[2024-01-25 19:47:35,725] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:47:35,726] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:47:35,727] [INFO] DQC Reference Directory: /var/lib/cwl/stgc0f27a58-42fb-4394-ad34-7cda29061090/dqc_reference
[2024-01-25 19:47:36,882] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:47:36,882] [INFO] Task started: Prodigal
[2024-01-25 19:47:36,882] [INFO] Running command: gunzip -c /var/lib/cwl/stg143fa257-5d5d-4c46-a799-bf559adc1a2c/GCF_014636475.1_ASM1463647v1_genomic.fna.gz | prodigal -d GCF_014636475.1_ASM1463647v1_genomic.fna/cds.fna -a GCF_014636475.1_ASM1463647v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:47:44,109] [INFO] Task succeeded: Prodigal
[2024-01-25 19:47:44,109] [INFO] Task started: HMMsearch
[2024-01-25 19:47:44,109] [INFO] Running command: hmmsearch --tblout GCF_014636475.1_ASM1463647v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc0f27a58-42fb-4394-ad34-7cda29061090/dqc_reference/reference_markers.hmm GCF_014636475.1_ASM1463647v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:47:44,332] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:47:44,333] [INFO] Found 6/6 markers.
[2024-01-25 19:47:44,362] [INFO] Query marker FASTA was written to GCF_014636475.1_ASM1463647v1_genomic.fna/markers.fasta
[2024-01-25 19:47:44,362] [INFO] Task started: Blastn
[2024-01-25 19:47:44,362] [INFO] Running command: blastn -query GCF_014636475.1_ASM1463647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0f27a58-42fb-4394-ad34-7cda29061090/dqc_reference/reference_markers.fasta -out GCF_014636475.1_ASM1463647v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:44,911] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:44,914] [INFO] Selected 27 target genomes.
[2024-01-25 19:47:44,914] [INFO] Target genome list was writen to GCF_014636475.1_ASM1463647v1_genomic.fna/target_genomes.txt
[2024-01-25 19:47:44,925] [INFO] Task started: fastANI
[2024-01-25 19:47:44,926] [INFO] Running command: fastANI --query /var/lib/cwl/stg143fa257-5d5d-4c46-a799-bf559adc1a2c/GCF_014636475.1_ASM1463647v1_genomic.fna.gz --refList GCF_014636475.1_ASM1463647v1_genomic.fna/target_genomes.txt --output GCF_014636475.1_ASM1463647v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:48:06,591] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:06,592] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc0f27a58-42fb-4394-ad34-7cda29061090/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:48:06,593] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc0f27a58-42fb-4394-ad34-7cda29061090/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:48:06,603] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:48:06,603] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:48:06,603] [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
Halobacillus andaensis	strain=CGMCC 1.12153	GCA_014636475.1	1176239	1176239	type	True	100.0	1297	1298	95	conclusive
Halobacillus andaensis	strain=DSM 25866	GCA_017874135.1	1176239	1176239	type	True	99.9996	1297	1298	95	conclusive
Halobacillus aidingensis	strain=CGMCC 1.3703	GCA_900104185.1	240303	240303	type	True	78.3563	181	1298	95	below_threshold
Halobacillus massiliensis	strain=Marseille-P3554	GCA_900166625.1	1926286	1926286	type	True	78.3298	308	1298	95	below_threshold
Halobacillus litoralis	strain=SL-4	GCA_009856445.1	45668	45668	suspected-type	True	78.0904	174	1298	95	below_threshold
Halobacillus dabanensis	strain=CGMCC 1.3704	GCA_900114165.1	240302	240302	type	True	78.069	175	1298	95	below_threshold
Halobacillus faecis	strain=NBRC 103569	GCA_007991335.1	360184	360184	type	True	78.068	163	1298	95	below_threshold
Halobacillus trueperi	strain=KCTC 3686	GCA_003386945.1	156205	156205	type	True	78.0332	182	1298	95	below_threshold
Halobacillus karajensis	strain=DSM 14948	GCA_900108515.1	195088	195088	type	True	77.9756	163	1298	95	below_threshold
Halobacillus ihumii	strain=Marseille-Q1234	GCA_902726645.1	2686092	2686092	type	True	77.9707	210	1298	95	below_threshold
Halobacillus alkaliphilus	strain=FP5	GCA_900113125.1	396056	396056	type	True	77.9542	189	1298	95	below_threshold
Halobacillus kuroshimensis	strain=DSM 18393	GCA_000425705.1	302481	302481	type	True	77.7549	141	1298	95	below_threshold
Pontibacillus salipaludis	strain=CGMCC 1.15353	GCA_014642405.1	1697394	1697394	type	True	77.5085	75	1298	95	below_threshold
Aquibacillus kalidii	strain=HU2P27	GCA_014280935.1	2762597	2762597	type	True	76.6917	59	1298	95	below_threshold
Oceanobacillus alkalisoli	strain=APA_J-2 (6-2)	GCA_021556485.1	2925113	2925113	type	True	76.2099	50	1298	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:48:06,604] [INFO] DFAST Taxonomy check result was written to GCF_014636475.1_ASM1463647v1_genomic.fna/tc_result.tsv
