[2024-01-24 14:54:56,520] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:54:56,523] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:54:56,523] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2fce5cb-3967-4a4b-977d-63b2fa215dbb/dqc_reference
[2024-01-24 14:54:57,951] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:54:57,952] [INFO] Task started: Prodigal
[2024-01-24 14:54:57,952] [INFO] Running command: gunzip -c /var/lib/cwl/stg4852276e-0b2c-43a0-8e9e-5c5b46aa2ac9/GCF_900113125.1_IMG-taxon_2654587900_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900113125.1_IMG-taxon_2654587900_annotated_assembly_genomic.fna/cds.fna -a GCF_900113125.1_IMG-taxon_2654587900_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:06,369] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:06,370] [INFO] Task started: HMMsearch
[2024-01-24 14:55:06,370] [INFO] Running command: hmmsearch --tblout GCF_900113125.1_IMG-taxon_2654587900_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2fce5cb-3967-4a4b-977d-63b2fa215dbb/dqc_reference/reference_markers.hmm GCF_900113125.1_IMG-taxon_2654587900_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:06,640] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:06,642] [INFO] Found 6/6 markers.
[2024-01-24 14:55:06,678] [INFO] Query marker FASTA was written to GCF_900113125.1_IMG-taxon_2654587900_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:55:06,679] [INFO] Task started: Blastn
[2024-01-24 14:55:06,679] [INFO] Running command: blastn -query GCF_900113125.1_IMG-taxon_2654587900_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2fce5cb-3967-4a4b-977d-63b2fa215dbb/dqc_reference/reference_markers.fasta -out GCF_900113125.1_IMG-taxon_2654587900_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:07,309] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:07,312] [INFO] Selected 28 target genomes.
[2024-01-24 14:55:07,313] [INFO] Target genome list was writen to GCF_900113125.1_IMG-taxon_2654587900_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:55:07,327] [INFO] Task started: fastANI
[2024-01-24 14:55:07,328] [INFO] Running command: fastANI --query /var/lib/cwl/stg4852276e-0b2c-43a0-8e9e-5c5b46aa2ac9/GCF_900113125.1_IMG-taxon_2654587900_annotated_assembly_genomic.fna.gz --refList GCF_900113125.1_IMG-taxon_2654587900_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900113125.1_IMG-taxon_2654587900_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:31,224] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:31,224] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2fce5cb-3967-4a4b-977d-63b2fa215dbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:31,224] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2fce5cb-3967-4a4b-977d-63b2fa215dbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:31,237] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:55:31,237] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:31,237] [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 alkaliphilus	strain=FP5	GCA_900113125.1	396056	396056	type	True	100.0	1311	1317	95	conclusive
Halobacillus halophilus	strain=type strain: DSM 2266	GCA_000284515.1	1570	1570	type	True	91.688	1162	1317	95	below_threshold
Halobacillus dabanensis	strain=CGMCC 1.3704	GCA_900114165.1	240302	240302	type	True	78.9039	264	1317	95	below_threshold
Halobacillus locisalis	strain=KCTC 3788	GCA_013694105.1	220753	220753	type	True	78.7016	223	1317	95	below_threshold
Halobacillus salinus	strain=HSL-3	GCA_004684905.1	192814	192814	type	True	78.5292	193	1317	95	below_threshold
Halobacillus litoralis	strain=SL-4	GCA_009856445.1	45668	45668	suspected-type	True	78.2723	265	1317	95	below_threshold
Halobacillus faecis	strain=NBRC 103569	GCA_007991335.1	360184	360184	type	True	78.2299	257	1317	95	below_threshold
Halobacillus andaensis	strain=CGMCC 1.12153	GCA_014636475.1	1176239	1176239	type	True	77.9239	195	1317	95	below_threshold
Halobacillus kuroshimensis	strain=DSM 18393	GCA_000425705.1	302481	302481	type	True	77.8906	216	1317	95	below_threshold
Halobacillus andaensis	strain=DSM 25866	GCA_017874135.1	1176239	1176239	type	True	77.8761	192	1317	95	below_threshold
Salimicrobium halophilum	strain=DSM 4771	GCA_900100295.1	86666	86666	type	True	77.52	83	1317	95	below_threshold
Terribacillus aidingensis	strain=CGMCC 1.8913	GCA_900215625.1	586416	586416	type	True	77.1752	50	1317	95	below_threshold
Sediminibacillus halophilus	strain=CGMCC 1.6199	GCA_900103695.1	482461	482461	type	True	77.164	53	1317	95	below_threshold
