[2024-01-25 20:02:20,515] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:02:20,519] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:02:20,519] [INFO] DQC Reference Directory: /var/lib/cwl/stgb30fa282-9a12-4761-bcdf-6370904a67f2/dqc_reference
[2024-01-25 20:02:21,677] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:02:21,678] [INFO] Task started: Prodigal
[2024-01-25 20:02:21,678] [INFO] Running command: gunzip -c /var/lib/cwl/stgae98ecb4-4d07-46e6-8332-d6ee4f63815a/GCF_024220175.1_ASM2422017v1_genomic.fna.gz | prodigal -d GCF_024220175.1_ASM2422017v1_genomic.fna/cds.fna -a GCF_024220175.1_ASM2422017v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:02:33,482] [INFO] Task succeeded: Prodigal
[2024-01-25 20:02:33,482] [INFO] Task started: HMMsearch
[2024-01-25 20:02:33,483] [INFO] Running command: hmmsearch --tblout GCF_024220175.1_ASM2422017v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb30fa282-9a12-4761-bcdf-6370904a67f2/dqc_reference/reference_markers.hmm GCF_024220175.1_ASM2422017v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:02:33,792] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:02:33,793] [INFO] Found 6/6 markers.
[2024-01-25 20:02:33,835] [INFO] Query marker FASTA was written to GCF_024220175.1_ASM2422017v1_genomic.fna/markers.fasta
[2024-01-25 20:02:33,835] [INFO] Task started: Blastn
[2024-01-25 20:02:33,835] [INFO] Running command: blastn -query GCF_024220175.1_ASM2422017v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb30fa282-9a12-4761-bcdf-6370904a67f2/dqc_reference/reference_markers.fasta -out GCF_024220175.1_ASM2422017v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:02:34,567] [INFO] Task succeeded: Blastn
[2024-01-25 20:02:34,570] [INFO] Selected 11 target genomes.
[2024-01-25 20:02:34,570] [INFO] Target genome list was writen to GCF_024220175.1_ASM2422017v1_genomic.fna/target_genomes.txt
[2024-01-25 20:02:34,575] [INFO] Task started: fastANI
[2024-01-25 20:02:34,575] [INFO] Running command: fastANI --query /var/lib/cwl/stgae98ecb4-4d07-46e6-8332-d6ee4f63815a/GCF_024220175.1_ASM2422017v1_genomic.fna.gz --refList GCF_024220175.1_ASM2422017v1_genomic.fna/target_genomes.txt --output GCF_024220175.1_ASM2422017v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:02:48,767] [INFO] Task succeeded: fastANI
[2024-01-25 20:02:48,767] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb30fa282-9a12-4761-bcdf-6370904a67f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:02:48,767] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb30fa282-9a12-4761-bcdf-6370904a67f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:02:48,775] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:02:48,775] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:02:48,775] [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
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	79.2831	818	1712	95	below_threshold
Baekduia soli	strain=BR7-21	GCA_007970665.1	496014	496014	type	True	78.5134	681	1712	95	below_threshold
Capillimicrobium parvum	strain=0166_1	GCA_021172045.1	2884022	2884022	type	True	77.8505	703	1712	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	77.5342	694	1712	95	below_threshold
Patulibacter medicamentivorans	strain=I11	GCA_000240225.2	1097667	1097667	type	True	77.3117	601	1712	95	below_threshold
Conexibacter woesei	strain=DSM 14684	GCA_000025265.1	191495	191495	type	True	77.2662	730	1712	95	below_threshold
Patulibacter minatonensis	strain=DSM 18081	GCA_000519325.1	298163	298163	type	True	77.2365	666	1712	95	below_threshold
Patulibacter americanus	strain=DSM 16676	GCA_000420025.1	588672	588672	type	True	77.0554	560	1712	95	below_threshold
Solirubrobacter pauli	strain=DSM 14954	GCA_003633755.1	166793	166793	type	True	77.0402	669	1712	95	below_threshold
Agrococcus carbonis	strain=DSM 22965	GCA_900104705.1	684552	684552	type	True	75.2669	332	1712	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	75.0938	250	1712	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:02:48,777] [INFO] DFAST Taxonomy check result was written to GCF_024220175.1_ASM2422017v1_genomic.fna/tc_result.tsv
[2024-01-25 20:02:48,777] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:02:48,777] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:02:48,778] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb30fa282-9a12-4761-bcdf-6370904a67f2/dqc_reference/checkm_data
[2024-01-25 20:02:48,778] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:02:48,828] [INFO] Task started: CheckM
[2024-01-25 20:02:48,828] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024220175.1_ASM2422017v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024220175.1_ASM2422017v1_genomic.fna/checkm_input GCF_024220175.1_ASM2422017v1_genomic.fna/checkm_result
[2024-01-25 20:03:50,521] [INFO] Task succeeded: CheckM
[2024-01-25 20:03:50,523] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:03:50,551] [INFO] ===== Completeness check finished =====
[2024-01-25 20:03:50,552] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:03:50,553] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024220175.1_ASM2422017v1_genomic.fna/markers.fasta)
[2024-01-25 20:03:50,553] [INFO] Task started: Blastn
[2024-01-25 20:03:50,553] [INFO] Running command: blastn -query GCF_024220175.1_ASM2422017v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb30fa282-9a12-4761-bcdf-6370904a67f2/dqc_reference/reference_markers_gtdb.fasta -out GCF_024220175.1_ASM2422017v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:51,883] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:51,886] [INFO] Selected 19 target genomes.
