[2024-01-25 20:05:50,441] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:05:50,443] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:05:50,443] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d8affd8-89fa-442c-a8e9-25f3a7ff26b8/dqc_reference
[2024-01-25 20:05:51,568] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:05:51,569] [INFO] Task started: Prodigal
[2024-01-25 20:05:51,569] [INFO] Running command: gunzip -c /var/lib/cwl/stge21cbd77-9135-450c-8693-2c3af866106b/GCF_017831975.1_ASM1783197v1_genomic.fna.gz | prodigal -d GCF_017831975.1_ASM1783197v1_genomic.fna/cds.fna -a GCF_017831975.1_ASM1783197v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:06:01,769] [INFO] Task succeeded: Prodigal
[2024-01-25 20:06:01,770] [INFO] Task started: HMMsearch
[2024-01-25 20:06:01,770] [INFO] Running command: hmmsearch --tblout GCF_017831975.1_ASM1783197v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d8affd8-89fa-442c-a8e9-25f3a7ff26b8/dqc_reference/reference_markers.hmm GCF_017831975.1_ASM1783197v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:06:01,977] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:06:01,978] [INFO] Found 6/6 markers.
[2024-01-25 20:06:02,011] [INFO] Query marker FASTA was written to GCF_017831975.1_ASM1783197v1_genomic.fna/markers.fasta
[2024-01-25 20:06:02,011] [INFO] Task started: Blastn
[2024-01-25 20:06:02,011] [INFO] Running command: blastn -query GCF_017831975.1_ASM1783197v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d8affd8-89fa-442c-a8e9-25f3a7ff26b8/dqc_reference/reference_markers.fasta -out GCF_017831975.1_ASM1783197v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:06:03,192] [INFO] Task succeeded: Blastn
[2024-01-25 20:06:03,195] [INFO] Selected 22 target genomes.
[2024-01-25 20:06:03,196] [INFO] Target genome list was writen to GCF_017831975.1_ASM1783197v1_genomic.fna/target_genomes.txt
[2024-01-25 20:06:03,216] [INFO] Task started: fastANI
[2024-01-25 20:06:03,216] [INFO] Running command: fastANI --query /var/lib/cwl/stge21cbd77-9135-450c-8693-2c3af866106b/GCF_017831975.1_ASM1783197v1_genomic.fna.gz --refList GCF_017831975.1_ASM1783197v1_genomic.fna/target_genomes.txt --output GCF_017831975.1_ASM1783197v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:06:22,704] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:22,704] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d8affd8-89fa-442c-a8e9-25f3a7ff26b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:06:22,705] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d8affd8-89fa-442c-a8e9-25f3a7ff26b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:06:22,717] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:06:22,717] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:06:22,717] [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
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	82.7648	764	1298	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	82.7354	710	1298	95	below_threshold
Microbacterium trichothecenolyticum	strain=DSM 8608	GCA_000956465.1	69370	69370	type	True	82.7038	805	1298	95	below_threshold
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	82.677	795	1298	95	below_threshold
Microbacterium kyungheense	strain=DSM 105492	GCA_006783905.1	1263636	1263636	type	True	82.5591	783	1298	95	below_threshold
Microbacterium helvum	strain=NEAU-LLC	GCA_014779795.1	2773713	2773713	type	True	82.5191	793	1298	95	below_threshold
Microbacterium flavescens	strain=JCM 3877	GCA_018588945.1	69366	69366	type	True	82.4919	726	1298	95	below_threshold
Microbacterium sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	82.477	779	1298	95	below_threshold
Microbacterium ureisolvens	strain=CFH S00084	GCA_015278315.1	2781186	2781186	type	True	82.4343	846	1298	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	82.3383	718	1298	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	82.1052	798	1298	95	below_threshold
Microbacterium thalassium	strain=DSM 12511	GCA_014208045.1	362649	362649	type	True	81.7751	700	1298	95	below_threshold
Microbacterium timonense	strain=Marseille-P5731	GCA_900292075.1	2086576	2086576	type	True	81.7017	716	1298	95	below_threshold
Microbacterium telephonicum	strain=S2T63	GCA_003651225.1	1714841	1714841	type	True	81.5086	629	1298	95	below_threshold
Microbacterium saccharophilum	strain=NBRC 108778	GCA_007992455.1	1213358	1213358	type	True	80.9525	603	1298	95	below_threshold
Microbacterium pullorum	strain=Sa4CUA7	GCA_014836535.1	2762236	2762236	type	True	80.9362	618	1298	95	below_threshold
Microbacterium proteolyticum	strain=CECT 8356	GCA_014192415.1	1572644	1572644	type	True	80.5979	549	1298	95	below_threshold
Microbacterium wangchenii	strain=dk512	GCA_004564355.1	2541726	2541726	type	True	80.5141	551	1298	95	below_threshold
Microbacterium lushaniae	strain=L-031	GCA_008727775.1	2614639	2614639	type	True	80.4019	557	1298	95	below_threshold
Microbacterium rhizomatis	strain=JCM 30598	GCA_008710745.1	1631477	1631477	type	True	80.1226	582	1298	95	below_threshold
