[2024-01-25 17:35:20,816] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:35:20,818] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:35:20,818] [INFO] DQC Reference Directory: /var/lib/cwl/stg5bcc9c18-7cae-4213-9afe-3d6158c9fe23/dqc_reference
[2024-01-25 17:35:21,938] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:35:21,939] [INFO] Task started: Prodigal
[2024-01-25 17:35:21,939] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c87f826-b582-4fb3-8a93-d1c59ac1028a/GCF_025002625.1_ASM2500262v1_genomic.fna.gz | prodigal -d GCF_025002625.1_ASM2500262v1_genomic.fna/cds.fna -a GCF_025002625.1_ASM2500262v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:35:30,395] [INFO] Task succeeded: Prodigal
[2024-01-25 17:35:30,395] [INFO] Task started: HMMsearch
[2024-01-25 17:35:30,395] [INFO] Running command: hmmsearch --tblout GCF_025002625.1_ASM2500262v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5bcc9c18-7cae-4213-9afe-3d6158c9fe23/dqc_reference/reference_markers.hmm GCF_025002625.1_ASM2500262v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:35:30,607] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:35:30,609] [INFO] Found 6/6 markers.
[2024-01-25 17:35:30,637] [INFO] Query marker FASTA was written to GCF_025002625.1_ASM2500262v1_genomic.fna/markers.fasta
[2024-01-25 17:35:30,637] [INFO] Task started: Blastn
[2024-01-25 17:35:30,637] [INFO] Running command: blastn -query GCF_025002625.1_ASM2500262v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bcc9c18-7cae-4213-9afe-3d6158c9fe23/dqc_reference/reference_markers.fasta -out GCF_025002625.1_ASM2500262v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:31,673] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:31,676] [INFO] Selected 15 target genomes.
[2024-01-25 17:35:31,676] [INFO] Target genome list was writen to GCF_025002625.1_ASM2500262v1_genomic.fna/target_genomes.txt
[2024-01-25 17:35:31,720] [INFO] Task started: fastANI
[2024-01-25 17:35:31,721] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c87f826-b582-4fb3-8a93-d1c59ac1028a/GCF_025002625.1_ASM2500262v1_genomic.fna.gz --refList GCF_025002625.1_ASM2500262v1_genomic.fna/target_genomes.txt --output GCF_025002625.1_ASM2500262v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:35:42,915] [INFO] Task succeeded: fastANI
[2024-01-25 17:35:42,915] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5bcc9c18-7cae-4213-9afe-3d6158c9fe23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:35:42,916] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5bcc9c18-7cae-4213-9afe-3d6158c9fe23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:35:42,926] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:35:42,926] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:35:42,926] [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 paraoxydans	strain=DSM 15019	GCA_900105335.1	199592	199592	suspected-type	True	89.9873	979	1118	95	below_threshold
Microbacterium paraoxydans	strain=NBRC 103076	GCA_001552495.1	199592	199592	suspected-type	True	89.9773	852	1118	95	below_threshold
Microbacterium algeriense	strain=G1	GCA_008868005.1	2615184	2615184	type	True	84.5114	870	1118	95	below_threshold
Microbacterium liquefaciens	strain=NBRC 15037	GCA_006539765.1	33918	33918	type	True	83.3564	735	1118	95	below_threshold
Microbacterium liquefaciens	strain=JCM 3879	GCA_014648755.1	33918	33918	type	True	83.3124	732	1118	95	below_threshold
Microbacterium oxydans	strain=NBRC 15586	GCA_006540085.1	82380	82380	suspected-type	True	83.2854	823	1118	95	below_threshold
Microbacterium oxydans	strain=DSM 20578	GCA_008868025.1	82380	82380	suspected-type	True	83.1945	831	1118	95	below_threshold
Microbacterium hydrocarbonoxydans	strain=NBRC 103074	GCA_001552455.1	273678	273678	suspected-type	True	82.5601	697	1118	95	below_threshold
Microbacterium hydrocarbonoxydans	strain=DSM 16089	GCA_900105205.1	273678	273678	suspected-type	True	82.5251	740	1118	95	below_threshold
Microbacterium saperdae	strain=JCM 1352	GCA_014646775.1	69368	69368	type	True	82.385	740	1118	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	81.0043	540	1118	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	80.946	583	1118	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	79.5243	432	1118	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	79.3786	459	1118	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	79.3425	480	1118	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:35:42,927] [INFO] DFAST Taxonomy check result was written to GCF_025002625.1_ASM2500262v1_genomic.fna/tc_result.tsv
[2024-01-25 17:35:42,928] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:35:42,928] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:35:42,928] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5bcc9c18-7cae-4213-9afe-3d6158c9fe23/dqc_reference/checkm_data
[2024-01-25 17:35:42,929] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:35:42,966] [INFO] Task started: CheckM
[2024-01-25 17:35:42,966] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025002625.1_ASM2500262v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025002625.1_ASM2500262v1_genomic.fna/checkm_input GCF_025002625.1_ASM2500262v1_genomic.fna/checkm_result
[2024-01-25 17:36:37,780] [INFO] Task succeeded: CheckM
[2024-01-25 17:36:37,781] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:36:37,810] [INFO] ===== Completeness check finished =====
[2024-01-25 17:36:37,811] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:36:37,812] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025002625.1_ASM2500262v1_genomic.fna/markers.fasta)
[2024-01-25 17:36:37,812] [INFO] Task started: Blastn
[2024-01-25 17:36:37,812] [INFO] Running command: blastn -query GCF_025002625.1_ASM2500262v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bcc9c18-7cae-4213-9afe-3d6158c9fe23/dqc_reference/reference_markers_gtdb.fasta -out GCF_025002625.1_ASM2500262v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:36:39,605] [INFO] Task succeeded: Blastn
[2024-01-25 17:36:39,608] [INFO] Selected 7 target genomes.
[2024-01-25 17:36:39,608] [INFO] Target genome list was writen to GCF_025002625.1_ASM2500262v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:36:39,637] [INFO] Task started: fastANI
[2024-01-25 17:36:39,637] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c87f826-b582-4fb3-8a93-d1c59ac1028a/GCF_025002625.1_ASM2500262v1_genomic.fna.gz --refList GCF_025002625.1_ASM2500262v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025002625.1_ASM2500262v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:36:46,029] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:46,035] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:36:46,035] [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_008271365.1	s__Microbacterium sp008271365	99.9439	1102	1118	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_019056515.1	s__Microbacterium sp001595495	90.059	954	1118	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.3631	98.29	96.93	0.91	0.85	10	-
GCF_900105335.1	s__Microbacterium paraoxydans	89.9873	979	1118	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.3631	99.12	98.76	0.96	0.92	5	-
GCF_002848265.1	s__Microbacterium sp002848265	89.8629	973	1118	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904066215.1	s__Microbacterium sp002456035	89.7857	968	1118	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.68	98.64	0.94	0.94	3	-
GCF_001866135.1	s__Microbacterium sp001866135	89.6994	959	1118	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.261	97.41	95.65	0.93	0.91	3	-
GCF_017939615.1	s__Microbacterium sp017939615	89.2866	949	1118	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 17:36:46,037] [INFO] GTDB search result was written to GCF_025002625.1_ASM2500262v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:36:46,037] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:36:46,040] [INFO] DFAST_QC result json was written to GCF_025002625.1_ASM2500262v1_genomic.fna/dqc_result.json
[2024-01-25 17:36:46,040] [INFO] DFAST_QC completed!
[2024-01-25 17:36:46,040] [INFO] Total running time: 0h1m25s