[2024-01-24 14:20:14,157] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:20:14,160] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:20:14,160] [INFO] DQC Reference Directory: /var/lib/cwl/stgca0bef4a-f739-42e1-b594-a9a7e09bb8d3/dqc_reference
[2024-01-24 14:20:15,562] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:20:15,563] [INFO] Task started: Prodigal
[2024-01-24 14:20:15,564] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb1c3482-6fbf-4b0f-a476-2e1b7ad5fd9b/GCF_008693095.1_ASM869309v1_genomic.fna.gz | prodigal -d GCF_008693095.1_ASM869309v1_genomic.fna/cds.fna -a GCF_008693095.1_ASM869309v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:23,420] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:23,421] [INFO] Task started: HMMsearch
[2024-01-24 14:20:23,421] [INFO] Running command: hmmsearch --tblout GCF_008693095.1_ASM869309v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca0bef4a-f739-42e1-b594-a9a7e09bb8d3/dqc_reference/reference_markers.hmm GCF_008693095.1_ASM869309v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:23,656] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:23,658] [INFO] Found 6/6 markers.
[2024-01-24 14:20:23,683] [INFO] Query marker FASTA was written to GCF_008693095.1_ASM869309v1_genomic.fna/markers.fasta
[2024-01-24 14:20:23,683] [INFO] Task started: Blastn
[2024-01-24 14:20:23,683] [INFO] Running command: blastn -query GCF_008693095.1_ASM869309v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca0bef4a-f739-42e1-b594-a9a7e09bb8d3/dqc_reference/reference_markers.fasta -out GCF_008693095.1_ASM869309v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:24,583] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:24,588] [INFO] Selected 21 target genomes.
[2024-01-24 14:20:24,589] [INFO] Target genome list was writen to GCF_008693095.1_ASM869309v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:24,608] [INFO] Task started: fastANI
[2024-01-24 14:20:24,608] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb1c3482-6fbf-4b0f-a476-2e1b7ad5fd9b/GCF_008693095.1_ASM869309v1_genomic.fna.gz --refList GCF_008693095.1_ASM869309v1_genomic.fna/target_genomes.txt --output GCF_008693095.1_ASM869309v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:33,760] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:33,761] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca0bef4a-f739-42e1-b594-a9a7e09bb8d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:33,762] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca0bef4a-f739-42e1-b594-a9a7e09bb8d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:33,789] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:33,789] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:33,790] [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 spheniscorum	strain=CCUG 45512	GCA_008693095.1	185761	185761	type	True	100.0	802	805	95	conclusive
Corynebacterium pollutisoli	strain=VDS11	GCA_900177745.1	1610489	1610489	type	True	78.4551	135	805	95	below_threshold
Corynebacterium humireducens	strain=DSM 45392	GCA_000819445.1	1223514	1223514	type	True	78.3436	130	805	95	below_threshold
Corynebacterium humireducens	strain=NBRC 106098	GCA_001571025.1	1223514	1223514	type	True	78.2887	127	805	95	below_threshold
Corynebacterium testudinoris	strain=DSM 44614	GCA_001021045.1	136857	136857	type	True	78.2394	127	805	95	below_threshold
Corynebacterium halotolerans	strain=DSM 44683	GCA_000688435.1	225326	225326	type	True	78.2372	141	805	95	below_threshold
Corynebacterium aquilae	strain=S-613	GCA_001941445.1	203263	203263	type	True	78.2367	136	805	95	below_threshold
Corynebacterium halotolerans	strain=YIM 70093 = DSM 44683	GCA_000341345.1	225326	225326	type	True	78.1923	143	805	95	below_threshold
Corynebacterium diphtheriae	strain=NCTC11397	GCA_001457455.1	1717	1717	type	True	78.1779	63	805	95	below_threshold
Corynebacterium diphtheriae	strain=DSM 44123	GCA_001913265.1	1717	1717	type	True	78.1596	66	805	95	below_threshold
Corynebacterium diphtheriae		GCA_902809765.1	1717	1717	type	True	78.1187	64	805	95	below_threshold
Corynebacterium diphtheriae subsp. diphtheriae	strain=FDAARGOS_1554	GCA_020736085.1	2315257	1717	type	True	78.0824	65	805	95	below_threshold
Corynebacterium occultum	strain=2039	GCA_009734425.1	2675219	2675219	type	True	77.982	159	805	95	below_threshold
Corynebacterium uberis	strain=18M0132	GCA_020616335.1	2883169	2883169	type	True	77.9745	124	805	95	below_threshold
Corynebacterium minutissimum	strain=NCTC10288	GCA_900478045.1	38301	38301	type	True	77.8771	96	805	95	below_threshold
Corynebacterium durum	strain=DSM 45333	GCA_013410305.1	61592	61592	type	True	77.6999	91	805	95	below_threshold
Corynebacterium vitaeruminis	strain=DSM 20294	GCA_000550805.1	38305	38305	type	True	77.6258	133	805	95	below_threshold
Corynebacterium lowii	strain=NML 130206	GCA_001412085.1	1544413	1544413	type	True	77.4627	129	805	95	below_threshold
Corynebacterium bouchesdurhonense	strain=SN14	GCA_900078305.2	1720192	1720192	type	True	77.123	91	805	95	below_threshold
Corynebacterium sphenisci	strain=DSM 44792	GCA_001941505.1	191493	191493	type	True	76.9414	106	805	95	below_threshold