Microbacterium azadirachtae	strain=DSM 23848	GCA_000956545.1	582680	582680	type	True	80.0128	521	1298	95	below_threshold
Microbacterium marinilacus	strain=YM11-607	GCA_019753765.1	415209	415209	type	True	79.773	506	1298	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:06:22,719] [INFO] DFAST Taxonomy check result was written to GCF_017831975.1_ASM1783197v1_genomic.fna/tc_result.tsv
[2024-01-25 20:06:22,719] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:06:22,720] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:06:22,720] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d8affd8-89fa-442c-a8e9-25f3a7ff26b8/dqc_reference/checkm_data
[2024-01-25 20:06:22,720] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:06:22,761] [INFO] Task started: CheckM
[2024-01-25 20:06:22,761] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017831975.1_ASM1783197v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017831975.1_ASM1783197v1_genomic.fna/checkm_input GCF_017831975.1_ASM1783197v1_genomic.fna/checkm_result
[2024-01-25 20:07:35,770] [INFO] Task succeeded: CheckM
[2024-01-25 20:07:35,771] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:07:35,800] [INFO] ===== Completeness check finished =====
[2024-01-25 20:07:35,800] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:07:35,801] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017831975.1_ASM1783197v1_genomic.fna/markers.fasta)
[2024-01-25 20:07:35,801] [INFO] Task started: Blastn
[2024-01-25 20:07:35,801] [INFO] Running command: blastn -query GCF_017831975.1_ASM1783197v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d8affd8-89fa-442c-a8e9-25f3a7ff26b8/dqc_reference/reference_markers_gtdb.fasta -out GCF_017831975.1_ASM1783197v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:37,803] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:37,806] [INFO] Selected 19 target genomes.
[2024-01-25 20:07:37,806] [INFO] Target genome list was writen to GCF_017831975.1_ASM1783197v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:07:37,833] [INFO] Task started: fastANI
[2024-01-25 20:07:37,833] [INFO] Running command: fastANI --query /var/lib/cwl/stge21cbd77-9135-450c-8693-2c3af866106b/GCF_017831975.1_ASM1783197v1_genomic.fna.gz --refList GCF_017831975.1_ASM1783197v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017831975.1_ASM1783197v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:07:54,921] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:54,932] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:07:54,933] [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_017831975.1	s__Microbacterium terrae	100.0	1298	1298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_005502885.1	s__Microbacterium sp005502885	82.7871	769	1298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015277855.1	s__Microbacterium sp015277855	82.7542	765	1298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422925.1	s__Microbacterium sp001422925	82.7326	857	1298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000956465.1	s__Microbacterium trichothecenolyticum	82.7143	804	1298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004010105.1	s__Microbacterium sp004010105	82.6604	490	1298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013282805.1	s__Microbacterium hominis_B	82.6549	770	1298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015278255.1	s__Microbacterium hibisci	82.6287	800	1298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779795.1	s__Microbacterium helvum	82.5394	791	1298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006783905.1	s__Microbacterium kyungheense	82.5394	786	1298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018588945.1	s__Microbacterium flavescens	82.5215	723	1298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380605.1	s__Microbacterium sp000380605	82.5099	791	1298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009858275.1	s__Microbacterium sp009858275	82.5031	775	1298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003999995.1	s__Microbacterium sp003999995	82.48	779	1298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015278315.1	s__Microbacterium ureisolvens	82.4474	845	1298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.97	99.97	1.00	1.00	2	-
GCF_001427145.1	s__Microbacterium sp001427145	82.4201	699	1298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012847295.1	s__Microbacterium sp012847295	82.0298	687	1298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014208045.1	s__Microbacterium thalassium	81.7934	699	1298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836535.1	s__Microbacterium sp014836535	80.9258	619	1298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:07:54,934] [INFO] GTDB search result was written to GCF_017831975.1_ASM1783197v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:07:54,934] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:07:54,938] [INFO] DFAST_QC result json was written to GCF_017831975.1_ASM1783197v1_genomic.fna/dqc_result.json
[2024-01-25 20:07:54,939] [INFO] DFAST_QC completed!
[2024-01-25 20:07:54,939] [INFO] Total running time: 0h2m4s