[2024-01-25 18:06:50,782] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:06:50,786] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:06:50,786] [INFO] DQC Reference Directory: /var/lib/cwl/stg628e5927-b852-4db0-8964-6cf98add7b2c/dqc_reference
[2024-01-25 18:06:52,083] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:06:52,084] [INFO] Task started: Prodigal
[2024-01-25 18:06:52,084] [INFO] Running command: gunzip -c /var/lib/cwl/stge0dc1a55-63e9-428f-9855-0ae4beb6776f/GCF_011382985.1_ASM1138298v1_genomic.fna.gz | prodigal -d GCF_011382985.1_ASM1138298v1_genomic.fna/cds.fna -a GCF_011382985.1_ASM1138298v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:07:01,155] [INFO] Task succeeded: Prodigal
[2024-01-25 18:07:01,156] [INFO] Task started: HMMsearch
[2024-01-25 18:07:01,156] [INFO] Running command: hmmsearch --tblout GCF_011382985.1_ASM1138298v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg628e5927-b852-4db0-8964-6cf98add7b2c/dqc_reference/reference_markers.hmm GCF_011382985.1_ASM1138298v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:07:01,353] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:07:01,354] [INFO] Found 6/6 markers.
[2024-01-25 18:07:01,380] [INFO] Query marker FASTA was written to GCF_011382985.1_ASM1138298v1_genomic.fna/markers.fasta
[2024-01-25 18:07:01,381] [INFO] Task started: Blastn
[2024-01-25 18:07:01,381] [INFO] Running command: blastn -query GCF_011382985.1_ASM1138298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg628e5927-b852-4db0-8964-6cf98add7b2c/dqc_reference/reference_markers.fasta -out GCF_011382985.1_ASM1138298v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:02,016] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:02,020] [INFO] Selected 19 target genomes.
[2024-01-25 18:07:02,021] [INFO] Target genome list was writen to GCF_011382985.1_ASM1138298v1_genomic.fna/target_genomes.txt
[2024-01-25 18:07:02,034] [INFO] Task started: fastANI
[2024-01-25 18:07:02,034] [INFO] Running command: fastANI --query /var/lib/cwl/stge0dc1a55-63e9-428f-9855-0ae4beb6776f/GCF_011382985.1_ASM1138298v1_genomic.fna.gz --refList GCF_011382985.1_ASM1138298v1_genomic.fna/target_genomes.txt --output GCF_011382985.1_ASM1138298v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:07:12,747] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:12,748] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg628e5927-b852-4db0-8964-6cf98add7b2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:07:12,748] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg628e5927-b852-4db0-8964-6cf98add7b2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:07:12,759] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:07:12,759] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:07:12,759] [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
Leucobacter coleopterorum	strain=HDW9A	GCA_011382985.1	2714933	2714933	type	True	100.0	1071	1071	95	conclusive
Leucobacter viscericola	strain=HDW9C	GCA_011299575.1	2714935	2714935	type	True	84.7784	755	1071	95	below_threshold
Leucobacter insecticola	strain=HDW9B	GCA_011382965.1	2714934	2714934	type	True	79.2245	325	1071	95	below_threshold
Leucobacter chironomi	strain=DSM 19883	GCA_000421845.1	491918	491918	type	True	79.0031	303	1071	95	below_threshold
Leucobacter luti	strain=RF6	GCA_016758235.1	340320	340320	suspected-type	True	78.8053	323	1071	95	below_threshold
Leucobacter musarum subsp. musarum	strain=CBX152	GCA_001273845.1	1461261	1930747	type	True	78.7365	273	1071	95	below_threshold
Leucobacter muris	strain=DSM 101948	GCA_004028235.1	1935379	1935379	type	True	78.6586	331	1071	95	below_threshold
Leucobacter luti	strain=RF6	GCA_004217175.1	340320	340320	suspected-type	True	78.6387	325	1071	95	below_threshold
Leucobacter japonicus	strain=CBX130	GCA_001273855.1	1461259	1461259	type	True	78.6269	273	1071	95	below_threshold
Leucobacter ruminantium	strain=A2	GCA_017565705.1	1289170	1289170	type	True	78.5622	263	1071	95	below_threshold
Leucobacter celer subsp. astrifaciens	strain=CBX151	GCA_001273835.1	1461260	668625	type	True	78.5597	341	1071	95	below_threshold
Leucobacter exalbidus	strain=DSM 22850	GCA_017834145.1	662960	662960	type	True	78.4643	255	1071	95	below_threshold
Leucobacter komagatae	strain=DSM 8803	GCA_006716085.1	55969	55969	type	True	78.4502	241	1071	95	below_threshold
Leucobacter salsicius	strain=M1-8	GCA_000350525.1	664638	664638	type	True	78.2492	256	1071	95	below_threshold
Microcella putealis	strain=CV2	GCA_004216575.1	337005	337005	type	True	77.8578	74	1071	95	below_threshold
Microcella putealis	strain=DSM 19627	GCA_006716545.1	337005	337005	type	True	77.7641	80	1071	95	below_threshold
Marisediminicola antarctica	strain=ZS314	GCA_009930795.1	674079	674079	type	True	77.1738	82	1071	95	below_threshold
Agrococcus lahaulensis	strain=DSM 17612	GCA_000425105.1	341722	341722	type	True	77.1436	100	1071	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:07:12,764] [INFO] DFAST Taxonomy check result was written to GCF_011382985.1_ASM1138298v1_genomic.fna/tc_result.tsv