Virgibacillus indicus	strain=P2-C2	GCA_002266285.1	2024554	2024554	type	True	76.6065	52	1317	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:31,239] [INFO] DFAST Taxonomy check result was written to GCF_900113125.1_IMG-taxon_2654587900_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:55:31,240] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:31,240] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:31,240] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2fce5cb-3967-4a4b-977d-63b2fa215dbb/dqc_reference/checkm_data
[2024-01-24 14:55:31,242] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:31,288] [INFO] Task started: CheckM
[2024-01-24 14:55:31,288] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900113125.1_IMG-taxon_2654587900_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900113125.1_IMG-taxon_2654587900_annotated_assembly_genomic.fna/checkm_input GCF_900113125.1_IMG-taxon_2654587900_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:56:02,205] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:02,207] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:02,225] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:02,225] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:02,226] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900113125.1_IMG-taxon_2654587900_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:56:02,226] [INFO] Task started: Blastn
[2024-01-24 14:56:02,226] [INFO] Running command: blastn -query GCF_900113125.1_IMG-taxon_2654587900_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2fce5cb-3967-4a4b-977d-63b2fa215dbb/dqc_reference/reference_markers_gtdb.fasta -out GCF_900113125.1_IMG-taxon_2654587900_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:03,016] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:03,021] [INFO] Selected 22 target genomes.
[2024-01-24 14:56:03,021] [INFO] Target genome list was writen to GCF_900113125.1_IMG-taxon_2654587900_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:03,044] [INFO] Task started: fastANI
[2024-01-24 14:56:03,044] [INFO] Running command: fastANI --query /var/lib/cwl/stg4852276e-0b2c-43a0-8e9e-5c5b46aa2ac9/GCF_900113125.1_IMG-taxon_2654587900_annotated_assembly_genomic.fna.gz --refList GCF_900113125.1_IMG-taxon_2654587900_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900113125.1_IMG-taxon_2654587900_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:21,277] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:21,294] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:21,295] [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_900113125.1	s__Halobacillus alkaliphilus	100.0	1311	1317	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000284515.1	s__Halobacillus halophilus	91.7152	1160	1317	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_900114165.1	s__Halobacillus dabanensis	78.8709	266	1317	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	78.7998	328	1317	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_004101865.1	s__Halobacillus litoralis_A	78.7074	295	1317	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_013694105.1	s__Halobacillus locisalis	78.7016	223	1317	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_004684905.1	s__Halobacillus salinus	78.5614	192	1317	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	98.08	98.08	0.93	0.93	2	-
GCF_000469135.2	s__Halobacillus sp001592845	78.4835	200	1317	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_000496835.1	s__Thalassobacillus devorans_B	78.2959	117	1317	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Thalassobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009856445.1	s__Halobacillus litoralis	78.2894	265	1317	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_015905325.1	s__Halobacillus sp015905325	78.2655	254	1317	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_900176565.1	s__Thalassobacillus devorans_A	77.9565	116	1317	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Thalassobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014636475.1	s__Halobacillus_A andaensis	77.9283	194	1317	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	-
GCF_000425705.1	s__Halobacillus kuroshimensis	77.8905	216	1317	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	98.79	98.79	0.92	0.92	2	-
GCF_900240285.1	s__Halobacillus_A sp900240285	77.8304	164	1317	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	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:21,296] [INFO] GTDB search result was written to GCF_900113125.1_IMG-taxon_2654587900_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:21,297] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:21,301] [INFO] DFAST_QC result json was written to GCF_900113125.1_IMG-taxon_2654587900_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:56:21,301] [INFO] DFAST_QC completed!
[2024-01-24 14:56:21,301] [INFO] Total running time: 0h1m25s