[2024-01-24 11:44:38,179] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:38,182] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:38,182] [INFO] DQC Reference Directory: /var/lib/cwl/stgb18cbf4d-ab25-4c85-a5c8-2011f5d96af1/dqc_reference
[2024-01-24 11:44:41,487] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:41,488] [INFO] Task started: Prodigal
[2024-01-24 11:44:41,488] [INFO] Running command: gunzip -c /var/lib/cwl/stgd7de9759-f0ac-48ab-acd3-0344e98d27fa/GCF_016908295.1_ASM1690829v1_genomic.fna.gz | prodigal -d GCF_016908295.1_ASM1690829v1_genomic.fna/cds.fna -a GCF_016908295.1_ASM1690829v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:51,359] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:51,360] [INFO] Task started: HMMsearch
[2024-01-24 11:44:51,360] [INFO] Running command: hmmsearch --tblout GCF_016908295.1_ASM1690829v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb18cbf4d-ab25-4c85-a5c8-2011f5d96af1/dqc_reference/reference_markers.hmm GCF_016908295.1_ASM1690829v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:51,642] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:51,643] [INFO] Found 6/6 markers.
[2024-01-24 11:44:51,679] [INFO] Query marker FASTA was written to GCF_016908295.1_ASM1690829v1_genomic.fna/markers.fasta
[2024-01-24 11:44:51,680] [INFO] Task started: Blastn
[2024-01-24 11:44:51,680] [INFO] Running command: blastn -query GCF_016908295.1_ASM1690829v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb18cbf4d-ab25-4c85-a5c8-2011f5d96af1/dqc_reference/reference_markers.fasta -out GCF_016908295.1_ASM1690829v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:52,277] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:52,281] [INFO] Selected 24 target genomes.
[2024-01-24 11:44:52,282] [INFO] Target genome list was writen to GCF_016908295.1_ASM1690829v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:52,386] [INFO] Task started: fastANI
[2024-01-24 11:44:52,386] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7de9759-f0ac-48ab-acd3-0344e98d27fa/GCF_016908295.1_ASM1690829v1_genomic.fna.gz --refList GCF_016908295.1_ASM1690829v1_genomic.fna/target_genomes.txt --output GCF_016908295.1_ASM1690829v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:45:07,488] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:07,489] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb18cbf4d-ab25-4c85-a5c8-2011f5d96af1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:45:07,490] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb18cbf4d-ab25-4c85-a5c8-2011f5d96af1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:45:07,507] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:45:07,507] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:45:07,507] [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
Thalassobacillus pellis	strain=DSM 22784	GCA_016908295.1	748008	748008	type	True	100.0	1341	1341	95	conclusive
Thalassobacillus devorans	strain=CECT 7046	GCA_011761345.1	279813	279813	type	True	78.3778	285	1341	95	below_threshold
Thalassobacillus devorans	strain=CCM 7282	GCA_014635125.1	279813	279813	type	True	78.3546	290	1341	95	below_threshold
Thalassobacillus cyri	strain=CCM7597	GCA_900107755.1	571932	571932	type	True	78.2799	315	1341	95	below_threshold
Halobacillus faecis	strain=NBRC 103569	GCA_007991335.1	360184	360184	type	True	77.4634	92	1341	95	below_threshold
Halobacillus halophilus	strain=type strain: DSM 2266	GCA_000284515.1	1570	1570	type	True	77.4597	111	1341	95	below_threshold
Halobacillus salinus	strain=HSL-3	GCA_004684905.1	192814	192814	type	True	77.3997	83	1341	95	below_threshold
Halobacillus karajensis	strain=DSM 14948	GCA_900108515.1	195088	195088	type	True	77.3884	136	1341	95	below_threshold
Halobacillus locisalis	strain=KCTC 3788	GCA_013694105.1	220753	220753	type	True	77.2808	76	1341	95	below_threshold
Halobacillus litoralis	strain=SL-4	GCA_009856445.1	45668	45668	suspected-type	True	76.9254	116	1341	95	below_threshold
Halobacillus kuroshimensis	strain=DSM 18393	GCA_000425705.1	302481	302481	type	True	76.768	101	1341	95	below_threshold
Gracilibacillus ureilyticus	strain=CGMCC 1.7727	GCA_900111195.1	531814	531814	type	True	76.6167	51	1341	95	below_threshold
Aquibacillus saliphilus	strain=KHM2	GCA_020404745.1	1909422	1909422	type	True	76.4225	53	1341	95	below_threshold
Gracilibacillus oryzae	strain=TD8	GCA_009498735.1	1672701	1672701	type	True	76.2306	52	1341	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:45:07,509] [INFO] DFAST Taxonomy check result was written to GCF_016908295.1_ASM1690829v1_genomic.fna/tc_result.tsv
