[2024-01-24 12:22:34,052] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:34,055] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:34,055] [INFO] DQC Reference Directory: /var/lib/cwl/stgd7840256-496e-410c-a72b-d797a96a2e7f/dqc_reference
[2024-01-24 12:22:35,711] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:35,712] [INFO] Task started: Prodigal
[2024-01-24 12:22:35,712] [INFO] Running command: gunzip -c /var/lib/cwl/stg89efd7d6-2b30-4ce0-af63-052aa2e2733f/GCF_021049245.1_ASM2104924v1_genomic.fna.gz | prodigal -d GCF_021049245.1_ASM2104924v1_genomic.fna/cds.fna -a GCF_021049245.1_ASM2104924v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:43,258] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:43,258] [INFO] Task started: HMMsearch
[2024-01-24 12:22:43,258] [INFO] Running command: hmmsearch --tblout GCF_021049245.1_ASM2104924v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd7840256-496e-410c-a72b-d797a96a2e7f/dqc_reference/reference_markers.hmm GCF_021049245.1_ASM2104924v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:43,468] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:43,471] [INFO] Found 6/6 markers.
[2024-01-24 12:22:43,501] [INFO] Query marker FASTA was written to GCF_021049245.1_ASM2104924v1_genomic.fna/markers.fasta
[2024-01-24 12:22:43,501] [INFO] Task started: Blastn
[2024-01-24 12:22:43,502] [INFO] Running command: blastn -query GCF_021049245.1_ASM2104924v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7840256-496e-410c-a72b-d797a96a2e7f/dqc_reference/reference_markers.fasta -out GCF_021049245.1_ASM2104924v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:44,041] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:44,043] [INFO] Selected 19 target genomes.
[2024-01-24 12:22:44,044] [INFO] Target genome list was writen to GCF_021049245.1_ASM2104924v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:44,092] [INFO] Task started: fastANI
[2024-01-24 12:22:44,092] [INFO] Running command: fastANI --query /var/lib/cwl/stg89efd7d6-2b30-4ce0-af63-052aa2e2733f/GCF_021049245.1_ASM2104924v1_genomic.fna.gz --refList GCF_021049245.1_ASM2104924v1_genomic.fna/target_genomes.txt --output GCF_021049245.1_ASM2104924v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:55,595] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:55,596] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd7840256-496e-410c-a72b-d797a96a2e7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:55,596] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd7840256-496e-410c-a72b-d797a96a2e7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:55,606] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:22:55,606] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:22:55,607] [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
Radiobacillus deserti	strain=TKL69	GCA_007301515.1	2594883	2594883	type	True	80.8732	637	1343	95	below_threshold
Halobacillus aidingensis	strain=CGMCC 1.3703	GCA_900104185.1	240303	240303	type	True	77.6759	55	1343	95	below_threshold
Halolactibacillus miurensis	strain=DSM 17074	GCA_900116255.1	306541	306541	type	True	77.6222	51	1343	95	below_threshold
Aquibacillus kalidii	strain=HU2P27	GCA_014280935.1	2762597	2762597	type	True	77.5708	152	1343	95	below_threshold
Aquibacillus sediminis	strain=BH258	GCA_005870085.1	2574734	2574734	type	True	77.5297	149	1343	95	below_threshold
Gracilibacillus lacisalsi	strain=DSM 19029	GCA_000377765.1	393087	393087	type	True	77.4922	92	1343	95	below_threshold
Aquibacillus albus	strain=DSM 23711	GCA_016908325.1	1168171	1168171	type	True	77.4772	144	1343	95	below_threshold
Pelagirhabdus alkalitolerans	strain=S5	GCA_900096905.1	1612202	1612202	type	True	77.4099	59	1343	95	below_threshold
Gracilibacillus kekensis	strain=CGMCC 1.10681	GCA_900143085.1	1027249	1027249	type	True	77.2913	90	1343	95	below_threshold
Paraliobacillus ryukyuensis	strain=DSM 15140	GCA_003315295.1	200904	200904	type	True	77.2745	98	1343	95	below_threshold
Virgibacillus profundi	strain=P3-H5	GCA_002287375.1	2024555	2024555	type	True	77.1861	73	1343	95	below_threshold
Virgibacillus pantothenticus	strain=DSM 26	GCA_001189575.1	1473	1473	type	True	76.9749	68	1343	95	below_threshold
Pontibacillus litoralis	strain=JSM 072002	GCA_000775615.1	516703	516703	type	True	76.9556	61	1343	95	below_threshold
Paraliobacillus sediminis	strain=126C4	GCA_003426055.1	1885916	1885916	type	True	76.9049	75	1343	95	below_threshold
Virgibacillus pantothenticus	strain=DSM 26	GCA_900156795.1	1473	1473	type	True	76.7982	67	1343	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:55,608] [INFO] DFAST Taxonomy check result was written to GCF_021049245.1_ASM2104924v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:55,609] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:55,609] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:55,609] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd7840256-496e-410c-a72b-d797a96a2e7f/dqc_reference/checkm_data
