[2024-01-24 12:14:33,761] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:33,763] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:33,763] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c91a00c-635c-4741-89ad-f9e726fdd85b/dqc_reference
[2024-01-24 12:14:35,048] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:35,049] [INFO] Task started: Prodigal
[2024-01-24 12:14:35,050] [INFO] Running command: gunzip -c /var/lib/cwl/stge8a61a1a-906d-40ca-a0ff-c44f4573802b/GCF_900166625.1_PRJEB19420_genomic.fna.gz | prodigal -d GCF_900166625.1_PRJEB19420_genomic.fna/cds.fna -a GCF_900166625.1_PRJEB19420_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:44,448] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:44,449] [INFO] Task started: HMMsearch
[2024-01-24 12:14:44,449] [INFO] Running command: hmmsearch --tblout GCF_900166625.1_PRJEB19420_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c91a00c-635c-4741-89ad-f9e726fdd85b/dqc_reference/reference_markers.hmm GCF_900166625.1_PRJEB19420_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:44,744] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:44,746] [INFO] Found 6/6 markers.
[2024-01-24 12:14:44,792] [INFO] Query marker FASTA was written to GCF_900166625.1_PRJEB19420_genomic.fna/markers.fasta
[2024-01-24 12:14:44,793] [INFO] Task started: Blastn
[2024-01-24 12:14:44,793] [INFO] Running command: blastn -query GCF_900166625.1_PRJEB19420_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c91a00c-635c-4741-89ad-f9e726fdd85b/dqc_reference/reference_markers.fasta -out GCF_900166625.1_PRJEB19420_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:45,376] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:45,380] [INFO] Selected 29 target genomes.
[2024-01-24 12:14:45,381] [INFO] Target genome list was writen to GCF_900166625.1_PRJEB19420_genomic.fna/target_genomes.txt
[2024-01-24 12:14:45,396] [INFO] Task started: fastANI
[2024-01-24 12:14:45,397] [INFO] Running command: fastANI --query /var/lib/cwl/stge8a61a1a-906d-40ca-a0ff-c44f4573802b/GCF_900166625.1_PRJEB19420_genomic.fna.gz --refList GCF_900166625.1_PRJEB19420_genomic.fna/target_genomes.txt --output GCF_900166625.1_PRJEB19420_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:07,017] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:07,017] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c91a00c-635c-4741-89ad-f9e726fdd85b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:07,017] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c91a00c-635c-4741-89ad-f9e726fdd85b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:07,029] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:07,029] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:07,029] [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 massiliensis	strain=Marseille-P3554	GCA_900166625.1	1926286	1926286	type	True	99.9982	1417	1437	95	conclusive
Metabacillus dongyingensis	strain=BY2G20	GCA_019933155.2	2874282	2874282	type	True	79.2992	58	1437	95	below_threshold
Halobacillus ihumii	strain=Marseille-Q1234	GCA_902726645.1	2686092	2686092	type	True	78.5511	193	1437	95	below_threshold
Halobacillus andaensis	strain=DSM 25866	GCA_017874135.1	1176239	1176239	type	True	78.4463	320	1437	95	below_threshold
Halobacillus andaensis	strain=CGMCC 1.12153	GCA_014636475.1	1176239	1176239	type	True	78.4449	320	1437	95	below_threshold
Halobacillus trueperi	strain=KCTC 3686	GCA_003386945.1	156205	156205	type	True	77.9542	156	1437	95	below_threshold
Halobacillus dabanensis	strain=CGMCC 1.3704	GCA_900114165.1	240302	240302	type	True	77.831	149	1437	95	below_threshold
Halobacillus faecis	strain=NBRC 103569	GCA_007991335.1	360184	360184	type	True	77.7412	146	1437	95	below_threshold
Sediminibacillus terrae	strain=JSM 102062	GCA_009602435.1	1562106	1562106	type	True	77.6672	64	1437	95	below_threshold
Halobacillus aidingensis	strain=CGMCC 1.3703	GCA_900104185.1	240303	240303	type	True	77.6642	184	1437	95	below_threshold
Aquibacillus sediminis	strain=BH258	GCA_005870085.1	2574734	2574734	type	True	77.5928	73	1437	95	below_threshold
Halobacillus locisalis	strain=KCTC 3788	GCA_013694105.1	220753	220753	type	True	77.327	126	1437	95	below_threshold
Thalassobacillus devorans	strain=CCM 7282	GCA_014635125.1	279813	279813	type	True	77.0414	134	1437	95	below_threshold
Thalassobacillus devorans	strain=CECT 7046	GCA_011761345.1	279813	279813	type	True	77.0298	133	1437	95	below_threshold
Aquibacillus kalidii	strain=HU2P27	GCA_014280935.1	2762597	2762597	type	True	76.8471	52	1437	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:07,031] [INFO] DFAST Taxonomy check result was written to GCF_900166625.1_PRJEB19420_genomic.fna/tc_result.tsv
