[2024-01-25 18:43:35,551] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:43:35,553] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:43:35,553] [INFO] DQC Reference Directory: /var/lib/cwl/stg5fa46276-052d-466a-9dab-9ed120ba2ffb/dqc_reference
[2024-01-25 18:43:36,734] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:43:36,735] [INFO] Task started: Prodigal
[2024-01-25 18:43:36,735] [INFO] Running command: gunzip -c /var/lib/cwl/stg9b573c6e-6550-4e15-b663-364d6dc1046b/GCF_011751765.2_ASM1175176v2_genomic.fna.gz | prodigal -d GCF_011751765.2_ASM1175176v2_genomic.fna/cds.fna -a GCF_011751765.2_ASM1175176v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:43:47,063] [INFO] Task succeeded: Prodigal
[2024-01-25 18:43:47,064] [INFO] Task started: HMMsearch
[2024-01-25 18:43:47,064] [INFO] Running command: hmmsearch --tblout GCF_011751765.2_ASM1175176v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5fa46276-052d-466a-9dab-9ed120ba2ffb/dqc_reference/reference_markers.hmm GCF_011751765.2_ASM1175176v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:43:47,274] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:43:47,275] [INFO] Found 6/6 markers.
[2024-01-25 18:43:47,305] [INFO] Query marker FASTA was written to GCF_011751765.2_ASM1175176v2_genomic.fna/markers.fasta
[2024-01-25 18:43:47,305] [INFO] Task started: Blastn
[2024-01-25 18:43:47,305] [INFO] Running command: blastn -query GCF_011751765.2_ASM1175176v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg5fa46276-052d-466a-9dab-9ed120ba2ffb/dqc_reference/reference_markers.fasta -out GCF_011751765.2_ASM1175176v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:48,091] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:48,093] [INFO] Selected 15 target genomes.
[2024-01-25 18:43:48,094] [INFO] Target genome list was writen to GCF_011751765.2_ASM1175176v2_genomic.fna/target_genomes.txt
[2024-01-25 18:43:48,100] [INFO] Task started: fastANI
[2024-01-25 18:43:48,100] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b573c6e-6550-4e15-b663-364d6dc1046b/GCF_011751765.2_ASM1175176v2_genomic.fna.gz --refList GCF_011751765.2_ASM1175176v2_genomic.fna/target_genomes.txt --output GCF_011751765.2_ASM1175176v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:43:57,844] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:57,845] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5fa46276-052d-466a-9dab-9ed120ba2ffb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:43:57,845] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5fa46276-052d-466a-9dab-9ed120ba2ffb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:43:57,854] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:43:57,854] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:43:57,855] [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 chengjingii	strain=HY60	GCA_011751765.2	2769067	2769067	type	True	100.0	1207	1207	95	conclusive
Microbacterium fandaimingii	strain=HY82	GCA_011751745.2	2708079	2708079	type	True	84.9513	885	1207	95	below_threshold
Microbacterium agarici	strain=DSM 21798	GCA_002563955.1	630514	630514	type	True	80.9383	652	1207	95	below_threshold
Microbacterium lindanitolerans	strain=DSM 22422	GCA_006788875.1	550448	550448	type	True	80.8292	648	1207	95	below_threshold
Microbacterium humi	strain=DSM 21799	GCA_900105715.1	640635	640635	type	True	79.0872	404	1207	95	below_threshold
Microbacterium esteraromaticum	strain=DSM 8609	GCA_016907315.1	57043	57043	suspected-type	True	77.698	133	1207	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	77.4186	161	1207	95	below_threshold
Agromyces lapidis	strain=JCM 14321	GCA_009749405.1	279574	279574	type	True	77.3112	200	1207	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	77.2466	143	1207	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	77.2222	168	1207	95	below_threshold
Microbacterium pullorum	strain=Sa4CUA7	GCA_014836535.1	2762236	2762236	type	True	77.1936	149	1207	95	below_threshold
Microbacterium aerolatum	strain=CCM 4955	GCA_014635005.1	153731	153731	type	True	77.1208	145	1207	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	77.0752	153	1207	95	below_threshold
Cryobacterium levicorallinum	strain=GMCC 1.11211	GCA_900113585.1	995038	995038	type	True	76.959	123	1207	95	below_threshold
Subtercola lobariae	strain=CGMCC 1.12976	GCA_014640255.1	1588641	1588641	type	True	76.6022	112	1207	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:43:57,857] [INFO] DFAST Taxonomy check result was written to GCF_011751765.2_ASM1175176v2_genomic.fna/tc_result.tsv
