[2024-01-24 13:57:32,141] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:32,143] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:32,143] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e1676c5-faee-4836-b6f5-88d30cf86e42/dqc_reference
[2024-01-24 13:57:33,545] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:33,546] [INFO] Task started: Prodigal
[2024-01-24 13:57:33,546] [INFO] Running command: gunzip -c /var/lib/cwl/stgaa8b74bd-2270-403b-a9fc-3748b5185357/GCF_019753765.1_ASM1975376v1_genomic.fna.gz | prodigal -d GCF_019753765.1_ASM1975376v1_genomic.fna/cds.fna -a GCF_019753765.1_ASM1975376v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:44,233] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:44,233] [INFO] Task started: HMMsearch
[2024-01-24 13:57:44,233] [INFO] Running command: hmmsearch --tblout GCF_019753765.1_ASM1975376v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e1676c5-faee-4836-b6f5-88d30cf86e42/dqc_reference/reference_markers.hmm GCF_019753765.1_ASM1975376v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:44,546] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:44,547] [INFO] Found 6/6 markers.
[2024-01-24 13:57:44,588] [INFO] Query marker FASTA was written to GCF_019753765.1_ASM1975376v1_genomic.fna/markers.fasta
[2024-01-24 13:57:44,589] [INFO] Task started: Blastn
[2024-01-24 13:57:44,589] [INFO] Running command: blastn -query GCF_019753765.1_ASM1975376v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e1676c5-faee-4836-b6f5-88d30cf86e42/dqc_reference/reference_markers.fasta -out GCF_019753765.1_ASM1975376v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:45,925] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:45,929] [INFO] Selected 11 target genomes.
[2024-01-24 13:57:45,929] [INFO] Target genome list was writen to GCF_019753765.1_ASM1975376v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:45,941] [INFO] Task started: fastANI
[2024-01-24 13:57:45,942] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa8b74bd-2270-403b-a9fc-3748b5185357/GCF_019753765.1_ASM1975376v1_genomic.fna.gz --refList GCF_019753765.1_ASM1975376v1_genomic.fna/target_genomes.txt --output GCF_019753765.1_ASM1975376v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:54,085] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:54,086] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e1676c5-faee-4836-b6f5-88d30cf86e42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:54,086] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e1676c5-faee-4836-b6f5-88d30cf86e42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:54,097] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:54,097] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:54,097] [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 marinilacus	strain=YM11-607	GCA_019753765.1	415209	415209	type	True	100.0	1283	1283	95	conclusive
Microbacterium stercoris	strain=NEAU-LLB	GCA_017592545.1	2820289	2820289	type	True	81.9915	663	1283	95	below_threshold
Microbacterium album	strain=CGMCC 1.15794	GCA_014643695.1	2053191	2053191	type	True	81.9015	618	1283	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_004564075.1	904291	904291	type	True	81.5373	576	1283	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_001689915.1	904291	904291	type	True	81.4081	575	1283	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_002741995.1	904291	904291	type	True	81.3248	582	1283	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	80.7249	540	1283	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	79.9751	431	1283	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	79.8005	501	1283	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	79.4711	499	1283	95	below_threshold
Microbacterium invictum	strain=DSM 19600	GCA_023155715.1	515415	515415	type	True	79.4236	452	1283	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:54,100] [INFO] DFAST Taxonomy check result was written to GCF_019753765.1_ASM1975376v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:54,100] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:54,101] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:54,101] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e1676c5-faee-4836-b6f5-88d30cf86e42/dqc_reference/checkm_data
[2024-01-24 13:57:54,102] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:54,141] [INFO] Task started: CheckM
[2024-01-24 13:57:54,142] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019753765.1_ASM1975376v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019753765.1_ASM1975376v1_genomic.fna/checkm_input GCF_019753765.1_ASM1975376v1_genomic.fna/checkm_result
[2024-01-24 13:58:44,792] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:44,793] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:44,816] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:44,816] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:44,817] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019753765.1_ASM1975376v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:44,817] [INFO] Task started: Blastn
[2024-01-24 13:58:44,817] [INFO] Running command: blastn -query GCF_019753765.1_ASM1975376v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e1676c5-faee-4836-b6f5-88d30cf86e42/dqc_reference/reference_markers_gtdb.fasta -out GCF_019753765.1_ASM1975376v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:46,827] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:46,831] [INFO] Selected 6 target genomes.
[2024-01-24 13:58:46,831] [INFO] Target genome list was writen to GCF_019753765.1_ASM1975376v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:46,834] [INFO] Task started: fastANI
[2024-01-24 13:58:46,835] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa8b74bd-2270-403b-a9fc-3748b5185357/GCF_019753765.1_ASM1975376v1_genomic.fna.gz --refList GCF_019753765.1_ASM1975376v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019753765.1_ASM1975376v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:51,512] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:51,519] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:58:51,519] [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_001426925.1	s__Microbacterium sp001426925	83.5718	652	1283	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.86	98.86	0.90	0.90	2	-
GCF_015235415.1	s__Microbacterium paludicola_A	83.5543	668	1283	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016805985.1	s__Microbacterium sp016805985	83.3205	702	1283	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017592545.1	s__Microbacterium sp017592545	81.986	663	1283	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643695.1	s__Microbacterium album	81.8895	619	1283	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004564075.1	s__Microbacterium sediminis	81.4898	580	1283	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.95	99.95	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:51,521] [INFO] GTDB search result was written to GCF_019753765.1_ASM1975376v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:51,521] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:51,524] [INFO] DFAST_QC result json was written to GCF_019753765.1_ASM1975376v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:51,524] [INFO] DFAST_QC completed!
[2024-01-24 13:58:51,525] [INFO] Total running time: 0h1m19s