[2024-01-24 13:32:35,079] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:35,081] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:35,081] [INFO] DQC Reference Directory: /var/lib/cwl/stg1be9eafe-38e5-404e-92bb-14625b65a6f6/dqc_reference
[2024-01-24 13:32:36,423] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:36,430] [INFO] Task started: Prodigal
[2024-01-24 13:32:36,431] [INFO] Running command: gunzip -c /var/lib/cwl/stg90343277-cf58-4b37-ac5d-064980e2fa8c/GCF_004795735.1_ASM479573v1_genomic.fna.gz | prodigal -d GCF_004795735.1_ASM479573v1_genomic.fna/cds.fna -a GCF_004795735.1_ASM479573v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:44,780] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:44,781] [INFO] Task started: HMMsearch
[2024-01-24 13:32:44,781] [INFO] Running command: hmmsearch --tblout GCF_004795735.1_ASM479573v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1be9eafe-38e5-404e-92bb-14625b65a6f6/dqc_reference/reference_markers.hmm GCF_004795735.1_ASM479573v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:45,083] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:45,084] [INFO] Found 6/6 markers.
[2024-01-24 13:32:45,108] [INFO] Query marker FASTA was written to GCF_004795735.1_ASM479573v1_genomic.fna/markers.fasta
[2024-01-24 13:32:45,108] [INFO] Task started: Blastn
[2024-01-24 13:32:45,109] [INFO] Running command: blastn -query GCF_004795735.1_ASM479573v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1be9eafe-38e5-404e-92bb-14625b65a6f6/dqc_reference/reference_markers.fasta -out GCF_004795735.1_ASM479573v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:45,989] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:45,993] [INFO] Selected 20 target genomes.
[2024-01-24 13:32:45,993] [INFO] Target genome list was writen to GCF_004795735.1_ASM479573v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:46,001] [INFO] Task started: fastANI
[2024-01-24 13:32:46,002] [INFO] Running command: fastANI --query /var/lib/cwl/stg90343277-cf58-4b37-ac5d-064980e2fa8c/GCF_004795735.1_ASM479573v1_genomic.fna.gz --refList GCF_004795735.1_ASM479573v1_genomic.fna/target_genomes.txt --output GCF_004795735.1_ASM479573v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:55,439] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:55,440] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1be9eafe-38e5-404e-92bb-14625b65a6f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:55,440] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1be9eafe-38e5-404e-92bb-14625b65a6f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:55,461] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:55,461] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:55,461] [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 endometrii	strain=LMM-1653	GCA_004795735.1	2488819	2488819	type	True	100.0	823	825	95	conclusive
Corynebacterium camporealensis	strain=CIP 105508	GCA_000766885.2	161896	161896	type	True	79.6066	224	825	95	below_threshold
Corynebacterium camporealensis	strain=DSM 44610	GCA_000980815.1	161896	161896	type	True	79.4858	227	825	95	below_threshold
Corynebacterium striatum	strain=NCTC764	GCA_900447675.1	43770	43770	type	True	79.2179	258	825	95	below_threshold
Corynebacterium striatum	strain=NBRC 15291	GCA_006538485.1	43770	43770	type	True	79.0423	256	825	95	below_threshold
Corynebacterium incognita	strain=Marseille-Q3630	GCA_014217255.1	2754725	2754725	type	True	78.973	223	825	95	below_threshold
Corynebacterium striatum	strain=FDAARGOS_1054	GCA_016403285.1	43770	43770	type	True	78.8676	263	825	95	below_threshold
Corynebacterium tuberculostearicum	strain=FDAARGOS_1117	GCA_016728365.1	38304	38304	type	True	78.8403	249	825	95	below_threshold
Corynebacterium tuberculostearicum	strain=DSM 44922	GCA_013408445.1	38304	38304	type	True	78.7789	253	825	95	below_threshold
Corynebacterium accolens	strain=DSM 44278	GCA_023520795.1	38284	38284	type	True	78.7295	218	825	95	below_threshold
Corynebacterium minutissimum	strain=NCTC10288	GCA_900478045.1	38301	38301	type	True	78.7222	231	825	95	below_threshold
Corynebacterium striatum	strain=ATCC 6940	GCA_000159135.1	43770	43770	type	True	78.6275	261	825	95	below_threshold
Corynebacterium minutissimum	strain=ATCC 23348	GCA_000805675.1	38301	38301	type	True	78.5403	229	825	95	below_threshold
Corynebacterium lizhenjunii	strain=ZJ-599	GCA_011038655.2	2709394	2709394	type	True	78.4695	207	825	95	below_threshold
Corynebacterium accolens	strain=ATCC 49725	GCA_000159115.1	38284	38284	type	True	78.3839	215	825	95	below_threshold
Corynebacterium phoceense	strain=MC1	GCA_900092335.1	1686286	1686286	type	True	78.329	266	825	95	below_threshold
Corynebacterium humireducens	strain=DSM 45392	GCA_000819445.1	1223514	1223514	type	True	78.3192	192	825	95	below_threshold
Corynebacterium frankenforstense	strain=ST18	GCA_001941485.1	1230998	1230998	type	True	78.1157	187	825	95	below_threshold
Corynebacterium humireducens	strain=NBRC 106098	GCA_001571025.1	1223514	1223514	type	True	77.846	180	825	95	below_threshold
Corynebacterium mastitidis	strain=DSM 44356	GCA_000375365.1	161890	161890	type	True	77.686	165	825	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:55,468] [INFO] DFAST Taxonomy check result was written to GCF_004795735.1_ASM479573v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:55,470] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:55,471] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:55,472] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1be9eafe-38e5-404e-92bb-14625b65a6f6/dqc_reference/checkm_data