[2024-01-25 19:48:06,605] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:48:06,605] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:48:06,605] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc0f27a58-42fb-4394-ad34-7cda29061090/dqc_reference/checkm_data
[2024-01-25 19:48:06,606] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:48:06,646] [INFO] Task started: CheckM
[2024-01-25 19:48:06,646] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014636475.1_ASM1463647v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014636475.1_ASM1463647v1_genomic.fna/checkm_input GCF_014636475.1_ASM1463647v1_genomic.fna/checkm_result
[2024-01-25 19:48:32,840] [INFO] Task succeeded: CheckM
[2024-01-25 19:48:32,841] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:48:32,858] [INFO] ===== Completeness check finished =====
[2024-01-25 19:48:32,858] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:48:32,859] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014636475.1_ASM1463647v1_genomic.fna/markers.fasta)
[2024-01-25 19:48:32,859] [INFO] Task started: Blastn
[2024-01-25 19:48:32,859] [INFO] Running command: blastn -query GCF_014636475.1_ASM1463647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0f27a58-42fb-4394-ad34-7cda29061090/dqc_reference/reference_markers_gtdb.fasta -out GCF_014636475.1_ASM1463647v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:48:33,665] [INFO] Task succeeded: Blastn
[2024-01-25 19:48:33,668] [INFO] Selected 23 target genomes.
[2024-01-25 19:48:33,668] [INFO] Target genome list was writen to GCF_014636475.1_ASM1463647v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:48:33,704] [INFO] Task started: fastANI
[2024-01-25 19:48:33,704] [INFO] Running command: fastANI --query /var/lib/cwl/stg143fa257-5d5d-4c46-a799-bf559adc1a2c/GCF_014636475.1_ASM1463647v1_genomic.fna.gz --refList GCF_014636475.1_ASM1463647v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014636475.1_ASM1463647v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:48:51,772] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:51,784] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:48:51,784] [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_014636475.1	s__Halobacillus_A andaensis	100.0	1297	1298	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus_A	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900240285.1	s__Halobacillus_A sp900240285	80.7217	669	1298	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902809865.1	s__Halobacillus_A sp902809865	78.9282	384	1298	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908235.1	s__Halobacillus_A seohaensis	78.6373	391	1298	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900166625.1	s__Halobacillus_A massiliensis	78.3298	308	1298	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015905325.1	s__Halobacillus sp015905325	78.1407	134	1298	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009856445.1	s__Halobacillus litoralis	78.095	175	1298	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	95.88	95.88	0.90	0.90	2	-
GCF_007991335.1	s__Halobacillus faecis	78.068	163	1298	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002097535.1	s__Halobacillus mangrovi	78.0668	209	1298	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000469135.2	s__Halobacillus sp001592845	78.0477	116	1298	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	99.23	99.19	0.95	0.95	3	-
GCF_900113125.1	s__Halobacillus alkaliphilus	77.9542	189	1298	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004078665.1	s__Halobacillus sp004078665	77.9451	144	1298	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284515.1	s__Halobacillus halophilus	77.9141	176	1298	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900108515.1	s__Halobacillus karajensis	77.9082	164	1298	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	99.38	99.37	0.93	0.93	4	-
GCF_014642405.1	s__Pontibacillus salipaludis	77.5085	75	1298	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Pontibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014280935.1	s__HU2P27 sp014280935	76.7666	57	1298	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__HU2P27	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:48:51,785] [INFO] GTDB search result was written to GCF_014636475.1_ASM1463647v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:48:51,786] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:48:51,789] [INFO] DFAST_QC result json was written to GCF_014636475.1_ASM1463647v1_genomic.fna/dqc_result.json
[2024-01-25 19:48:51,790] [INFO] DFAST_QC completed!
[2024-01-25 19:48:51,790] [INFO] Total running time: 0h1m16s