[2024-01-25 18:07:12,765] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:07:12,765] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:07:12,765] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg628e5927-b852-4db0-8964-6cf98add7b2c/dqc_reference/checkm_data
[2024-01-25 18:07:12,766] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:07:12,800] [INFO] Task started: CheckM
[2024-01-25 18:07:12,800] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011382985.1_ASM1138298v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011382985.1_ASM1138298v1_genomic.fna/checkm_input GCF_011382985.1_ASM1138298v1_genomic.fna/checkm_result
[2024-01-25 18:07:41,808] [INFO] Task succeeded: CheckM
[2024-01-25 18:07:41,809] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:07:41,835] [INFO] ===== Completeness check finished =====
[2024-01-25 18:07:41,836] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:07:41,836] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011382985.1_ASM1138298v1_genomic.fna/markers.fasta)
[2024-01-25 18:07:41,836] [INFO] Task started: Blastn
[2024-01-25 18:07:41,836] [INFO] Running command: blastn -query GCF_011382985.1_ASM1138298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg628e5927-b852-4db0-8964-6cf98add7b2c/dqc_reference/reference_markers_gtdb.fasta -out GCF_011382985.1_ASM1138298v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:42,797] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:42,800] [INFO] Selected 20 target genomes.
[2024-01-25 18:07:42,800] [INFO] Target genome list was writen to GCF_011382985.1_ASM1138298v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:07:42,817] [INFO] Task started: fastANI
[2024-01-25 18:07:42,817] [INFO] Running command: fastANI --query /var/lib/cwl/stge0dc1a55-63e9-428f-9855-0ae4beb6776f/GCF_011382985.1_ASM1138298v1_genomic.fna.gz --refList GCF_011382985.1_ASM1138298v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011382985.1_ASM1138298v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:07:55,251] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:55,263] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:07:55,264] [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_011382985.1	s__Leucobacter coleopterorum	100.0	1071	1071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011299575.1	s__Leucobacter viscericola	84.7784	755	1071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011382965.1	s__Leucobacter insecticola	79.2309	323	1071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421845.1	s__Leucobacter chironomi	78.958	302	1071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004028235.1	s__Leucobacter muris	78.6703	331	1071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	98.77	98.77	0.90	0.90	2	-
GCF_000633415.1	s__Leucobacter sp000633415	78.6602	305	1071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217175.1	s__Leucobacter luti	78.6387	325	1071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001273835.1	s__Leucobacter celer	78.5763	339	1071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017565705.1	s__Leucobacter ruminantium	78.5622	263	1071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003917135.1	s__Leucobacter chromiireducens_A	78.5228	294	1071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003569785.1	s__Leucobacter sp003569785	78.4938	303	1071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716085.1	s__Leucobacter komagatae	78.4667	240	1071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000980875.1	s__Leucobacter sp000980875	78.431	284	1071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900163635.1	s__Leucobacter sp900163635	78.4058	228	1071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016522535.1	s__Leucobacter sp016522535	78.3557	259	1071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017990305.1	s__Leucobacter sp017990305	78.212	123	1071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339635.1	s__Leucobacter luti_A	78.1445	226	1071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	98.22	98.22	0.92	0.92	2	-
GCF_017161405.1	s__Cx-87 sp014529995	77.9758	199	1071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cx-87	95.0	98.78	98.17	0.90	0.87	4	-
GCF_014530035.1	s__Leucobacter sp014530035	77.8693	167	1071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009765225.1	s__Leifsonia sp009765225	76.9473	98	1071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:07:55,265] [INFO] GTDB search result was written to GCF_011382985.1_ASM1138298v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:07:55,266] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:07:55,271] [INFO] DFAST_QC result json was written to GCF_011382985.1_ASM1138298v1_genomic.fna/dqc_result.json
[2024-01-25 18:07:55,271] [INFO] DFAST_QC completed!
[2024-01-25 18:07:55,271] [INFO] Total running time: 0h1m4s