[2024-01-24 13:36:45,291] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:45,294] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:45,294] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb840a6e-2430-497b-9499-06e02bb9b043/dqc_reference
[2024-01-24 13:36:46,593] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:46,594] [INFO] Task started: Prodigal
[2024-01-24 13:36:46,594] [INFO] Running command: gunzip -c /var/lib/cwl/stg4edc094e-af33-4ee8-bbbc-5c61ed575188/GCF_000159115.1_ASM15911v1_genomic.fna.gz | prodigal -d GCF_000159115.1_ASM15911v1_genomic.fna/cds.fna -a GCF_000159115.1_ASM15911v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:54,245] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:54,245] [INFO] Task started: HMMsearch
[2024-01-24 13:36:54,246] [INFO] Running command: hmmsearch --tblout GCF_000159115.1_ASM15911v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb840a6e-2430-497b-9499-06e02bb9b043/dqc_reference/reference_markers.hmm GCF_000159115.1_ASM15911v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:54,468] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:54,469] [INFO] Found 6/6 markers.
[2024-01-24 13:36:54,491] [INFO] Query marker FASTA was written to GCF_000159115.1_ASM15911v1_genomic.fna/markers.fasta
[2024-01-24 13:36:54,491] [INFO] Task started: Blastn
[2024-01-24 13:36:54,491] [INFO] Running command: blastn -query GCF_000159115.1_ASM15911v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb840a6e-2430-497b-9499-06e02bb9b043/dqc_reference/reference_markers.fasta -out GCF_000159115.1_ASM15911v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:55,462] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:55,465] [INFO] Selected 8 target genomes.
[2024-01-24 13:36:55,465] [INFO] Target genome list was writen to GCF_000159115.1_ASM15911v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:55,474] [INFO] Task started: fastANI
[2024-01-24 13:36:55,475] [INFO] Running command: fastANI --query /var/lib/cwl/stg4edc094e-af33-4ee8-bbbc-5c61ed575188/GCF_000159115.1_ASM15911v1_genomic.fna.gz --refList GCF_000159115.1_ASM15911v1_genomic.fna/target_genomes.txt --output GCF_000159115.1_ASM15911v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:00,230] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:00,231] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb840a6e-2430-497b-9499-06e02bb9b043/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:00,231] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb840a6e-2430-497b-9499-06e02bb9b043/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:00,239] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:37:00,240] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:00,240] [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
Corynebacterium accolens	strain=ATCC 49725	GCA_000159115.1	38284	38284	type	True	99.9998	802	804	95	conclusive
Corynebacterium accolens	strain=DSM 44278	GCA_023520795.1	38284	38284	type	True	99.9524	803	804	95	conclusive
Corynebacterium macginleyi	strain=CCUG 32361	GCA_003688935.1	38290	38290	type	True	88.0285	666	804	95	below_threshold
Corynebacterium macginleyi	strain=FDAARGOS_1195	GCA_016889465.1	38290	38290	type	True	87.9114	694	804	95	below_threshold
Corynebacterium tuberculostearicum	strain=FDAARGOS_1117	GCA_016728365.1	38304	38304	type	True	81.873	539	804	95	below_threshold
Corynebacterium camporealensis	strain=DSM 44610	GCA_000980815.1	161896	161896	type	True	79.2233	317	804	95	below_threshold
Corynebacterium massiliense	strain=DSM 45435	GCA_000420605.1	441501	441501	type	True	78.7738	255	804	95	below_threshold
Corynebacterium flavescens	strain=OJ8	GCA_001941465.1	28028	28028	type	True	78.6426	259	804	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:00,242] [INFO] DFAST Taxonomy check result was written to GCF_000159115.1_ASM15911v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:00,242] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:00,242] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:00,243] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb840a6e-2430-497b-9499-06e02bb9b043/dqc_reference/checkm_data
[2024-01-24 13:37:00,244] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:00,276] [INFO] Task started: CheckM
[2024-01-24 13:37:00,276] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000159115.1_ASM15911v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000159115.1_ASM15911v1_genomic.fna/checkm_input GCF_000159115.1_ASM15911v1_genomic.fna/checkm_result
[2024-01-24 13:37:28,708] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:28,710] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:28,728] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:28,728] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:28,729] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000159115.1_ASM15911v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:28,729] [INFO] Task started: Blastn
[2024-01-24 13:37:28,730] [INFO] Running command: blastn -query GCF_000159115.1_ASM15911v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb840a6e-2430-497b-9499-06e02bb9b043/dqc_reference/reference_markers_gtdb.fasta -out GCF_000159115.1_ASM15911v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:30,014] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:30,018] [INFO] Selected 11 target genomes.
[2024-01-24 13:37:30,018] [INFO] Target genome list was writen to GCF_000159115.1_ASM15911v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:30,030] [INFO] Task started: fastANI
[2024-01-24 13:37:30,030] [INFO] Running command: fastANI --query /var/lib/cwl/stg4edc094e-af33-4ee8-bbbc-5c61ed575188/GCF_000159115.1_ASM15911v1_genomic.fna.gz --refList GCF_000159115.1_ASM15911v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000159115.1_ASM15911v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:36,057] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:36,067] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:36,067] [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_000159115.1	s__Corynebacterium accolens	99.9998	802	804	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.20	96.99	0.95	0.94	10	conclusive
GCF_000478175.1	s__Corynebacterium sp000478175	93.5714	731	804	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.95	99.95	0.99	0.98	3	-
GCF_003688935.1	s__Corynebacterium macginleyi	88.0138	667	804	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.68	97.89	0.95	0.93	26	-
GCF_013408445.1	s__Corynebacterium tuberculostearicum	81.789	539	804	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	96.3332	98.29	96.59	0.96	0.92	3	-
GCA_900539985.1	s__Corynebacterium sp900539985	81.7813	480	804	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.98	99.98	0.92	0.92	2	-
GCF_016894265.1	s__Corynebacterium tuberculostearicum_D	81.7386	543	804	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.1108	N/A	N/A	N/A	N/A	1	-
GCF_000175635.1	s__Corynebacterium tuberculostearicum_C	81.6969	530	804	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	96.3332	96.71	96.71	0.91	0.91	2	-
GCF_002154655.1	s__Corynebacterium kefirresidentii	81.1163	512	804	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.23	95.39	0.90	0.89	9	-
GCF_000980815.1	s__Corynebacterium camporealensis	79.2233	317	804	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.96	99.96	1.00	1.00	2	-
GCF_008693105.1	s__Corynebacterium flavescens	78.4991	256	804	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.46	98.96	0.96	0.94	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:37:36,070] [INFO] GTDB search result was written to GCF_000159115.1_ASM15911v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:36,070] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:36,074] [INFO] DFAST_QC result json was written to GCF_000159115.1_ASM15911v1_genomic.fna/dqc_result.json
[2024-01-24 13:37:36,074] [INFO] DFAST_QC completed!
[2024-01-24 13:37:36,075] [INFO] Total running time: 0h0m51s