[2023-06-30 06:58:44,065] [INFO] DFAST_QC pipeline started.
[2023-06-30 06:58:44,068] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 06:58:44,068] [INFO] DQC Reference Directory: /var/lib/cwl/stgd11c038d-61c6-4507-b0c1-d39c078cf28a/dqc_reference
[2023-06-30 06:58:45,857] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 06:58:45,859] [INFO] Task started: Prodigal
[2023-06-30 06:58:45,860] [INFO] Running command: gunzip -c /var/lib/cwl/stg5d03a9c3-3196-41b8-be28-62051d69b9b6/GCA_019423945.1_ASM1942394v1_genomic.fna.gz | prodigal -d GCA_019423945.1_ASM1942394v1_genomic.fna/cds.fna -a GCA_019423945.1_ASM1942394v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 06:58:51,935] [INFO] Task succeeded: Prodigal
[2023-06-30 06:58:51,935] [INFO] Task started: HMMsearch
[2023-06-30 06:58:51,936] [INFO] Running command: hmmsearch --tblout GCA_019423945.1_ASM1942394v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd11c038d-61c6-4507-b0c1-d39c078cf28a/dqc_reference/reference_markers.hmm GCA_019423945.1_ASM1942394v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 06:58:52,205] [INFO] Task succeeded: HMMsearch
[2023-06-30 06:58:52,206] [INFO] Found 6/6 markers.
[2023-06-30 06:58:52,232] [INFO] Query marker FASTA was written to GCA_019423945.1_ASM1942394v1_genomic.fna/markers.fasta
[2023-06-30 06:58:52,232] [INFO] Task started: Blastn
[2023-06-30 06:58:52,232] [INFO] Running command: blastn -query GCA_019423945.1_ASM1942394v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd11c038d-61c6-4507-b0c1-d39c078cf28a/dqc_reference/reference_markers.fasta -out GCA_019423945.1_ASM1942394v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 06:58:53,178] [INFO] Task succeeded: Blastn
[2023-06-30 06:58:53,182] [INFO] Selected 18 target genomes.
[2023-06-30 06:58:53,183] [INFO] Target genome list was writen to GCA_019423945.1_ASM1942394v1_genomic.fna/target_genomes.txt
[2023-06-30 06:58:53,184] [INFO] Task started: fastANI
[2023-06-30 06:58:53,184] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d03a9c3-3196-41b8-be28-62051d69b9b6/GCA_019423945.1_ASM1942394v1_genomic.fna.gz --refList GCA_019423945.1_ASM1942394v1_genomic.fna/target_genomes.txt --output GCA_019423945.1_ASM1942394v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 06:59:02,286] [INFO] Task succeeded: fastANI
[2023-06-30 06:59:02,287] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd11c038d-61c6-4507-b0c1-d39c078cf28a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 06:59:02,287] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd11c038d-61c6-4507-b0c1-d39c078cf28a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 06:59:02,304] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 06:59:02,305] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 06:59:02,305] [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
Rothia mucilaginosa	strain=ATCC 25296	GCA_000175615.1	43675	43675	suspected-type	True	94.9217	662	723	95	below_threshold
Rothia dentocariosa	strain=NCTC10917	GCA_900455895.1	2047	2047	type	True	78.8649	198	723	95	below_threshold
Rothia dentocariosa	strain=ATCC 17931	GCA_000164695.2	2047	2047	type	True	78.816	199	723	95	below_threshold
Rothia aeria	strain=FDAARGOS_1137	GCA_016726365.1	172042	172042	type	True	78.6368	253	723	95	below_threshold
Rothia aerolata	strain=CCM 8669	GCA_014635585.1	1812262	1812262	type	True	78.3948	168	723	95	below_threshold
Rothia terrae	strain=LMG 23708	GCA_012396615.1	396015	396015	type	True	78.1563	128	723	95	below_threshold
Kocuria rhizophila	strain=TA68	GCA_003667225.1	72000	72000	type	True	77.278	95	723	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	77.1426	78	723	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_017353495.1	2816859	2816859	type	True	77.0447	82	723	95	below_threshold
Arthrobacter pullicola	strain=Sa2BUA2	GCA_014836875.1	2762224	2762224	type	True	76.9698	88	723	95	below_threshold
Arthrobacter luteolus	strain=DSM 13067	GCA_008973725.1	98672	98672	type	True	76.8825	92	723	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	76.87	90	723	95	below_threshold
Galactobacter valiniphilus	strain=JZ R-35	GCA_003575975.1	2676122	2676122	type	True	76.8288	95	723	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	76.8163	90	723	95	below_threshold
