[2024-01-24 14:55:08,463] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:08,466] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:08,467] [INFO] DQC Reference Directory: /var/lib/cwl/stgf972a431-a400-4ad5-af96-3456a1036139/dqc_reference
[2024-01-24 14:55:10,010] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:10,011] [INFO] Task started: Prodigal
[2024-01-24 14:55:10,011] [INFO] Running command: gunzip -c /var/lib/cwl/stg6218e770-8136-4cea-9957-cdbb707ed08f/GCF_013307245.1_ASM1330724v1_genomic.fna.gz | prodigal -d GCF_013307245.1_ASM1330724v1_genomic.fna/cds.fna -a GCF_013307245.1_ASM1330724v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:15,183] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:15,184] [INFO] Task started: HMMsearch
[2024-01-24 14:55:15,184] [INFO] Running command: hmmsearch --tblout GCF_013307245.1_ASM1330724v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf972a431-a400-4ad5-af96-3456a1036139/dqc_reference/reference_markers.hmm GCF_013307245.1_ASM1330724v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:15,438] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:15,440] [INFO] Found 6/6 markers.
[2024-01-24 14:55:15,464] [INFO] Query marker FASTA was written to GCF_013307245.1_ASM1330724v1_genomic.fna/markers.fasta
[2024-01-24 14:55:15,465] [INFO] Task started: Blastn
[2024-01-24 14:55:15,465] [INFO] Running command: blastn -query GCF_013307245.1_ASM1330724v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf972a431-a400-4ad5-af96-3456a1036139/dqc_reference/reference_markers.fasta -out GCF_013307245.1_ASM1330724v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:16,067] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:16,071] [INFO] Selected 17 target genomes.
[2024-01-24 14:55:16,071] [INFO] Target genome list was writen to GCF_013307245.1_ASM1330724v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:16,097] [INFO] Task started: fastANI
[2024-01-24 14:55:16,097] [INFO] Running command: fastANI --query /var/lib/cwl/stg6218e770-8136-4cea-9957-cdbb707ed08f/GCF_013307245.1_ASM1330724v1_genomic.fna.gz --refList GCF_013307245.1_ASM1330724v1_genomic.fna/target_genomes.txt --output GCF_013307245.1_ASM1330724v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:24,207] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:24,207] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf972a431-a400-4ad5-af96-3456a1036139/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:24,207] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf972a431-a400-4ad5-af96-3456a1036139/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:24,225] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:55:24,225] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:24,226] [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
Polynucleobacter antarcticus	strain=LimPoW16	GCA_013307245.1	1743162	1743162	type	True	100.0	718	718	95	conclusive
Polynucleobacter arcticus	strain=UK-Long2-W17	GCA_013307205.1	1743165	1743165	type	True	79.6919	299	718	95	below_threshold
Polynucleobacter aenigmaticus	strain=MWH-K35W1	GCA_002206635.1	1743164	1743164	type	True	79.5915	310	718	95	below_threshold
Polynucleobacter duraquae	strain=MWH-MoK4	GCA_000973625.1	1835254	1835254	type	True	79.5674	328	718	95	below_threshold
Polynucleobacter hallstattensis	strain=MWH-Hall10	GCA_018881835.1	1855586	1855586	type	True	79.5415	331	718	95	below_threshold
Polynucleobacter corsicus	strain=AP-Melu-1000-A1	GCA_018688255.1	2081042	2081042	type	True	79.4936	338	718	95	below_threshold
Polynucleobacter bastaniensis	strain=AP-Basta-1000A-D1	GCA_018882205.1	2081039	2081039	type	True	79.4769	316	718	95	below_threshold
Polynucleobacter sinensis	strain=MWH-HuW1	GCA_001595985.1	1743157	1743157	type	True	79.3957	309	718	95	below_threshold
Polynucleobacter parvulilacunae	strain=Ross1-W9	GCA_018881715.1	1855631	1855631	type	True	79.2402	257	718	95	below_threshold
Polynucleobacter finlandensis	strain=MWH-Mekk-B1	GCA_018881755.1	1855894	1855894	type	True	79.1539	263	718	95	below_threshold
Polynucleobacter ibericus	strain=es-MAR-2	GCA_018687955.1	1819725	1819725	type	True	79.0826	272	718	95	below_threshold
Polynucleobacter hirudinilacicola	strain=MWH-EgelM1-30-B4	GCA_002192535.1	1743166	1743166	type	True	79.0762	271	718	95	below_threshold
Polynucleobacter campilacus	strain=MWH-Feld-100	GCA_002206625.1	1743163	1743163	type	True	79.0714	262	718	95	below_threshold
Polynucleobacter alcilacus	strain=UK-Pondora-W15	GCA_018881545.1	1819739	1819739	type	True	78.93	263	718	95	below_threshold
Polynucleobacter nymphae	strain=AP-Mumm-500A-B3	GCA_018882155.1	2081043	2081043	type	True	78.9213	252	718	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:24,228] [INFO] DFAST Taxonomy check result was written to GCF_013307245.1_ASM1330724v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:24,229] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:24,229] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:24,229] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf972a431-a400-4ad5-af96-3456a1036139/dqc_reference/checkm_data
