[2024-01-25 18:06:50,347] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:06:50,349] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:06:50,349] [INFO] DQC Reference Directory: /var/lib/cwl/stg53aaa0a5-55f6-42ea-9f5b-387165b3fc0c/dqc_reference
[2024-01-25 18:06:51,521] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:06:51,522] [INFO] Task started: Prodigal
[2024-01-25 18:06:51,522] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c826797-81f5-4599-9229-9c108506585b/GCF_001552115.1_ASM155211v1_genomic.fna.gz | prodigal -d GCF_001552115.1_ASM155211v1_genomic.fna/cds.fna -a GCF_001552115.1_ASM155211v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:07:01,372] [INFO] Task succeeded: Prodigal
[2024-01-25 18:07:01,372] [INFO] Task started: HMMsearch
[2024-01-25 18:07:01,373] [INFO] Running command: hmmsearch --tblout GCF_001552115.1_ASM155211v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53aaa0a5-55f6-42ea-9f5b-387165b3fc0c/dqc_reference/reference_markers.hmm GCF_001552115.1_ASM155211v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:07:01,593] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:07:01,595] [INFO] Found 6/6 markers.
[2024-01-25 18:07:01,623] [INFO] Query marker FASTA was written to GCF_001552115.1_ASM155211v1_genomic.fna/markers.fasta
[2024-01-25 18:07:01,623] [INFO] Task started: Blastn
[2024-01-25 18:07:01,623] [INFO] Running command: blastn -query GCF_001552115.1_ASM155211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53aaa0a5-55f6-42ea-9f5b-387165b3fc0c/dqc_reference/reference_markers.fasta -out GCF_001552115.1_ASM155211v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:02,663] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:02,666] [INFO] Selected 13 target genomes.
[2024-01-25 18:07:02,666] [INFO] Target genome list was writen to GCF_001552115.1_ASM155211v1_genomic.fna/target_genomes.txt
[2024-01-25 18:07:02,669] [INFO] Task started: fastANI
[2024-01-25 18:07:02,669] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c826797-81f5-4599-9229-9c108506585b/GCF_001552115.1_ASM155211v1_genomic.fna.gz --refList GCF_001552115.1_ASM155211v1_genomic.fna/target_genomes.txt --output GCF_001552115.1_ASM155211v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:07:12,570] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:12,571] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53aaa0a5-55f6-42ea-9f5b-387165b3fc0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:07:12,571] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53aaa0a5-55f6-42ea-9f5b-387165b3fc0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:07:12,579] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 18:07:12,580] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 18:07:12,580] [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
Glutamicibacter mysorens	strain=NBRC 103060	GCA_001552115.1	257984	257984	type	True	100.0	1134	1135	95	inconclusive
Glutamicibacter mysorens	strain=DSM 12798	GCA_002797775.1	257984	257984	type	True	99.9983	1135	1135	95	inconclusive
Glutamicibacter nicotianae	strain=NBRC 14234	GCA_006539525.1	37929	37929	type	True	97.6563	982	1135	95	inconclusive
Glutamicibacter arilaitensis	strain=Re117	GCA_000197735.1	256701	256701	type	True	85.5097	873	1135	95	below_threshold
Glutamicibacter mishrai	strain=S5-52	GCA_012221945.1	1775880	1775880	type	True	83.5992	715	1135	95	below_threshold
Glutamicibacter protophormiae	strain=DSM 20168	GCA_017876615.1	37930	37930	type	True	83.041	733	1135	95	below_threshold
Glutamicibacter protophormiae	strain=JCM 1973	GCA_014647495.1	37930	37930	type	True	82.992	728	1135	95	below_threshold
Glutamicibacter halophytocola	strain=KLBMP 5180	GCA_001302565.1	1933880	1933880	type	True	82.873	724	1135	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	78.2118	294	1135	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	77.5355	175	1135	95	below_threshold
Georgenia wutianyii	strain=Z294	GCA_006349365.1	2585135	2585135	type	True	76.6226	101	1135	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	76.5694	99	1135	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	76.4882	119	1135	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:07:12,581] [INFO] DFAST Taxonomy check result was written to GCF_001552115.1_ASM155211v1_genomic.fna/tc_result.tsv
[2024-01-25 18:07:12,582] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:07:12,582] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:07:12,582] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53aaa0a5-55f6-42ea-9f5b-387165b3fc0c/dqc_reference/checkm_data
[2024-01-25 18:07:12,583] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:07:12,618] [INFO] Task started: CheckM
[2024-01-25 18:07:12,618] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001552115.1_ASM155211v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001552115.1_ASM155211v1_genomic.fna/checkm_input GCF_001552115.1_ASM155211v1_genomic.fna/checkm_result
[2024-01-25 18:07:42,665] [INFO] Task succeeded: CheckM
[2024-01-25 18:07:42,666] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:07:42,686] [INFO] ===== Completeness check finished =====
[2024-01-25 18:07:42,686] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:07:42,686] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001552115.1_ASM155211v1_genomic.fna/markers.fasta)
[2024-01-25 18:07:42,687] [INFO] Task started: Blastn
[2024-01-25 18:07:42,687] [INFO] Running command: blastn -query GCF_001552115.1_ASM155211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53aaa0a5-55f6-42ea-9f5b-387165b3fc0c/dqc_reference/reference_markers_gtdb.fasta -out GCF_001552115.1_ASM155211v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:44,313] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:44,315] [INFO] Selected 8 target genomes.
[2024-01-25 18:07:44,316] [INFO] Target genome list was writen to GCF_001552115.1_ASM155211v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:07:44,317] [INFO] Task started: fastANI
[2024-01-25 18:07:44,317] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c826797-81f5-4599-9229-9c108506585b/GCF_001552115.1_ASM155211v1_genomic.fna.gz --refList GCF_001552115.1_ASM155211v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001552115.1_ASM155211v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:07:50,877] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:50,883] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:07:50,883] [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_006539525.1	s__Glutamicibacter nicotianae	97.6563	982	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	97.59	96.22	0.88	0.85	10	conclusive
GCF_002979865.1	s__Glutamicibacter sp002979865	88.3761	955	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.88	98.56	0.94	0.92	3	-
GCF_000197735.1	s__Glutamicibacter arilaitensis	85.5097	873	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.79	97.54	0.91	0.83	7	-
GCF_012221945.1	s__Glutamicibacter mishrai	83.5985	716	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	97.84	97.11	0.89	0.89	3	-
GCF_003309065.1	s__Glutamicibacter soli	83.3555	743	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.33	97.69	0.91	0.87	6	-
GCF_014647495.1	s__Glutamicibacter protophormiae	82.9746	730	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.76	97.53	0.93	0.87	3	-
GCF_001302565.1	s__Glutamicibacter halophytocola	82.8772	723	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.28	98.01	0.91	0.89	4	-
GCF_900094805.1	s__Glutamicibacter sp900094805	81.8585	602	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:07:50,884] [INFO] GTDB search result was written to GCF_001552115.1_ASM155211v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:07:50,885] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:07:50,888] [INFO] DFAST_QC result json was written to GCF_001552115.1_ASM155211v1_genomic.fna/dqc_result.json
[2024-01-25 18:07:50,888] [INFO] DFAST_QC completed!
[2024-01-25 18:07:50,889] [INFO] Total running time: 0h1m1s