[2024-01-25 18:43:57,857] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:43:57,857] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:43:57,857] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5fa46276-052d-466a-9dab-9ed120ba2ffb/dqc_reference/checkm_data
[2024-01-25 18:43:57,858] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:43:57,895] [INFO] Task started: CheckM
[2024-01-25 18:43:57,895] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011751765.2_ASM1175176v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011751765.2_ASM1175176v2_genomic.fna/checkm_input GCF_011751765.2_ASM1175176v2_genomic.fna/checkm_result
[2024-01-25 18:44:33,061] [INFO] Task succeeded: CheckM
[2024-01-25 18:44:33,062] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:44:33,077] [INFO] ===== Completeness check finished =====
[2024-01-25 18:44:33,077] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:44:33,078] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011751765.2_ASM1175176v2_genomic.fna/markers.fasta)
[2024-01-25 18:44:33,078] [INFO] Task started: Blastn
[2024-01-25 18:44:33,078] [INFO] Running command: blastn -query GCF_011751765.2_ASM1175176v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg5fa46276-052d-466a-9dab-9ed120ba2ffb/dqc_reference/reference_markers_gtdb.fasta -out GCF_011751765.2_ASM1175176v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:34,308] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:34,316] [INFO] Selected 16 target genomes.
[2024-01-25 18:44:34,316] [INFO] Target genome list was writen to GCF_011751765.2_ASM1175176v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:44:34,325] [INFO] Task started: fastANI
[2024-01-25 18:44:34,325] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b573c6e-6550-4e15-b663-364d6dc1046b/GCF_011751765.2_ASM1175176v2_genomic.fna.gz --refList GCF_011751765.2_ASM1175176v2_genomic.fna/target_genomes_gtdb.txt --output GCF_011751765.2_ASM1175176v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:44:44,628] [INFO] Task succeeded: fastANI
[2024-01-25 18:44:44,639] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:44:44,639] [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_011751765.2	s__Microbacterium_A chengjingii	100.0	1207	1207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium_A	95.0	98.92	98.92	0.94	0.94	2	conclusive
GCF_011751745.2	s__Microbacterium_A fandaimingii	84.9299	888	1207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium_A	95.0	98.82	98.82	0.94	0.94	2	-
GCF_002563955.1	s__Microbacterium_A agarici	80.9638	653	1207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium_A	95.0	97.53	97.53	0.93	0.93	2	-
GCF_900105715.1	s__Microbacterium_A humi	79.0302	404	1207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004078635.1	s__Labedella phragmitis	77.6876	175	1207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Labedella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645655.1	s__Agromyces bauzanensis	77.6325	149	1207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014675.1	s__Labedella gwakjiensis	77.4929	168	1207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Labedella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015277895.1	s__Microbacterium sp015277895	77.4539	145	1207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003668565.1	s__Mycetocola_A zhadangensis	77.4301	159	1207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004959775.1	s__Agromyces sp004959775	77.3544	183	1207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002705755.3	s__Microbacterium esteraromaticum_A	77.3182	139	1207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.15	98.15	0.64	0.64	2	-
GCF_002362255.1	s__Microbacterium sp002362255	77.3101	141	1207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009749405.1	s__Agromyces lapidis	77.2854	202	1207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613995.1	s__Microbacterium sp018613995	77.2309	118	1207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013297645.1	s__JAAFHU01 sp013297645	77.1525	101	1207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__JAAFHU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003243275.1	s__Protaetiibacter sp003243275	77.1337	131	1207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:44:44,640] [INFO] GTDB search result was written to GCF_011751765.2_ASM1175176v2_genomic.fna/result_gtdb.tsv
[2024-01-25 18:44:44,641] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:44:44,644] [INFO] DFAST_QC result json was written to GCF_011751765.2_ASM1175176v2_genomic.fna/dqc_result.json
[2024-01-25 18:44:44,644] [INFO] DFAST_QC completed!
[2024-01-25 18:44:44,644] [INFO] Total running time: 0h1m9s