCF_014287465.1_ASM1428746v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50486ab7-10a8-4ead-82b8-3881cd959b48/dqc_reference/reference_markers_gtdb.fasta -out GCF_014287465.1_ASM1428746v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:09,325] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:09,328] [INFO] Selected 14 target genomes.
[2024-01-24 15:03:09,329] [INFO] Target genome list was writen to GCF_014287465.1_ASM1428746v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:09,342] [INFO] Task started: fastANI
[2024-01-24 15:03:09,342] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b7636b4-5978-47e2-8ba6-2d8441018d26/GCF_014287465.1_ASM1428746v1_genomic.fna.gz --refList GCF_014287465.1_ASM1428746v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014287465.1_ASM1428746v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:19,862] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:19,879] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:19,879] [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_018310345.1	s__Ornithinibacillus massiliensis	99.2046	1198	1237	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	99.20	99.20	0.97	0.97	2	conclusive
GCF_001038485.1	s__Ornithinibacillus californiensis	79.4572	489	1237	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000577245.1	s__Ornithinibacillus sp000577245	79.0571	450	1237	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184735.1	s__Ornithinibacillus globulus_B	78.9236	429	1237	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482485.1	s__Ornithinibacillus globulus	78.8791	426	1237	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000190475.1	s__Ornithinibacillus scapharcae	78.8072	384	1237	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001038425.2	s__Ornithinibacillus contaminans	78.559	339	1237	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900240995.1	s__OESV01 sp900240995	76.8738	60	1237	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_C;f__Bacillaceae_J;g__OESV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003944835.1	s__HMF5848 sp003944835	76.6504	52	1237	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__HMF5848;g__HMF5848	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:03:19,883] [INFO] GTDB search result was written to GCF_014287465.1_ASM1428746v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:19,884] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:19,890] [INFO] DFAST_QC result json was written to GCF_014287465.1_ASM1428746v1_genomic.fna/dqc_result.json
[2024-01-24 15:03:19,890] [INFO] DFAST_QC completed!
[2024-01-24 15:03:19,890] [INFO] Total running time: 0h1m3s