[2024-01-25 17:49:20,641] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:49:20,642] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:49:20,642] [INFO] DQC Reference Directory: /var/lib/cwl/stg90e6615e-26ae-47bc-bc23-0716763e4afb/dqc_reference
[2024-01-25 17:49:21,770] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:49:21,770] [INFO] Task started: Prodigal
[2024-01-25 17:49:21,770] [INFO] Running command: gunzip -c /var/lib/cwl/stg5cd9e7fe-f809-4898-8edd-8310b6492b89/GCF_013694105.1_ASM1369410v1_genomic.fna.gz | prodigal -d GCF_013694105.1_ASM1369410v1_genomic.fna/cds.fna -a GCF_013694105.1_ASM1369410v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:49:29,832] [INFO] Task succeeded: Prodigal
[2024-01-25 17:49:29,833] [INFO] Task started: HMMsearch
[2024-01-25 17:49:29,833] [INFO] Running command: hmmsearch --tblout GCF_013694105.1_ASM1369410v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90e6615e-26ae-47bc-bc23-0716763e4afb/dqc_reference/reference_markers.hmm GCF_013694105.1_ASM1369410v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:49:30,065] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:49:30,066] [INFO] Found 6/6 markers.
[2024-01-25 17:49:30,097] [INFO] Query marker FASTA was written to GCF_013694105.1_ASM1369410v1_genomic.fna/markers.fasta
[2024-01-25 17:49:30,098] [INFO] Task started: Blastn
[2024-01-25 17:49:30,098] [INFO] Running command: blastn -query GCF_013694105.1_ASM1369410v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90e6615e-26ae-47bc-bc23-0716763e4afb/dqc_reference/reference_markers.fasta -out GCF_013694105.1_ASM1369410v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:49:30,659] [INFO] Task succeeded: Blastn
[2024-01-25 17:49:30,664] [INFO] Selected 25 target genomes.
[2024-01-25 17:49:30,664] [INFO] Target genome list was writen to GCF_013694105.1_ASM1369410v1_genomic.fna/target_genomes.txt
[2024-01-25 17:49:30,688] [INFO] Task started: fastANI
[2024-01-25 17:49:30,688] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cd9e7fe-f809-4898-8edd-8310b6492b89/GCF_013694105.1_ASM1369410v1_genomic.fna.gz --refList GCF_013694105.1_ASM1369410v1_genomic.fna/target_genomes.txt --output GCF_013694105.1_ASM1369410v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:49:47,869] [INFO] Task succeeded: fastANI
[2024-01-25 17:49:47,870] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90e6615e-26ae-47bc-bc23-0716763e4afb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:49:47,870] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90e6615e-26ae-47bc-bc23-0716763e4afb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:49:47,879] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:49:47,879] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:49:47,879] [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 locisalis	strain=KCTC 3788	GCA_013694105.1	220753	220753	type	True	100.0	1239	1240	95	conclusive
Halobacillus salinus	strain=HSL-3	GCA_004684905.1	192814	192814	type	True	79.5435	453	1240	95	below_threshold
Halobacillus litoralis	strain=SL-4	GCA_009856445.1	45668	45668	suspected-type	True	78.916	271	1240	95	below_threshold
Halobacillus halophilus	strain=type strain: DSM 2266	GCA_000284515.1	1570	1570	type	True	78.6493	241	1240	95	below_threshold
Halobacillus aidingensis	strain=CGMCC 1.3703	GCA_900104185.1	240303	240303	type	True	78.535	309	1240	95	below_threshold
Halobacillus faecis	strain=NBRC 103569	GCA_007991335.1	360184	360184	type	True	78.498	296	1240	95	below_threshold
Halobacillus trueperi	strain=KCTC 3686	GCA_003386945.1	156205	156205	type	True	78.4742	318	1240	95	below_threshold
Halobacillus alkaliphilus	strain=FP5	GCA_900113125.1	396056	396056	type	True	78.3963	234	1240	95	below_threshold
Halobacillus kuroshimensis	strain=DSM 18393	GCA_000425705.1	302481	302481	type	True	78.0023	232	1240	95	below_threshold
Thalassobacillus pellis	strain=DSM 22784	GCA_016908295.1	748008	748008	type	True	77.8948	72	1240	95	below_threshold
Halobacillus andaensis	strain=CGMCC 1.12153	GCA_014636475.1	1176239	1176239	type	True	77.8457	161	1240	95	below_threshold
Halobacillus andaensis	strain=DSM 25866	GCA_017874135.1	1176239	1176239	type	True	77.7993	159	1240	95	below_threshold
Sediminibacillus terrae	strain=JSM 102062	GCA_009602435.1	1562106	1562106	type	True	77.0969	54	1240	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:49:47,880] [INFO] DFAST Taxonomy check result was written to GCF_013694105.1_ASM1369410v1_genomic.fna/tc_result.tsv