[2024-01-24 12:22:55,610] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:55,651] [INFO] Task started: CheckM
[2024-01-24 12:22:55,651] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021049245.1_ASM2104924v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021049245.1_ASM2104924v1_genomic.fna/checkm_input GCF_021049245.1_ASM2104924v1_genomic.fna/checkm_result
[2024-01-24 12:23:21,769] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:21,770] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:21,785] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:21,785] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:21,785] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021049245.1_ASM2104924v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:21,786] [INFO] Task started: Blastn
[2024-01-24 12:23:21,786] [INFO] Running command: blastn -query GCF_021049245.1_ASM2104924v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7840256-496e-410c-a72b-d797a96a2e7f/dqc_reference/reference_markers_gtdb.fasta -out GCF_021049245.1_ASM2104924v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:22,517] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:22,520] [INFO] Selected 24 target genomes.
[2024-01-24 12:23:22,520] [INFO] Target genome list was writen to GCF_021049245.1_ASM2104924v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:22,533] [INFO] Task started: fastANI
[2024-01-24 12:23:22,533] [INFO] Running command: fastANI --query /var/lib/cwl/stg89efd7d6-2b30-4ce0-af63-052aa2e2733f/GCF_021049245.1_ASM2104924v1_genomic.fna.gz --refList GCF_021049245.1_ASM2104924v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021049245.1_ASM2104924v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:38,582] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:38,603] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:23:38,603] [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_007301515.1	s__Radiobacillus deserti	80.9023	636	1343	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Radiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000750635.1	s__Oceanobacillus jeddahense	79.1375	65	1343	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003176895.1	s__Gracilibacillus dipsosauri	77.8271	78	1343	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	99.23	99.13	0.93	0.92	3	-
GCF_001368815.1	s__Paraliobacillus sp001368815	77.8161	81	1343	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000821245.2	s__Sediminibacillus senegalensis	77.8015	119	1343	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_900116255.1	s__Halolactibacillus miurensis	77.6875	50	1343	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Halolactibacillus	95.0	99.76	99.51	0.98	0.95	3	-
GCF_014280935.1	s__HU2P27 sp014280935	77.5619	152	1343	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_000377765.1	s__Gracilibacillus lacisalsi	77.5197	92	1343	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	95.88	95.36	0.83	0.81	4	-
GCF_016908325.1	s__Aquibacillus albus	77.5185	139	1343	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Aquibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111195.1	s__Gracilibacillus ureilyticus	77.4843	75	1343	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_900096905.1	s__Pelagirhabdus alkalitolerans	77.4099	59	1343	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Pelagirhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315295.1	s__Paraliobacillus ryukyuensis	77.2745	98	1343	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	98.18	98.18	0.92	0.92	2	-
GCF_002287375.1	s__Virgibacillus_G profundi	77.2647	70	1343	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_G	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003369565.1	s__Oceanobacillus chungangensis	77.1149	77	1343	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002584535.1	s__Bacillus_A cereus_AW	77.0102	52	1343	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.12	98.24	0.93	0.90	5	-
GCF_000775615.1	s__Pontibacillus litoralis	76.9556	61	1343	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_016909015.1	s__Gracilibacillus alcaliphilus	76.954	72	1343	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_003612345.1	s__Virgibacillus sp003612345	76.8309	61	1343	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	100.00	100.00	1.00	0.99	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:38,606] [INFO] GTDB search result was written to GCF_021049245.1_ASM2104924v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:38,607] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:38,610] [INFO] DFAST_QC result json was written to GCF_021049245.1_ASM2104924v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:38,610] [INFO] DFAST_QC completed!
[2024-01-24 12:23:38,610] [INFO] Total running time: 0h1m5s