[2024-01-24 13:42:57,281] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:42:57,283] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:42:57,284] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f2b3e09-5d0c-41e9-a059-408fcb0005cf/dqc_reference
[2024-01-24 13:42:58,502] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:42:58,502] [INFO] Task started: Prodigal
[2024-01-24 13:42:58,503] [INFO] Running command: gunzip -c /var/lib/cwl/stga73ef374-d6c3-4fef-896b-54c1862399ff/GCF_008693075.1_ASM869307v1_genomic.fna.gz | prodigal -d GCF_008693075.1_ASM869307v1_genomic.fna/cds.fna -a GCF_008693075.1_ASM869307v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:43:06,764] [INFO] Task succeeded: Prodigal
[2024-01-24 13:43:06,764] [INFO] Task started: HMMsearch
[2024-01-24 13:43:06,764] [INFO] Running command: hmmsearch --tblout GCF_008693075.1_ASM869307v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f2b3e09-5d0c-41e9-a059-408fcb0005cf/dqc_reference/reference_markers.hmm GCF_008693075.1_ASM869307v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:43:06,981] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:43:06,982] [INFO] Found 6/6 markers.
[2024-01-24 13:43:07,010] [INFO] Query marker FASTA was written to GCF_008693075.1_ASM869307v1_genomic.fna/markers.fasta
[2024-01-24 13:43:07,010] [INFO] Task started: Blastn
[2024-01-24 13:43:07,010] [INFO] Running command: blastn -query GCF_008693075.1_ASM869307v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f2b3e09-5d0c-41e9-a059-408fcb0005cf/dqc_reference/reference_markers.fasta -out GCF_008693075.1_ASM869307v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:07,813] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:07,817] [INFO] Selected 18 target genomes.
[2024-01-24 13:43:07,817] [INFO] Target genome list was writen to GCF_008693075.1_ASM869307v1_genomic.fna/target_genomes.txt
[2024-01-24 13:43:07,840] [INFO] Task started: fastANI
[2024-01-24 13:43:07,841] [INFO] Running command: fastANI --query /var/lib/cwl/stga73ef374-d6c3-4fef-896b-54c1862399ff/GCF_008693075.1_ASM869307v1_genomic.fna.gz --refList GCF_008693075.1_ASM869307v1_genomic.fna/target_genomes.txt --output GCF_008693075.1_ASM869307v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:43:17,195] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:17,195] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f2b3e09-5d0c-41e9-a059-408fcb0005cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:43:17,196] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f2b3e09-5d0c-41e9-a059-408fcb0005cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:43:17,214] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:43:17,214] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:43:17,215] [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 phocae	strain=CCUG 38205T	GCA_008693075.1	161895	161895	type	True	100.0	884	886	95	conclusive
Corynebacterium phocae	strain=M408/89/1	GCA_001941565.1	161895	161895	type	True	99.9976	884	886	95	conclusive
Corynebacterium tuberculostearicum	strain=FDAARGOS_1117	GCA_016728365.1	38304	38304	type	True	78.1837	172	886	95	below_threshold
Corynebacterium lizhenjunii	strain=ZJ-599	GCA_011038655.2	2709394	2709394	type	True	78.0622	232	886	95	below_threshold
Corynebacterium phoceense	strain=MC1	GCA_900092335.1	1686286	1686286	type	True	77.9351	212	886	95	below_threshold
Corynebacterium aurimucosum	strain=DSM 44532	GCA_024138775.1	169292	169292	suspected-type	True	77.8906	197	886	95	below_threshold
Corynebacterium aurimucosum	strain=FDAARGOS_1109	GCA_016728705.1	169292	169292	suspected-type	True	77.8657	200	886	95	below_threshold
Corynebacterium striatum	strain=NBRC 15291	GCA_006538485.1	43770	43770	type	True	77.7567	201	886	95	below_threshold
Corynebacterium minutissimum	strain=NBRC 15361	GCA_001552395.1	38301	38301	type	True	77.7282	176	886	95	below_threshold
Corynebacterium minutissimum	strain=ATCC 23348	GCA_000805675.1	38301	38301	type	True	77.7266	177	886	95	below_threshold
Corynebacterium minutissimum	strain=NCTC10288	GCA_900478045.1	38301	38301	type	True	77.7212	180	886	95	below_threshold
Corynebacterium striatum	strain=FDAARGOS_1054	GCA_016403285.1	43770	43770	type	True	77.7123	201	886	95	below_threshold
Corynebacterium striatum	strain=NCTC764	GCA_900447675.1	43770	43770	type	True	77.6906	202	886	95	below_threshold
Corynebacterium flavescens	strain=CCUG 28791T	GCA_008693105.1	28028	28028	type	True	77.6089	150	886	95	below_threshold
Corynebacterium flavescens	strain=OJ8	GCA_001941465.1	28028	28028	type	True	77.5687	156	886	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:43:17,217] [INFO] DFAST Taxonomy check result was written to GCF_008693075.1_ASM869307v1_genomic.fna/tc_result.tsv
[2024-01-24 13:43:17,217] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:43:17,217] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:43:17,218] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f2b3e09-5d0c-41e9-a059-408fcb0005cf/dqc_reference/checkm_data