[2024-01-25 17:49:47,881] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:49:47,881] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:49:47,881] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90e6615e-26ae-47bc-bc23-0716763e4afb/dqc_reference/checkm_data
[2024-01-25 17:49:47,882] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:49:47,919] [INFO] Task started: CheckM
[2024-01-25 17:49:47,920] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013694105.1_ASM1369410v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013694105.1_ASM1369410v1_genomic.fna/checkm_input GCF_013694105.1_ASM1369410v1_genomic.fna/checkm_result
[2024-01-25 17:50:16,336] [INFO] Task succeeded: CheckM
[2024-01-25 17:50:16,337] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:50:16,357] [INFO] ===== Completeness check finished =====
[2024-01-25 17:50:16,357] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:50:16,357] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013694105.1_ASM1369410v1_genomic.fna/markers.fasta)
[2024-01-25 17:50:16,358] [INFO] Task started: Blastn
[2024-01-25 17:50:16,358] [INFO] Running command: blastn -query GCF_013694105.1_ASM1369410v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90e6615e-26ae-47bc-bc23-0716763e4afb/dqc_reference/reference_markers_gtdb.fasta -out GCF_013694105.1_ASM1369410v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:17,118] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:17,121] [INFO] Selected 20 target genomes.
[2024-01-25 17:50:17,121] [INFO] Target genome list was writen to GCF_013694105.1_ASM1369410v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:50:17,135] [INFO] Task started: fastANI
[2024-01-25 17:50:17,135] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cd9e7fe-f809-4898-8edd-8310b6492b89/GCF_013694105.1_ASM1369410v1_genomic.fna.gz --refList GCF_013694105.1_ASM1369410v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013694105.1_ASM1369410v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:50:33,562] [INFO] Task succeeded: fastANI
[2024-01-25 17:50:33,572] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:50:33,573] [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_013694105.1	s__Halobacillus locisalis	100.0	1239	1240	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_004684905.1	s__Halobacillus salinus	79.5622	451	1240	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_009856445.1	s__Halobacillus litoralis	78.9073	273	1240	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_000469135.2	s__Halobacillus sp001592845	78.8744	217	1240	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	99.23	99.19	0.95	0.95	3	-
GCA_004078665.1	s__Halobacillus sp004078665	78.7876	332	1240	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_015905325.1	s__Halobacillus sp015905325	78.6262	265	1240	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	78.615	244	1240	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_002097535.1	s__Halobacillus mangrovi	78.5709	285	1240	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_900104185.1	s__Halobacillus aidingensis	78.5266	306	1240	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	96.52	96.52	0.91	0.91	2	-
GCF_007991335.1	s__Halobacillus faecis	78.4979	296	1240	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_009856415.1	s__Halobacillus litoralis_C	78.4684	327	1240	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	78.4248	274	1240	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_900114165.1	s__Halobacillus dabanensis	78.4102	269	1240	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_000425705.1	s__Halobacillus kuroshimensis	78.0023	232	1240	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_014636475.1	s__Halobacillus_A andaensis	77.7922	159	1240	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_002844535.1	s__Halalkalibacillus_A sediminis	77.6432	51	1240	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Halalkalibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900162695.1	s__Lentibacillus siamensis	77.0758	50	1240	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:50:33,574] [INFO] GTDB search result was written to GCF_013694105.1_ASM1369410v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:50:33,575] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:50:33,578] [INFO] DFAST_QC result json was written to GCF_013694105.1_ASM1369410v1_genomic.fna/dqc_result.json
[2024-01-25 17:50:33,578] [INFO] DFAST_QC completed!
[2024-01-25 17:50:33,578] [INFO] Total running time: 0h1m13s