[2024-01-24 11:34:41,522] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:41,526] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:41,527] [INFO] DQC Reference Directory: /var/lib/cwl/stg13575a7c-0a8d-495b-ae6c-73fbada842b7/dqc_reference
[2024-01-24 11:34:42,837] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:42,838] [INFO] Task started: Prodigal
[2024-01-24 11:34:42,838] [INFO] Running command: gunzip -c /var/lib/cwl/stgbeb5fb54-12c0-4527-841c-39d171efbfeb/GCF_014191305.1_ASM1419130v1_genomic.fna.gz | prodigal -d GCF_014191305.1_ASM1419130v1_genomic.fna/cds.fna -a GCF_014191305.1_ASM1419130v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:53,944] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:53,945] [INFO] Task started: HMMsearch
[2024-01-24 11:34:53,945] [INFO] Running command: hmmsearch --tblout GCF_014191305.1_ASM1419130v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13575a7c-0a8d-495b-ae6c-73fbada842b7/dqc_reference/reference_markers.hmm GCF_014191305.1_ASM1419130v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:54,225] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:54,226] [INFO] Found 6/6 markers.
[2024-01-24 11:34:54,259] [INFO] Query marker FASTA was written to GCF_014191305.1_ASM1419130v1_genomic.fna/markers.fasta
[2024-01-24 11:34:54,259] [INFO] Task started: Blastn
[2024-01-24 11:34:54,259] [INFO] Running command: blastn -query GCF_014191305.1_ASM1419130v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13575a7c-0a8d-495b-ae6c-73fbada842b7/dqc_reference/reference_markers.fasta -out GCF_014191305.1_ASM1419130v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:55,351] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:55,355] [INFO] Selected 18 target genomes.
[2024-01-24 11:34:55,355] [INFO] Target genome list was writen to GCF_014191305.1_ASM1419130v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:55,363] [INFO] Task started: fastANI
[2024-01-24 11:34:55,363] [INFO] Running command: fastANI --query /var/lib/cwl/stgbeb5fb54-12c0-4527-841c-39d171efbfeb/GCF_014191305.1_ASM1419130v1_genomic.fna.gz --refList GCF_014191305.1_ASM1419130v1_genomic.fna/target_genomes.txt --output GCF_014191305.1_ASM1419130v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:08,592] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:08,592] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13575a7c-0a8d-495b-ae6c-73fbada842b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:08,593] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13575a7c-0a8d-495b-ae6c-73fbada842b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:08,608] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:08,608] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:08,608] [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
Pseudoclavibacter helvolus	strain=DSM 20419	GCA_014191305.1	255205	255205	type	True	100.0	1269	1272	95	conclusive
Pseudoclavibacter terrae	strain=THG-MD12	GCA_008831075.1	1530195	1530195	type	True	87.1739	950	1272	95	below_threshold
Pseudoclavibacter chungangensis	strain=DSM 23821	GCA_013410545.1	587635	587635	type	True	79.4579	425	1272	95	below_threshold
Pseudoclavibacter chungangensis	strain=DSM 23821	GCA_008831135.1	587635	587635	type	True	79.1714	417	1272	95	below_threshold
Pseudoclavibacter alba	strain=NBRC 15616	GCA_001570905.1	272241	272241	type	True	78.4926	209	1272	95	below_threshold
Pseudoclavibacter endophyticus	strain=CGMCC 1.15081	GCA_014640595.1	1778590	1778590	type	True	78.2725	296	1272	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	78.2412	293	1272	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	78.0479	280	1272	95	below_threshold
Gulosibacter faecalis	strain=B187	GCA_000381765.1	272240	272240	type	True	78.0027	308	1272	95	below_threshold
Agromyces protaetiae	strain=FW100M-8	GCA_004135405.1	2509455	2509455	type	True	77.8732	315	1272	95	below_threshold
Agromyces salentinus	strain=JCM 14323	GCA_009749395.1	269421	269421	type	True	77.8259	329	1272	95	below_threshold
Microbacterium immunditiarum	strain=DSM 24662	GCA_013409785.1	337480	337480	type	True	77.763	246	1272	95	below_threshold