[2024-01-24 13:43:17,219] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:43:17,247] [INFO] Task started: CheckM
[2024-01-24 13:43:17,247] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008693075.1_ASM869307v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008693075.1_ASM869307v1_genomic.fna/checkm_input GCF_008693075.1_ASM869307v1_genomic.fna/checkm_result
[2024-01-24 13:43:45,878] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:45,879] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:45,899] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:45,899] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:45,900] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008693075.1_ASM869307v1_genomic.fna/markers.fasta)
[2024-01-24 13:43:45,900] [INFO] Task started: Blastn
[2024-01-24 13:43:45,900] [INFO] Running command: blastn -query GCF_008693075.1_ASM869307v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f2b3e09-5d0c-41e9-a059-408fcb0005cf/dqc_reference/reference_markers_gtdb.fasta -out GCF_008693075.1_ASM869307v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:47,053] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:47,057] [INFO] Selected 22 target genomes.
[2024-01-24 13:43:47,058] [INFO] Target genome list was writen to GCF_008693075.1_ASM869307v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:47,097] [INFO] Task started: fastANI
[2024-01-24 13:43:47,098] [INFO] Running command: fastANI --query /var/lib/cwl/stga73ef374-d6c3-4fef-896b-54c1862399ff/GCF_008693075.1_ASM869307v1_genomic.fna.gz --refList GCF_008693075.1_ASM869307v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008693075.1_ASM869307v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:57,865] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:57,892] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:57,892] [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_001941565.1	s__Corynebacterium phocae	99.9976	884	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_013408445.1	s__Corynebacterium tuberculostearicum	78.2746	172	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	96.3332	98.29	96.59	0.96	0.92	3	-
GCF_016894265.1	s__Corynebacterium tuberculostearicum_D	78.1844	177	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.1108	N/A	N/A	N/A	N/A	1	-
GCF_001815935.1	s__Corynebacterium sp001815935	78.0866	218	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011038655.2	s__Corynebacterium lizhenjunii	78.0622	232	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.69	98.69	0.97	0.97	2	-
GCF_001836165.1	s__Corynebacterium sp001836165	78.0012	190	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.96	97.92	0.93	0.93	3	-
GCF_000478175.1	s__Corynebacterium sp000478175	78.0008	171	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.95	99.95	0.99	0.98	3	-
GCF_002861385.1	s__Corynebacterium aurimucosum_C	77.9727	190	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.04	96.50	0.91	0.89	28	-
GCF_000175635.1	s__Corynebacterium tuberculostearicum_C	77.9615	184	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	96.3332	96.71	96.71	0.91	0.91	2	-
GCF_900092335.1	s__Corynebacterium phoceense	77.9407	211	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.96	96.08	0.95	0.92	11	-
GCF_016127015.1	s__Corynebacterium aurimucosum_E	77.9189	180	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.91	96.45	0.92	0.89	6	-
GCA_900539985.1	s__Corynebacterium sp900539985	77.8799	163	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.98	99.98	0.92	0.92	2	-
GCF_016728705.1	s__Corynebacterium sp001807205	77.8657	200	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.15	96.83	0.93	0.90	8	-
GCF_000159135.1	s__Corynebacterium striatum	77.8461	199	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.44	95.19	0.92	0.85	41	-
GCF_000805675.1	s__Corynebacterium minutissimum	77.7266	177	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.99	99.99	1.00	1.00	6	-
GCF_001812805.1	s__Corynebacterium sp001812805	77.6856	185	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008693105.1	s__Corynebacterium flavescens	77.6359	148	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.46	98.96	0.96	0.94	6	-
GCF_001586215.1	s__Corynebacterium simulans	77.5871	187	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.78	97.47	0.94	0.92	11	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:57,893] [INFO] GTDB search result was written to GCF_008693075.1_ASM869307v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:57,894] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:57,897] [INFO] DFAST_QC result json was written to GCF_008693075.1_ASM869307v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:57,897] [INFO] DFAST_QC completed!
[2024-01-24 13:43:57,898] [INFO] Total running time: 0h1m1s