[2024-01-24 11:45:07,510] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:45:07,510] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:45:07,510] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb18cbf4d-ab25-4c85-a5c8-2011f5d96af1/dqc_reference/checkm_data
[2024-01-24 11:45:07,511] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:45:07,552] [INFO] Task started: CheckM
[2024-01-24 11:45:07,552] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016908295.1_ASM1690829v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016908295.1_ASM1690829v1_genomic.fna/checkm_input GCF_016908295.1_ASM1690829v1_genomic.fna/checkm_result
[2024-01-24 11:45:41,763] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:41,765] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:41,785] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:41,785] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:41,785] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016908295.1_ASM1690829v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:41,786] [INFO] Task started: Blastn
[2024-01-24 11:45:41,786] [INFO] Running command: blastn -query GCF_016908295.1_ASM1690829v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb18cbf4d-ab25-4c85-a5c8-2011f5d96af1/dqc_reference/reference_markers_gtdb.fasta -out GCF_016908295.1_ASM1690829v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:42,602] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:42,606] [INFO] Selected 21 target genomes.
[2024-01-24 11:45:42,607] [INFO] Target genome list was writen to GCF_016908295.1_ASM1690829v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:42,623] [INFO] Task started: fastANI
[2024-01-24 11:45:42,623] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7de9759-f0ac-48ab-acd3-0344e98d27fa/GCF_016908295.1_ASM1690829v1_genomic.fna.gz --refList GCF_016908295.1_ASM1690829v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016908295.1_ASM1690829v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:57,408] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:57,426] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:57,426] [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_016908295.1	s__Thalassobacillus pellis	100.0	1341	1341	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Thalassobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000496835.1	s__Thalassobacillus devorans_B	78.672	297	1341	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_011761345.1	s__Thalassobacillus devorans	78.3923	284	1341	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Thalassobacillus	95.0	100.00	100.00	1.00	1.00	4	-
GCF_900176565.1	s__Thalassobacillus devorans_A	78.3207	291	1341	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_900107755.1	s__Thalassobacillus cyri	78.3181	312	1341	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_000284515.1	s__Halobacillus halophilus	77.5911	109	1341	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_000821245.2	s__Sediminibacillus senegalensis	77.4279	78	1341	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Sediminibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108515.1	s__Halobacillus karajensis	77.3884	136	1341	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_013694105.1	s__Halobacillus locisalis	77.2808	76	1341	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	77.1167	129	1341	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	77.0468	98	1341	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	76.8087	94	1341	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_900162695.1	s__Lentibacillus siamensis	76.6592	59	1341	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111195.1	s__Gracilibacillus ureilyticus	76.6167	51	1341	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_009498735.1	s__Gracilibacillus sp009498735	76.2306	52	1341	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_000377765.1	s__Gracilibacillus lacisalsi	76.2181	53	1341	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	95.88	95.36	0.83	0.81	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:57,428] [INFO] GTDB search result was written to GCF_016908295.1_ASM1690829v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:57,428] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:57,432] [INFO] DFAST_QC result json was written to GCF_016908295.1_ASM1690829v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:57,432] [INFO] DFAST_QC completed!
[2024-01-24 11:45:57,432] [INFO] Total running time: 0h1m19s