[2024-01-24 14:06:31,065] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:31,067] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:31,067] [INFO] DQC Reference Directory: /var/lib/cwl/stg841c659b-eda3-4f3c-8609-fb802412ff6d/dqc_reference
[2024-01-24 14:06:32,428] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:32,429] [INFO] Task started: Prodigal
[2024-01-24 14:06:32,429] [INFO] Running command: gunzip -c /var/lib/cwl/stg749fa589-33f5-4ac3-9551-a02069434ed3/GCF_001591345.1_ASM159134v1_genomic.fna.gz | prodigal -d GCF_001591345.1_ASM159134v1_genomic.fna/cds.fna -a GCF_001591345.1_ASM159134v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:54,794] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:54,795] [INFO] Task started: HMMsearch
[2024-01-24 14:06:54,795] [INFO] Running command: hmmsearch --tblout GCF_001591345.1_ASM159134v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg841c659b-eda3-4f3c-8609-fb802412ff6d/dqc_reference/reference_markers.hmm GCF_001591345.1_ASM159134v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:55,151] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:55,152] [INFO] Found 6/6 markers.
[2024-01-24 14:06:55,216] [INFO] Query marker FASTA was written to GCF_001591345.1_ASM159134v1_genomic.fna/markers.fasta
[2024-01-24 14:06:55,216] [INFO] Task started: Blastn
[2024-01-24 14:06:55,216] [INFO] Running command: blastn -query GCF_001591345.1_ASM159134v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg841c659b-eda3-4f3c-8609-fb802412ff6d/dqc_reference/reference_markers.fasta -out GCF_001591345.1_ASM159134v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:56,313] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:56,317] [INFO] Selected 12 target genomes.
[2024-01-24 14:06:56,317] [INFO] Target genome list was writen to GCF_001591345.1_ASM159134v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:56,331] [INFO] Task started: fastANI
[2024-01-24 14:06:56,332] [INFO] Running command: fastANI --query /var/lib/cwl/stg749fa589-33f5-4ac3-9551-a02069434ed3/GCF_001591345.1_ASM159134v1_genomic.fna.gz --refList GCF_001591345.1_ASM159134v1_genomic.fna/target_genomes.txt --output GCF_001591345.1_ASM159134v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:13,422] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:13,422] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg841c659b-eda3-4f3c-8609-fb802412ff6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:13,423] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg841c659b-eda3-4f3c-8609-fb802412ff6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:13,433] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:07:13,434] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:13,434] [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
Variovorax boronicumulans	strain=NBRC 103145	GCA_001591345.1	436515	436515	type	True	100.0	2096	2111	95	conclusive
Variovorax guangxiensis	strain=DSM 27352	GCA_003952165.1	1775474	1775474	type	True	88.6986	1506	2111	95	below_threshold
Variovorax gossypii	strain=DSM 100435	GCA_003965815.1	1679495	1679495	type	True	88.4201	1285	2111	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	87.9761	1407	2111	95	below_threshold
Variovorax beijingensis	strain=502	GCA_003951285.1	2496117	2496117	type	True	87.8547	1387	2111	95	below_threshold
Variovorax soli	strain=NBRC 106424	GCA_001591385.1	376815	376815	type	True	83.7782	1074	2111	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	81.0734	768	2111	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	81.0624	773	2111	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.9795	782	2111	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	80.7071	839	2111	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	78.8069	494	2111	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	78.71	623	2111	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:13,435] [INFO] DFAST Taxonomy check result was written to GCF_001591345.1_ASM159134v1_genomic.fna/tc_result.tsv
[2024-01-24 14:07:13,436] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:13,436] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:13,436] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg841c659b-eda3-4f3c-8609-fb802412ff6d/dqc_reference/checkm_data
[2024-01-24 14:07:13,437] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:13,502] [INFO] Task started: CheckM
[2024-01-24 14:07:13,503] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001591345.1_ASM159134v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001591345.1_ASM159134v1_genomic.fna/checkm_input GCF_001591345.1_ASM159134v1_genomic.fna/checkm_result
[2024-01-24 14:08:54,227] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:54,228] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:54,253] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:54,253] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:54,254] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001591345.1_ASM159134v1_genomic.fna/markers.fasta)
[2024-01-24 14:08:54,254] [INFO] Task started: Blastn
[2024-01-24 14:08:54,254] [INFO] Running command: blastn -query GCF_001591345.1_ASM159134v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg841c659b-eda3-4f3c-8609-fb802412ff6d/dqc_reference/reference_markers_gtdb.fasta -out GCF_001591345.1_ASM159134v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:56,515] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:56,519] [INFO] Selected 10 target genomes.
[2024-01-24 14:08:56,519] [INFO] Target genome list was writen to GCF_001591345.1_ASM159134v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:56,545] [INFO] Task started: fastANI
[2024-01-24 14:08:56,546] [INFO] Running command: fastANI --query /var/lib/cwl/stg749fa589-33f5-4ac3-9551-a02069434ed3/GCF_001591345.1_ASM159134v1_genomic.fna.gz --refList GCF_001591345.1_ASM159134v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001591345.1_ASM159134v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:09:15,944] [INFO] Task succeeded: fastANI
[2024-01-24 14:09:15,955] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:09:15,956] [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_001591345.1	s__Variovorax boronicumulans	100.0	2096	2111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	97.15	97.07	0.92	0.90	8	conclusive
GCF_002754375.1	s__Variovorax sp002754375	94.6362	1777	2111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	95.39	95.37	0.86	0.85	3	-
GCF_009498455.1	s__Variovorax paradoxus_H	94.1111	1769	2111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426505.1	s__Variovorax sp001426505	93.9655	1548	2111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016082275.1	s__Variovorax sp016082275	89.1188	1521	2111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053685.1	s__Variovorax sp003053685	88.8276	1529	2111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	100.00	100.00	1.00	1.00	5	-
GCF_016405905.1	s__Variovorax sp016405905	88.7072	1478	2111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003019815.1	s__Variovorax sp003019815	88.5295	1510	2111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	99.10	98.33	0.94	0.92	3	-
GCF_001425205.1	s__Variovorax sp001425205	88.4769	1355	2111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014302995.1	s__Variovorax sp014302995	88.4174	1578	2111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:09:15,957] [INFO] GTDB search result was written to GCF_001591345.1_ASM159134v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:09:15,958] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:09:15,961] [INFO] DFAST_QC result json was written to GCF_001591345.1_ASM159134v1_genomic.fna/dqc_result.json
[2024-01-24 14:09:15,961] [INFO] DFAST_QC completed!
[2024-01-24 14:09:15,962] [INFO] Total running time: 0h2m45s