Corynebacterium suicordis	strain=DSM 45110	GCA_015351405.1	203264	203264	type	True	76.6232	68	805	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:33,792] [INFO] DFAST Taxonomy check result was written to GCF_008693095.1_ASM869309v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:33,793] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:33,793] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:33,793] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca0bef4a-f739-42e1-b594-a9a7e09bb8d3/dqc_reference/checkm_data
[2024-01-24 14:20:33,795] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:33,824] [INFO] Task started: CheckM
[2024-01-24 14:20:33,824] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008693095.1_ASM869309v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008693095.1_ASM869309v1_genomic.fna/checkm_input GCF_008693095.1_ASM869309v1_genomic.fna/checkm_result
[2024-01-24 14:21:00,881] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:00,882] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:00,903] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:00,904] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:00,904] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008693095.1_ASM869309v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:00,905] [INFO] Task started: Blastn
[2024-01-24 14:21:00,905] [INFO] Running command: blastn -query GCF_008693095.1_ASM869309v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca0bef4a-f739-42e1-b594-a9a7e09bb8d3/dqc_reference/reference_markers_gtdb.fasta -out GCF_008693095.1_ASM869309v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:02,168] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:02,175] [INFO] Selected 21 target genomes.
[2024-01-24 14:21:02,176] [INFO] Target genome list was writen to GCF_008693095.1_ASM869309v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:02,197] [INFO] Task started: fastANI
[2024-01-24 14:21:02,197] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb1c3482-6fbf-4b0f-a476-2e1b7ad5fd9b/GCF_008693095.1_ASM869309v1_genomic.fna.gz --refList GCF_008693095.1_ASM869309v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008693095.1_ASM869309v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:12,077] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:12,100] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:12,101] [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_900113445.1	s__Corynebacterium spheniscorum	99.9851	791	805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.99	99.99	0.98	0.98	2	conclusive
GCF_900177745.1	s__Corynebacterium pollutisoli	78.4551	135	805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.83	98.83	0.98	0.98	2	-
GCF_000819445.1	s__Corynebacterium humireducens	78.3436	130	805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.80	97.60	0.97	0.93	3	-
GCF_001021045.1	s__Corynebacterium testudinoris	78.2394	127	805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001941445.1	s__Corynebacterium aquilae	78.2367	136	805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003955685.1	s__Corynebacterium sp003955685	78.1942	130	805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341345.1	s__Corynebacterium halotolerans	78.1923	143	805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001457455.1	s__Corynebacterium diphtheriae	78.1187	64	805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.05	95.03	0.92	0.83	346	-
GCF_002994655.1	s__Corynebacterium sp002994655	78.0164	130	805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009734425.1	s__Corynebacterium sp009734425	77.982	159	805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900092335.1	s__Corynebacterium phoceense	77.8356	88	805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.96	96.08	0.95	0.92	11	-
GCF_013410305.1	s__Corynebacterium durum	77.6999	91	805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.07	97.26	0.97	0.94	4	-
GCF_000550805.1	s__Corynebacterium vitaeruminis	77.6258	133	805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.86	98.60	0.94	0.94	3	-
GCF_003716585.1	s__Corynebacterium alimapuense	77.5482	99	805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009734385.1	s__Corynebacterium sp009734385	77.4662	85	805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001412085.1	s__Corynebacterium lowii	77.4627	129	805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078305.2	s__Corynebacterium bouchesdurhonense	77.1531	90	805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_016127015.1	s__Corynebacterium aurimucosum_E	77.1312	96	805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.91	96.45	0.92	0.89	6	-
GCF_000175635.1	s__Corynebacterium tuberculostearicum_C	77.0032	103	805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	96.3332	96.71	96.71	0.91	0.91	2	-
GCF_001941505.1	s__Corynebacterium sphenisci	76.9414	106	805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019114175.1	s__Corynebacterium gallistercoris	76.5268	77	805	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 14:21:12,102] [INFO] GTDB search result was written to GCF_008693095.1_ASM869309v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:12,103] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:12,107] [INFO] DFAST_QC result json was written to GCF_008693095.1_ASM869309v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:12,108] [INFO] DFAST_QC completed!
[2024-01-24 14:21:12,108] [INFO] Total running time: 0h0m58s