Agromyces tardus	strain=SJ-23	GCA_003710805.1	2583849	2583849	type	True	77.7393	333	1272	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	77.6682	294	1272	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	77.4337	318	1272	95	below_threshold
Amnibacterium setariae	strain=DD4a	GCA_003581425.1	2306585	2306585	type	True	77.3805	260	1272	95	below_threshold
Amnibacterium kyonggiense	strain=DSM 24782	GCA_004364555.1	595671	595671	type	True	77.1614	240	1272	95	below_threshold
Amycolatopsis roodepoortensis	strain=DSM 46661	GCA_014873915.1	700274	700274	type	True	76.0326	174	1272	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:08,610] [INFO] DFAST Taxonomy check result was written to GCF_014191305.1_ASM1419130v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:08,611] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:08,611] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:08,611] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13575a7c-0a8d-495b-ae6c-73fbada842b7/dqc_reference/checkm_data
[2024-01-24 11:35:08,613] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:08,652] [INFO] Task started: CheckM
[2024-01-24 11:35:08,653] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014191305.1_ASM1419130v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014191305.1_ASM1419130v1_genomic.fna/checkm_input GCF_014191305.1_ASM1419130v1_genomic.fna/checkm_result
[2024-01-24 11:35:44,523] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:44,524] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:44,548] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:44,548] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:44,549] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014191305.1_ASM1419130v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:44,549] [INFO] Task started: Blastn
[2024-01-24 11:35:44,549] [INFO] Running command: blastn -query GCF_014191305.1_ASM1419130v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13575a7c-0a8d-495b-ae6c-73fbada842b7/dqc_reference/reference_markers_gtdb.fasta -out GCF_014191305.1_ASM1419130v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:46,157] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:46,161] [INFO] Selected 5 target genomes.
[2024-01-24 11:35:46,161] [INFO] Target genome list was writen to GCF_014191305.1_ASM1419130v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:46,166] [INFO] Task started: fastANI
[2024-01-24 11:35:46,166] [INFO] Running command: fastANI --query /var/lib/cwl/stgbeb5fb54-12c0-4527-841c-39d171efbfeb/GCF_014191305.1_ASM1419130v1_genomic.fna.gz --refList GCF_014191305.1_ASM1419130v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014191305.1_ASM1419130v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:35:51,341] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:51,347] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:35:51,347] [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_014191305.1	s__Pseudoclavibacter helvolus	100.0	1270	1272	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudoclavibacter	95.0	98.40	98.37	0.85	0.85	3	conclusive
GCF_002931075.1	s__Pseudoclavibacter sp002931075	89.492	975	1272	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudoclavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002931555.1	s__Pseudoclavibacter sp002931555	87.2488	936	1272	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudoclavibacter	95.0	98.27	98.05	0.90	0.88	3	-
GCF_008831075.1	s__Pseudoclavibacter terrae	87.1739	950	1272	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudoclavibacter	95.0	96.82	96.82	0.88	0.88	2	-
GCF_002931055.1	s__Pseudoclavibacter sp002931055	86.4523	925	1272	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudoclavibacter	95.0	97.65	95.42	0.90	0.86	11	-
--------------------------------------------------------------------------------
[2024-01-24 11:35:51,349] [INFO] GTDB search result was written to GCF_014191305.1_ASM1419130v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:35:51,350] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:35:51,353] [INFO] DFAST_QC result json was written to GCF_014191305.1_ASM1419130v1_genomic.fna/dqc_result.json
[2024-01-24 11:35:51,353] [INFO] DFAST_QC completed!
[2024-01-24 11:35:51,353] [INFO] Total running time: 0h1m10s