[2024-01-24 12:36:58,145] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:58,147] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:58,147] [INFO] DQC Reference Directory: /var/lib/cwl/stg03bbb756-e09e-4a0d-be9a-a5a9bf0a1196/dqc_reference
[2024-01-24 12:36:59,600] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:59,601] [INFO] Task started: Prodigal
[2024-01-24 12:36:59,602] [INFO] Running command: gunzip -c /var/lib/cwl/stgb0a6dc82-3cfb-4657-8ad0-3e901f47743e/GCF_013184495.1_ASM1318449v1_genomic.fna.gz | prodigal -d GCF_013184495.1_ASM1318449v1_genomic.fna/cds.fna -a GCF_013184495.1_ASM1318449v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:08,252] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:08,253] [INFO] Task started: HMMsearch
[2024-01-24 12:37:08,253] [INFO] Running command: hmmsearch --tblout GCF_013184495.1_ASM1318449v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03bbb756-e09e-4a0d-be9a-a5a9bf0a1196/dqc_reference/reference_markers.hmm GCF_013184495.1_ASM1318449v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:08,582] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:08,583] [INFO] Found 6/6 markers.
[2024-01-24 12:37:08,617] [INFO] Query marker FASTA was written to GCF_013184495.1_ASM1318449v1_genomic.fna/markers.fasta
[2024-01-24 12:37:08,617] [INFO] Task started: Blastn
[2024-01-24 12:37:08,617] [INFO] Running command: blastn -query GCF_013184495.1_ASM1318449v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03bbb756-e09e-4a0d-be9a-a5a9bf0a1196/dqc_reference/reference_markers.fasta -out GCF_013184495.1_ASM1318449v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:09,235] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:09,239] [INFO] Selected 22 target genomes.
[2024-01-24 12:37:09,239] [INFO] Target genome list was writen to GCF_013184495.1_ASM1318449v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:09,269] [INFO] Task started: fastANI
[2024-01-24 12:37:09,270] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0a6dc82-3cfb-4657-8ad0-3e901f47743e/GCF_013184495.1_ASM1318449v1_genomic.fna.gz --refList GCF_013184495.1_ASM1318449v1_genomic.fna/target_genomes.txt --output GCF_013184495.1_ASM1318449v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:22,539] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:22,540] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03bbb756-e09e-4a0d-be9a-a5a9bf0a1196/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:22,540] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03bbb756-e09e-4a0d-be9a-a5a9bf0a1196/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:22,549] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:22,550] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:22,550] [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
Sporosarcina jiandibaonis	strain=LAM9210	GCA_013184495.1	2715535	2715535	type	True	100.0	1198	1199	95	conclusive
Sporosarcina ureilytica	strain=LMG 22257	GCA_001753205.1	298596	298596	type	True	77.6855	240	1199	95	below_threshold
Sporosarcina limicola	strain=DSM 13886	GCA_014873855.1	34101	34101	type	True	77.1715	155	1199	95	below_threshold
Filibacter tadaridae		GCA_900609045.1	2483811	2483811	type	True	76.9726	134	1199	95	below_threshold
Sporosarcina gallistercoris	strain=Sa3CUA8	GCA_014836415.1	2762245	2762245	type	True	76.4241	64	1199	95	below_threshold
Psychrobacillus glaciei	strain=PB01	GCA_008973485.1	2283160	2283160	type	True	76.3882	80	1199	95	below_threshold
Sporosarcina quadrami	strain=Sa2YVA2	GCA_014836615.1	2762234	2762234	type	True	76.3766	116	1199	95	below_threshold
Planococcus ruber	strain=CGMCC 1.19134	GCA_022819085.1	2027871	2027871	type	True	76.218	54	1199	95	below_threshold
Psychrobacillus psychrotolerans	strain=DSM 11706	GCA_900115805.1	126156	126156	type	True	76.1219	65	1199	95	below_threshold
Paenisporosarcina antarctica	strain=CGMCC 1.6503	GCA_004367585.1	417367	417367	type	True	76.0651	70	1199	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:22,552] [INFO] DFAST Taxonomy check result was written to GCF_013184495.1_ASM1318449v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:22,553] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:22,553] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:22,553] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03bbb756-e09e-4a0d-be9a-a5a9bf0a1196/dqc_reference/checkm_data
[2024-01-24 12:37:22,555] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:22,598] [INFO] Task started: CheckM
[2024-01-24 12:37:22,598] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013184495.1_ASM1318449v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013184495.1_ASM1318449v1_genomic.fna/checkm_input GCF_013184495.1_ASM1318449v1_genomic.fna/checkm_result
[2024-01-24 12:37:54,062] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:54,064] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:54,085] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:54,086] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:54,086] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013184495.1_ASM1318449v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:54,087] [INFO] Task started: Blastn
[2024-01-24 12:37:54,087] [INFO] Running command: blastn -query GCF_013184495.1_ASM1318449v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03bbb756-e09e-4a0d-be9a-a5a9bf0a1196/dqc_reference/reference_markers_gtdb.fasta -out GCF_013184495.1_ASM1318449v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:54,907] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:54,911] [INFO] Selected 12 target genomes.
[2024-01-24 12:37:54,911] [INFO] Target genome list was writen to GCF_013184495.1_ASM1318449v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:54,919] [INFO] Task started: fastANI
[2024-01-24 12:37:54,919] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0a6dc82-3cfb-4657-8ad0-3e901f47743e/GCF_013184495.1_ASM1318449v1_genomic.fna.gz --refList GCF_013184495.1_ASM1318449v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013184495.1_ASM1318449v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:03,654] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:03,668] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:03,668] [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_013184495.1	s__Sporosarcina sp013184495	100.0	1198	1199	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018309085.1	s__Sporosarcina sp018309085	87.2393	922	1199	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017921835.1	s__Sporosarcina sp017921835	84.8333	867	1199	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001753205.1	s__Sporosarcina ureilytica	77.6811	238	1199	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900457495.1	s__Sporosarcina pasteurii	77.6379	246	1199	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013408665.1	s__Sporosarcina sp013408665	77.3192	182	1199	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016820585.1	s__Sporosarcina sp016820585	77.19	173	1199	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873855.1	s__Sporosarcina limicola	77.1715	155	1199	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017498505.1	s__Sporosarcina sp017498505	77.0163	98	1199	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008369195.1	s__Sporosarcina sp008369195	77.0003	185	1199	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009650995.1	s__Sporosarcina sp009650995	76.7559	67	1199	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836615.1	s__Sporosarcina sp014836615	76.3766	116	1199	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:03,670] [INFO] GTDB search result was written to GCF_013184495.1_ASM1318449v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:03,670] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:03,674] [INFO] DFAST_QC result json was written to GCF_013184495.1_ASM1318449v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:03,674] [INFO] DFAST_QC completed!
[2024-01-24 12:38:03,674] [INFO] Total running time: 0h1m6s