[2024-01-25 20:03:51,886] [INFO] Target genome list was writen to GCF_024220175.1_ASM2422017v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:03:51,911] [INFO] Task started: fastANI
[2024-01-25 20:03:51,911] [INFO] Running command: fastANI --query /var/lib/cwl/stgae98ecb4-4d07-46e6-8332-d6ee4f63815a/GCF_024220175.1_ASM2422017v1_genomic.fna.gz --refList GCF_024220175.1_ASM2422017v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024220175.1_ASM2422017v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:04:08,539] [INFO] Task succeeded: fastANI
[2024-01-25 20:04:08,552] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:04:08,553] [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_003044185.1	s__SEOHO-28 sp003044185	79.3229	813	1712	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__SEOHO-28	95.0	98.17	98.17	0.92	0.92	2	-
GCA_013695395.1	s__SEOHO-28 sp013695395	79.263	415	1712	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__SEOHO-28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806205.1	s__SEOHO-28 sp902806205	78.7653	512	1712	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__SEOHO-28	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017084525.1	s__Baekduia sp017084525	78.747	715	1712	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Baekduia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009699245.1	s__F1-60-MAGs163 sp009699245	78.5047	348	1712	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__F1-60-MAGs163	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007970665.1	s__Baekduia soli	78.4901	685	1712	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Baekduia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013813955.1	s__CADCVQ01 sp013813955	78.4524	276	1712	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__CADCVQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016215085.1	s__Baekduia sp016215085	78.2952	536	1712	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Baekduia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882425.1	s__F1-60-MAGs163 sp017882425	78.1769	454	1712	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__F1-60-MAGs163	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000424625.1	s__Baekduia woesei_A	78.0226	730	1712	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Baekduia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806175.1	s__CADCVQ01 sp902806175	77.9967	540	1712	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__CADCVQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013815355.1	s__Palsa-744 sp013815355	77.6395	277	1712	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Palsa-744	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199525.1	s__Conexibacter arvalis	77.5154	701	1712	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Conexibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806215.1	s__CADCVT01 sp902806215	77.4951	494	1712	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__CADCVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017916475.1	s__Patulibacter sp017916475	77.0927	602	1712	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Patulibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005788585.1	s__SYBY01 sp005788585	77.0241	436	1712	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__SYBY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018263295.1	s__RHKX01 sp018263295	76.7752	319	1712	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__70-9;g__RHKX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015655225.1	s__Conexibacter sp015655225	76.4908	395	1712	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Conexibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016861045.1	s__RHKX01 sp008363375	76.4248	405	1712	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__70-9;g__RHKX01	95.0	99.36	99.36	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:04:08,554] [INFO] GTDB search result was written to GCF_024220175.1_ASM2422017v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:04:08,561] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:04:08,565] [INFO] DFAST_QC result json was written to GCF_024220175.1_ASM2422017v1_genomic.fna/dqc_result.json
[2024-01-25 20:04:08,565] [INFO] DFAST_QC completed!
[2024-01-25 20:04:08,565] [INFO] Total running time: 0h1m48s