[2024-01-24 11:51:11,459] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:11,467] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:11,468] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e446bb1-dd91-4e4d-8e99-fac024a40f9a/dqc_reference
[2024-01-24 11:51:12,920] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:12,921] [INFO] Task started: Prodigal
[2024-01-24 11:51:12,921] [INFO] Running command: gunzip -c /var/lib/cwl/stgb1876a32-e3b4-4ebe-9540-983c9ac51741/GCF_006539465.1_ASM653946v1_genomic.fna.gz | prodigal -d GCF_006539465.1_ASM653946v1_genomic.fna/cds.fna -a GCF_006539465.1_ASM653946v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:20,730] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:20,731] [INFO] Task started: HMMsearch
[2024-01-24 11:51:20,731] [INFO] Running command: hmmsearch --tblout GCF_006539465.1_ASM653946v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e446bb1-dd91-4e4d-8e99-fac024a40f9a/dqc_reference/reference_markers.hmm GCF_006539465.1_ASM653946v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:20,977] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:20,978] [INFO] Found 6/6 markers.
[2024-01-24 11:51:21,007] [INFO] Query marker FASTA was written to GCF_006539465.1_ASM653946v1_genomic.fna/markers.fasta
[2024-01-24 11:51:21,007] [INFO] Task started: Blastn
[2024-01-24 11:51:21,007] [INFO] Running command: blastn -query GCF_006539465.1_ASM653946v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e446bb1-dd91-4e4d-8e99-fac024a40f9a/dqc_reference/reference_markers.fasta -out GCF_006539465.1_ASM653946v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:21,844] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:21,850] [INFO] Selected 9 target genomes.
[2024-01-24 11:51:21,850] [INFO] Target genome list was writen to GCF_006539465.1_ASM653946v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:21,854] [INFO] Task started: fastANI
[2024-01-24 11:51:21,855] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1876a32-e3b4-4ebe-9540-983c9ac51741/GCF_006539465.1_ASM653946v1_genomic.fna.gz --refList GCF_006539465.1_ASM653946v1_genomic.fna/target_genomes.txt --output GCF_006539465.1_ASM653946v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:26,824] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:26,825] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e446bb1-dd91-4e4d-8e99-fac024a40f9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:26,825] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e446bb1-dd91-4e4d-8e99-fac024a40f9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:26,833] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:51:26,834] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:26,834] [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 flavescens	strain=NBRC 14136	GCA_006539465.1	28028	28028	type	True	100.0	835	841	95	conclusive
Corynebacterium flavescens	strain=CCUG 28791T	GCA_008693105.1	28028	28028	type	True	99.9996	838	841	95	conclusive
Corynebacterium flavescens	strain=OJ8	GCA_001941465.1	28028	28028	type	True	99.9893	832	841	95	conclusive
Corynebacterium striatum	strain=NBRC 15291	GCA_006538485.1	43770	43770	type	True	78.839	288	841	95	below_threshold
Corynebacterium striatum	strain=FDAARGOS_1054	GCA_016403285.1	43770	43770	type	True	78.8162	287	841	95	below_threshold
Corynebacterium aurimucosum	strain=FDAARGOS_1109	GCA_016728705.1	169292	169292	suspected-type	True	78.4899	297	841	95	below_threshold
Corynebacterium aurimucosum	strain=DSM 44532	GCA_024138775.1	169292	169292	suspected-type	True	78.4847	291	841	95	below_threshold
Corynebacterium phoceense	strain=MC1	GCA_900092335.1	1686286	1686286	type	True	78.3225	256	841	95	below_threshold
Corynebacterium lizhenjunii	strain=ZJ-599	GCA_011038655.2	2709394	2709394	type	True	78.0398	174	841	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:26,835] [INFO] DFAST Taxonomy check result was written to GCF_006539465.1_ASM653946v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:26,837] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:26,837] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:26,837] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e446bb1-dd91-4e4d-8e99-fac024a40f9a/dqc_reference/checkm_data
[2024-01-24 11:51:26,838] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:26,868] [INFO] Task started: CheckM
[2024-01-24 11:51:26,868] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006539465.1_ASM653946v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006539465.1_ASM653946v1_genomic.fna/checkm_input GCF_006539465.1_ASM653946v1_genomic.fna/checkm_result
[2024-01-24 11:51:53,056] [INFO] Task succeeded: CheckM
[2024-01-24 11:51:53,057] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:51:53,078] [INFO] ===== Completeness check finished =====
[2024-01-24 11:51:53,078] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:51:53,079] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006539465.1_ASM653946v1_genomic.fna/markers.fasta)
[2024-01-24 11:51:53,079] [INFO] Task started: Blastn
[2024-01-24 11:51:53,079] [INFO] Running command: blastn -query GCF_006539465.1_ASM653946v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e446bb1-dd91-4e4d-8e99-fac024a40f9a/dqc_reference/reference_markers_gtdb.fasta -out GCF_006539465.1_ASM653946v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:54,290] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:54,293] [INFO] Selected 14 target genomes.
[2024-01-24 11:51:54,294] [INFO] Target genome list was writen to GCF_006539465.1_ASM653946v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:51:54,306] [INFO] Task started: fastANI
[2024-01-24 11:51:54,306] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1876a32-e3b4-4ebe-9540-983c9ac51741/GCF_006539465.1_ASM653946v1_genomic.fna.gz --refList GCF_006539465.1_ASM653946v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006539465.1_ASM653946v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:01,248] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:01,259] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:01,259] [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_008693105.1	s__Corynebacterium flavescens	99.9996	838	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.46	98.96	0.96	0.94	6	conclusive
GCF_016894265.1	s__Corynebacterium tuberculostearicum_D	78.9529	239	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.1108	N/A	N/A	N/A	N/A	1	-
GCF_002861385.1	s__Corynebacterium aurimucosum_C	78.8461	296	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.04	96.50	0.91	0.89	28	-
GCF_000159135.1	s__Corynebacterium striatum	78.8237	285	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.44	95.19	0.92	0.85	41	-
GCF_001836165.1	s__Corynebacterium sp001836165	78.7755	287	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.96	97.92	0.93	0.93	3	-
GCF_001586215.1	s__Corynebacterium simulans	78.7669	275	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.78	97.47	0.94	0.92	11	-
GCF_000175635.1	s__Corynebacterium tuberculostearicum_C	78.6647	255	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	96.3332	96.71	96.71	0.91	0.91	2	-
GCA_900539985.1	s__Corynebacterium sp900539985	78.6471	233	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.98	99.98	0.92	0.92	2	-
GCF_000022905.1	s__Corynebacterium aurimucosum	78.6166	287	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCF_016728705.1	s__Corynebacterium sp001807205	78.4899	297	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.15	96.83	0.93	0.90	8	-
GCF_900092335.1	s__Corynebacterium phoceense	78.3225	256	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.96	96.08	0.95	0.92	11	-
GCF_011038655.2	s__Corynebacterium lizhenjunii	78.0398	174	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.69	98.69	0.97	0.97	2	-
GCF_903645305.1	s__Corynebacterium sp001764565	77.3828	110	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.10	98.10	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:01,260] [INFO] GTDB search result was written to GCF_006539465.1_ASM653946v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:01,261] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:01,268] [INFO] DFAST_QC result json was written to GCF_006539465.1_ASM653946v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:01,268] [INFO] DFAST_QC completed!
[2024-01-24 11:52:01,268] [INFO] Total running time: 0h0m50s