[2024-01-24 13:32:55,474] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:55,509] [INFO] Task started: CheckM
[2024-01-24 13:32:55,509] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004795735.1_ASM479573v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004795735.1_ASM479573v1_genomic.fna/checkm_input GCF_004795735.1_ASM479573v1_genomic.fna/checkm_result
[2024-01-24 13:33:25,753] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:25,754] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:25,820] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:25,820] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:25,821] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004795735.1_ASM479573v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:25,821] [INFO] Task started: Blastn
[2024-01-24 13:33:25,821] [INFO] Running command: blastn -query GCF_004795735.1_ASM479573v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1be9eafe-38e5-404e-92bb-14625b65a6f6/dqc_reference/reference_markers_gtdb.fasta -out GCF_004795735.1_ASM479573v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:27,171] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:27,180] [INFO] Selected 21 target genomes.
[2024-01-24 13:33:27,180] [INFO] Target genome list was writen to GCF_004795735.1_ASM479573v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:27,208] [INFO] Task started: fastANI
[2024-01-24 13:33:27,209] [INFO] Running command: fastANI --query /var/lib/cwl/stg90343277-cf58-4b37-ac5d-064980e2fa8c/GCF_004795735.1_ASM479573v1_genomic.fna.gz --refList GCF_004795735.1_ASM479573v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004795735.1_ASM479573v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:37,403] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:37,422] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:37,423] [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_004795735.1	s__Corynebacterium endometrii	100.0	824	825	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002861385.1	s__Corynebacterium aurimucosum_C	79.0413	251	825	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.04	96.50	0.91	0.89	28	-
GCF_001586215.1	s__Corynebacterium simulans	78.9998	253	825	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.78	97.47	0.94	0.92	11	-
GCF_000022905.1	s__Corynebacterium aurimucosum	78.9079	259	825	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCF_000988205.1	s__Corynebacterium minutissimum_A	78.8626	238	825	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.53	96.09	0.91	0.89	16	-
GCF_016127015.1	s__Corynebacterium aurimucosum_E	78.8619	241	825	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.91	96.45	0.92	0.89	6	-
GCF_000550785.1	s__Corynebacterium casei	78.8301	205	825	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.86	98.58	0.94	0.92	5	-
GCF_000478175.1	s__Corynebacterium sp000478175	78.8266	219	825	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.95	99.95	0.99	0.98	3	-
GCF_013408445.1	s__Corynebacterium tuberculostearicum	78.7786	253	825	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	96.3332	98.29	96.59	0.96	0.92	3	-
GCF_000159135.1	s__Corynebacterium striatum	78.6967	256	825	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.44	95.19	0.92	0.85	41	-
GCF_011038655.2	s__Corynebacterium lizhenjunii	78.6291	205	825	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.69	98.69	0.97	0.97	2	-
GCF_001812805.1	s__Corynebacterium sp001812805	78.6047	205	825	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000805675.1	s__Corynebacterium minutissimum	78.5849	226	825	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.99	99.99	1.00	1.00	6	-
GCF_000175635.1	s__Corynebacterium tuberculostearicum_C	78.4771	234	825	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	78.4665	217	825	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.98	99.98	0.92	0.92	2	-
GCF_000819445.1	s__Corynebacterium humireducens	78.4541	191	825	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.80	97.60	0.97	0.93	3	-
GCF_000159115.1	s__Corynebacterium accolens	78.4458	210	825	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.20	96.99	0.95	0.94	10	-
GCF_900092335.1	s__Corynebacterium phoceense	78.3431	264	825	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.96	96.08	0.95	0.92	11	-
GCF_001941485.1	s__Corynebacterium frankenforstense	78.0582	185	825	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000375365.1	s__Corynebacterium mastitidis	77.7054	164	825	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.64	96.64	0.96	0.96	2	-
GCA_012838985.1	s__Corynebacterium sp012838985	77.0813	152	825	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:37,425] [INFO] GTDB search result was written to GCF_004795735.1_ASM479573v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:37,426] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:37,433] [INFO] DFAST_QC result json was written to GCF_004795735.1_ASM479573v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:37,433] [INFO] DFAST_QC completed!
[2024-01-24 13:33:37,433] [INFO] Total running time: 0h1m2s