[2024-01-24 12:37:25,114] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:25,116] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:25,116] [INFO] DQC Reference Directory: /var/lib/cwl/stge17ba1e0-1b0d-47cc-805b-7450f1db9d80/dqc_reference
[2024-01-24 12:37:26,458] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:26,458] [INFO] Task started: Prodigal
[2024-01-24 12:37:26,459] [INFO] Running command: gunzip -c /var/lib/cwl/stg109761e5-7add-453d-91f0-8ab255b5cbe2/GCF_011751745.2_ASM1175174v2_genomic.fna.gz | prodigal -d GCF_011751745.2_ASM1175174v2_genomic.fna/cds.fna -a GCF_011751745.2_ASM1175174v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:37,930] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:37,930] [INFO] Task started: HMMsearch
[2024-01-24 12:37:37,930] [INFO] Running command: hmmsearch --tblout GCF_011751745.2_ASM1175174v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge17ba1e0-1b0d-47cc-805b-7450f1db9d80/dqc_reference/reference_markers.hmm GCF_011751745.2_ASM1175174v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:38,178] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:38,180] [INFO] Found 6/6 markers.
[2024-01-24 12:37:38,215] [INFO] Query marker FASTA was written to GCF_011751745.2_ASM1175174v2_genomic.fna/markers.fasta
[2024-01-24 12:37:38,216] [INFO] Task started: Blastn
[2024-01-24 12:37:38,216] [INFO] Running command: blastn -query GCF_011751745.2_ASM1175174v2_genomic.fna/markers.fasta -db /var/lib/cwl/stge17ba1e0-1b0d-47cc-805b-7450f1db9d80/dqc_reference/reference_markers.fasta -out GCF_011751745.2_ASM1175174v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:39,131] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:39,134] [INFO] Selected 12 target genomes.
[2024-01-24 12:37:39,134] [INFO] Target genome list was writen to GCF_011751745.2_ASM1175174v2_genomic.fna/target_genomes.txt
[2024-01-24 12:37:39,140] [INFO] Task started: fastANI
[2024-01-24 12:37:39,141] [INFO] Running command: fastANI --query /var/lib/cwl/stg109761e5-7add-453d-91f0-8ab255b5cbe2/GCF_011751745.2_ASM1175174v2_genomic.fna.gz --refList GCF_011751745.2_ASM1175174v2_genomic.fna/target_genomes.txt --output GCF_011751745.2_ASM1175174v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:47,147] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:47,148] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge17ba1e0-1b0d-47cc-805b-7450f1db9d80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:47,148] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge17ba1e0-1b0d-47cc-805b-7450f1db9d80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:47,163] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:47,163] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:47,164] [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 fandaimingii	strain=HY82	GCA_011751745.2	2708079	2708079	type	True	100.0	1207	1207	95	conclusive
Microbacterium chengjingii	strain=HY60	GCA_011751765.2	2769067	2769067	type	True	84.9986	880	1207	95	below_threshold
Microbacterium lindanitolerans	strain=DSM 22422	GCA_006788875.1	550448	550448	type	True	81.5124	705	1207	95	below_threshold
Microbacterium agarici	strain=DSM 21798	GCA_002563955.1	630514	630514	type	True	81.4164	698	1207	95	below_threshold
Microbacterium humi	strain=DSM 21799	GCA_900105715.1	640635	640635	type	True	79.5385	496	1207	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	77.5638	236	1207	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	77.4337	242	1207	95	below_threshold
Clavibacter zhangzhiyongii	strain=DM1	GCA_014775655.1	2768071	2768071	type	True	77.2524	170	1207	95	below_threshold
Microbacterium invictum	strain=DSM 19600	GCA_023155715.1	515415	515415	type	True	77.237	192	1207	95	below_threshold
Microbacterium invictum	strain=JCM 17023	GCA_015278285.1	515415	515415	type	True	77.1968	193	1207	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	77.0553	191	1207	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_001689915.1	904291	904291	type	True	76.8796	177	1207	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:47,165] [INFO] DFAST Taxonomy check result was written to GCF_011751745.2_ASM1175174v2_genomic.fna/tc_result.tsv
[2024-01-24 12:37:47,166] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:47,166] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:47,166] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge17ba1e0-1b0d-47cc-805b-7450f1db9d80/dqc_reference/checkm_data
[2024-01-24 12:37:47,167] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:47,203] [INFO] Task started: CheckM
[2024-01-24 12:37:47,203] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011751745.2_ASM1175174v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011751745.2_ASM1175174v2_genomic.fna/checkm_input GCF_011751745.2_ASM1175174v2_genomic.fna/checkm_result
[2024-01-24 12:38:27,895] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:27,897] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:27,916] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:27,917] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:27,917] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011751745.2_ASM1175174v2_genomic.fna/markers.fasta)
[2024-01-24 12:38:27,918] [INFO] Task started: Blastn
[2024-01-24 12:38:27,918] [INFO] Running command: blastn -query GCF_011751745.2_ASM1175174v2_genomic.fna/markers.fasta -db /var/lib/cwl/stge17ba1e0-1b0d-47cc-805b-7450f1db9d80/dqc_reference/reference_markers_gtdb.fasta -out GCF_011751745.2_ASM1175174v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:29,220] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:29,224] [INFO] Selected 14 target genomes.
[2024-01-24 12:38:29,224] [INFO] Target genome list was writen to GCF_011751745.2_ASM1175174v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:29,236] [INFO] Task started: fastANI
[2024-01-24 12:38:29,236] [INFO] Running command: fastANI --query /var/lib/cwl/stg109761e5-7add-453d-91f0-8ab255b5cbe2/GCF_011751745.2_ASM1175174v2_genomic.fna.gz --refList GCF_011751745.2_ASM1175174v2_genomic.fna/target_genomes_gtdb.txt --output GCF_011751745.2_ASM1175174v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:38,097] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:38,109] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:38,109] [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_011751745.2	s__Microbacterium_A fandaimingii	100.0	1207	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	conclusive
GCF_011751765.2	s__Microbacterium_A chengjingii	84.9776	882	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	-
GCF_002563955.1	s__Microbacterium_A agarici	81.4125	699	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	79.5894	495	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_003990045.1	s__Labedella endophytica	77.6611	215	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_004078635.1	s__Labedella phragmitis	77.6193	224	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_008122505.1	s__Agromyces sp008122505	77.5658	235	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_902809835.1	s__Agromyces sp902809835	77.5638	206	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_009647605.1	s__Agromyces sp009647605	77.4473	240	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_003668565.1	s__Mycetocola_A zhadangensis	77.362	174	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_001513675.1	s__Microbacterium sp001513675	77.3443	203	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_014775655.1	s__Clavibacter zhangzhiyongii	77.1858	167	1207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	98.40	98.40	0.96	0.96	2	-
GCF_002362255.1	s__Microbacterium sp002362255	77.1421	185	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_003384945.1	s__Clavibacter sp003384945	77.0506	179	1207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:38,111] [INFO] GTDB search result was written to GCF_011751745.2_ASM1175174v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:38,112] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:38,115] [INFO] DFAST_QC result json was written to GCF_011751745.2_ASM1175174v2_genomic.fna/dqc_result.json
[2024-01-24 12:38:38,116] [INFO] DFAST_QC completed!
[2024-01-24 12:38:38,116] [INFO] Total running time: 0h1m13s