[2024-01-24 14:55:24,231] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:24,256] [INFO] Task started: CheckM
[2024-01-24 14:55:24,256] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013307245.1_ASM1330724v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013307245.1_ASM1330724v1_genomic.fna/checkm_input GCF_013307245.1_ASM1330724v1_genomic.fna/checkm_result
[2024-01-24 14:55:46,963] [INFO] Task succeeded: CheckM
[2024-01-24 14:55:46,964] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:55:46,985] [INFO] ===== Completeness check finished =====
[2024-01-24 14:55:46,985] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:55:46,986] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013307245.1_ASM1330724v1_genomic.fna/markers.fasta)
[2024-01-24 14:55:46,986] [INFO] Task started: Blastn
[2024-01-24 14:55:46,986] [INFO] Running command: blastn -query GCF_013307245.1_ASM1330724v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf972a431-a400-4ad5-af96-3456a1036139/dqc_reference/reference_markers_gtdb.fasta -out GCF_013307245.1_ASM1330724v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:47,872] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:47,929] [INFO] Selected 20 target genomes.
[2024-01-24 14:55:47,930] [INFO] Target genome list was writen to GCF_013307245.1_ASM1330724v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:55:47,954] [INFO] Task started: fastANI
[2024-01-24 14:55:47,954] [INFO] Running command: fastANI --query /var/lib/cwl/stg6218e770-8136-4cea-9957-cdbb707ed08f/GCF_013307245.1_ASM1330724v1_genomic.fna.gz --refList GCF_013307245.1_ASM1330724v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013307245.1_ASM1330724v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:55:56,911] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:56,926] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:55:56,927] [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_013307245.1	s__Polynucleobacter sp013307245	100.0	718	718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018687575.1	s__Polynucleobacter asymbioticus_C	79.9687	316	718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882405.1	s__Polynucleobacter sp018882405	79.8017	328	718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881905.1	s__Polynucleobacter sp018881905	79.7693	324	718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013307205.1	s__Polynucleobacter asymbioticus_A	79.6919	299	718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000342265.1	s__Polynucleobacter sp000342265	79.66	338	718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018688335.1	s__Polynucleobacter sp018688335	79.6363	324	718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	95.20	95.20	0.89	0.89	2	-
GCF_018688495.1	s__Polynucleobacter sp018688495	79.6299	333	718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	97.81	97.81	0.94	0.94	2	-
GCF_018882365.1	s__Polynucleobacter sp018882365	79.6178	331	718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882335.1	s__Polynucleobacter sp018882335	79.6065	311	718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882055.1	s__Polynucleobacter sp018882055	79.5844	321	718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001830325.1	s__Polynucleobacter sp001830325	79.5658	309	718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018882295.1	s__Polynucleobacter sp018882295	79.539	331	718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900095165.1	s__Polynucleobacter necessarius_J	79.5162	302	718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882325.1	s__Polynucleobacter sp018882325	79.4799	330	718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018688315.1	s__Polynucleobacter sp018688315	79.4292	242	718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001595985.1	s__Polynucleobacter sinensis	79.3957	309	718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900096755.1	s__Polynucleobacter necessarius_K	78.8394	241	718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903845455.1	s__Polynucleobacter sp903845455	78.2195	206	718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	98.50	98.25	0.75	0.69	7	-
--------------------------------------------------------------------------------
[2024-01-24 14:55:56,930] [INFO] GTDB search result was written to GCF_013307245.1_ASM1330724v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:55:56,930] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:55:56,934] [INFO] DFAST_QC result json was written to GCF_013307245.1_ASM1330724v1_genomic.fna/dqc_result.json
[2024-01-24 14:55:56,934] [INFO] DFAST_QC completed!
[2024-01-24 14:55:56,934] [INFO] Total running time: 0h0m48s