[2024-01-24 12:15:07,032] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:07,032] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:07,032] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c91a00c-635c-4741-89ad-f9e726fdd85b/dqc_reference/checkm_data
[2024-01-24 12:15:07,034] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:07,077] [INFO] Task started: CheckM
[2024-01-24 12:15:07,078] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900166625.1_PRJEB19420_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900166625.1_PRJEB19420_genomic.fna/checkm_input GCF_900166625.1_PRJEB19420_genomic.fna/checkm_result
[2024-01-24 12:15:39,443] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:39,445] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:39,475] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:39,476] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:39,476] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900166625.1_PRJEB19420_genomic.fna/markers.fasta)
[2024-01-24 12:15:39,477] [INFO] Task started: Blastn
[2024-01-24 12:15:39,477] [INFO] Running command: blastn -query GCF_900166625.1_PRJEB19420_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c91a00c-635c-4741-89ad-f9e726fdd85b/dqc_reference/reference_markers_gtdb.fasta -out GCF_900166625.1_PRJEB19420_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:40,258] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:40,262] [INFO] Selected 26 target genomes.
[2024-01-24 12:15:40,263] [INFO] Target genome list was writen to GCF_900166625.1_PRJEB19420_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:40,278] [INFO] Task started: fastANI
[2024-01-24 12:15:40,278] [INFO] Running command: fastANI --query /var/lib/cwl/stge8a61a1a-906d-40ca-a0ff-c44f4573802b/GCF_900166625.1_PRJEB19420_genomic.fna.gz --refList GCF_900166625.1_PRJEB19420_genomic.fna/target_genomes_gtdb.txt --output GCF_900166625.1_PRJEB19420_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:58,902] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:58,921] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:58,921] [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_900166625.1	s__Halobacillus_A massiliensis	99.9982	1418	1437	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	conclusive
GCF_902809865.1	s__Halobacillus_A sp902809865	81.1926	762	1437	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_000469135.2	s__Halobacillus sp001592845	79.3301	134	1437	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_009858175.1	s__Pontibacillus sp009858175	79.276	75	1437	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_900240285.1	s__Halobacillus_A sp900240285	78.8018	294	1437	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_014636475.1	s__Halobacillus_A andaensis	78.4331	321	1437	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_900176565.1	s__Thalassobacillus devorans_A	78.2639	120	1437	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_016908235.1	s__Halobacillus_A seohaensis	78.0916	230	1437	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_900166655.1	s__Halobacillus_A hunanensis	78.0273	190	1437	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_007991335.1	s__Halobacillus faecis	77.7775	146	1437	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_009602435.1	s__Sediminibacillus terrae	77.6941	64	1437	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Sediminibacillus	95.0	99.15	99.14	0.93	0.93	3	-
GCF_005870085.1	s__BH258 sp005870085	77.674	71	1437	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__BH258	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104185.1	s__Halobacillus aidingensis	77.6619	183	1437	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_009856415.1	s__Halobacillus litoralis_C	77.6596	159	1437	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_010993965.1	s__Gracilibacillus sp010993965	77.6493	52	1437	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014280935.1	s__HU2P27 sp014280935	76.8547	52	1437	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__HU2P27	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003318295.1	s__Maribacillus taeanensis	76.2123	50	1437	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__UBA6769;g__Maribacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:58,923] [INFO] GTDB search result was written to GCF_900166625.1_PRJEB19420_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:58,924] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:58,928] [INFO] DFAST_QC result json was written to GCF_900166625.1_PRJEB19420_genomic.fna/dqc_result.json
[2024-01-24 12:15:58,928] [INFO] DFAST_QC completed!
[2024-01-24 12:15:58,928] [INFO] Total running time: 0h1m25s