Kocuria palustris	strain=TAGA27	GCA_016907795.1	71999	71999	type	True	76.8084	100	723	95	below_threshold
Paeniglutamicibacter psychrophenolicus	strain=DSM 15454	GCA_017876575.1	257454	257454	type	True	76.6116	87	723	95	below_threshold
Neomicrococcus aestuarii	strain=DSM 105783	GCA_014201135.1	556325	556325	type	True	76.395	54	723	95	below_threshold
Nesterenkonia jeotgali	strain=DSM 19081	GCA_014138825.1	317018	317018	type	True	76.2043	59	723	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 06:59:02,308] [INFO] DFAST Taxonomy check result was written to GCA_019423945.1_ASM1942394v1_genomic.fna/tc_result.tsv
[2023-06-30 06:59:02,308] [INFO] ===== Taxonomy check completed =====
[2023-06-30 06:59:02,309] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 06:59:02,309] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd11c038d-61c6-4507-b0c1-d39c078cf28a/dqc_reference/checkm_data
[2023-06-30 06:59:02,311] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 06:59:02,347] [INFO] Task started: CheckM
[2023-06-30 06:59:02,348] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019423945.1_ASM1942394v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019423945.1_ASM1942394v1_genomic.fna/checkm_input GCA_019423945.1_ASM1942394v1_genomic.fna/checkm_result
[2023-06-30 06:59:27,408] [INFO] Task succeeded: CheckM
[2023-06-30 06:59:27,410] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 06:59:27,432] [INFO] ===== Completeness check finished =====
[2023-06-30 06:59:27,432] [INFO] ===== Start GTDB Search =====
[2023-06-30 06:59:27,433] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019423945.1_ASM1942394v1_genomic.fna/markers.fasta)
[2023-06-30 06:59:27,433] [INFO] Task started: Blastn
[2023-06-30 06:59:27,433] [INFO] Running command: blastn -query GCA_019423945.1_ASM1942394v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd11c038d-61c6-4507-b0c1-d39c078cf28a/dqc_reference/reference_markers_gtdb.fasta -out GCA_019423945.1_ASM1942394v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 06:59:28,716] [INFO] Task succeeded: Blastn
[2023-06-30 06:59:28,720] [INFO] Selected 6 target genomes.
[2023-06-30 06:59:28,720] [INFO] Target genome list was writen to GCA_019423945.1_ASM1942394v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 06:59:28,721] [INFO] Task started: fastANI
[2023-06-30 06:59:28,721] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d03a9c3-3196-41b8-be28-62051d69b9b6/GCA_019423945.1_ASM1942394v1_genomic.fna.gz --refList GCA_019423945.1_ASM1942394v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019423945.1_ASM1942394v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 06:59:32,267] [INFO] Task succeeded: fastANI
[2023-06-30 06:59:32,274] [INFO] Found 6 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-30 06:59:32,274] [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_001808955.1	s__Rothia sp001808955	95.5953	680	723	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	96.04	95.53	0.94	0.90	20	inconclusive
GCF_001548235.1	s__Rothia mucilaginosa_B	95.0091	681	723	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	95.72	95.51	0.97	0.96	3	inconclusive
GCF_000175615.1	s__Rothia mucilaginosa	94.9217	662	723	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	95.99	95.33	0.94	0.89	44	-
GCA_015265375.1	s__Rothia sp015265375	94.2636	624	723	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	95.30	95.30	0.97	0.97	2	-
GCF_001061665.1	s__Rothia mucilaginosa_A	89.0249	619	723	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	97.28	96.59	0.94	0.92	10	-
GCF_901875305.1	s__Rothia sp902373285	87.945	616	723	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	97.53	97.34	0.97	0.96	6	-
--------------------------------------------------------------------------------
[2023-06-30 06:59:32,276] [INFO] GTDB search result was written to GCA_019423945.1_ASM1942394v1_genomic.fna/result_gtdb.tsv
[2023-06-30 06:59:32,277] [INFO] ===== GTDB Search completed =====
[2023-06-30 06:59:32,280] [INFO] DFAST_QC result json was written to GCA_019423945.1_ASM1942394v1_genomic.fna/dqc_result.json
[2023-06-30 06:59:32,280] [INFO] DFAST_QC completed!
[2023-06-30 06:59:32,280] [INFO] Total running time: 0h0m48s