[2024-01-25 19:00:50,524] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:00:50,525] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:00:50,526] [INFO] DQC Reference Directory: /var/lib/cwl/stge494aa32-1393-4d7f-b629-0b2358e0e79d/dqc_reference
[2024-01-25 19:00:51,649] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:00:51,650] [INFO] Task started: Prodigal
[2024-01-25 19:00:51,650] [INFO] Running command: gunzip -c /var/lib/cwl/stga9f9dd1c-966a-4b71-87ae-eea86d68215a/GCF_030440575.1_ASM3044057v1_genomic.fna.gz | prodigal -d GCF_030440575.1_ASM3044057v1_genomic.fna/cds.fna -a GCF_030440575.1_ASM3044057v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:00:59,613] [INFO] Task succeeded: Prodigal
[2024-01-25 19:00:59,613] [INFO] Task started: HMMsearch
[2024-01-25 19:00:59,613] [INFO] Running command: hmmsearch --tblout GCF_030440575.1_ASM3044057v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge494aa32-1393-4d7f-b629-0b2358e0e79d/dqc_reference/reference_markers.hmm GCF_030440575.1_ASM3044057v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:00:59,791] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:00:59,792] [INFO] Found 6/6 markers.
[2024-01-25 19:00:59,814] [INFO] Query marker FASTA was written to GCF_030440575.1_ASM3044057v1_genomic.fna/markers.fasta
[2024-01-25 19:00:59,814] [INFO] Task started: Blastn
[2024-01-25 19:00:59,815] [INFO] Running command: blastn -query GCF_030440575.1_ASM3044057v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge494aa32-1393-4d7f-b629-0b2358e0e79d/dqc_reference/reference_markers.fasta -out GCF_030440575.1_ASM3044057v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:01:00,637] [INFO] Task succeeded: Blastn
[2024-01-25 19:01:00,641] [INFO] Selected 22 target genomes.
[2024-01-25 19:01:00,641] [INFO] Target genome list was writen to GCF_030440575.1_ASM3044057v1_genomic.fna/target_genomes.txt
[2024-01-25 19:01:00,657] [INFO] Task started: fastANI
[2024-01-25 19:01:00,657] [INFO] Running command: fastANI --query /var/lib/cwl/stga9f9dd1c-966a-4b71-87ae-eea86d68215a/GCF_030440575.1_ASM3044057v1_genomic.fna.gz --refList GCF_030440575.1_ASM3044057v1_genomic.fna/target_genomes.txt --output GCF_030440575.1_ASM3044057v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:01:10,414] [INFO] Task succeeded: fastANI
[2024-01-25 19:01:10,414] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge494aa32-1393-4d7f-b629-0b2358e0e79d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:01:10,414] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge494aa32-1393-4d7f-b629-0b2358e0e79d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:01:10,428] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:01:10,428] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:01:10,428] [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 ciconiae	strain=DSM 44920	GCA_000372385.1	227319	227319	type	True	99.9847	835	861	95	conclusive
Corynebacterium aquilae	strain=S-613	GCA_001941445.1	203263	203263	type	True	78.8725	176	861	95	below_threshold
Corynebacterium vitaeruminis	strain=DSM 20294	GCA_000550805.1	38305	38305	type	True	78.567	210	861	95	below_threshold
Corynebacterium halotolerans	strain=YIM 70093 = DSM 44683	GCA_000341345.1	225326	225326	type	True	78.5557	204	861	95	below_threshold
Corynebacterium tapiri	strain=LMG 28165	GCA_006334925.1	1448266	1448266	type	True	78.5168	120	861	95	below_threshold
Corynebacterium occultum	strain=2039	GCA_009734425.1	2675219	2675219	type	True	78.4924	183	861	95	below_threshold
Corynebacterium frankenforstense	strain=ST18	GCA_001941485.1	1230998	1230998	type	True	78.3849	201	861	95	below_threshold
Corynebacterium ureicelerivorans	strain=IMMIB RIV-2301	GCA_000747315.1	401472	401472	type	True	78.2728	134	861	95	below_threshold
Corynebacterium marinum	strain=DSM 44953	GCA_000835165.1	349751	349751	type	True	78.2554	183	861	95	below_threshold
Corynebacterium testudinoris	strain=DSM 44614	GCA_001021045.1	136857	136857	type	True	78.1998	171	861	95	below_threshold
Corynebacterium epidermidicanis	strain=DSM 45586	GCA_001021025.1	1050174	1050174	type	True	78.124	114	861	95	below_threshold
Corynebacterium marinum	strain=CGMCC 1.6998	GCA_014645275.1	349751	349751	type	True	78.0623	182	861	95	below_threshold
Corynebacterium halotolerans	strain=DSM 44683	GCA_000688435.1	225326	225326	type	True	78.0017	197	861	95	below_threshold
Corynebacterium bouchesdurhonense	strain=SN14	GCA_900078305.2	1720192	1720192	type	True	77.9853	160	861	95	below_threshold
Corynebacterium glutamicum	strain=ATCC 13032	GCA_011761195.1	1718	1718	type	True	77.8421	113	861	95	below_threshold
Corynebacterium haemomassiliense	strain=Marseille-Q3615	GCA_013978595.1	2754726	2754726	type	True	77.8209	166	861	95	below_threshold
Corynebacterium yudongzhengii	strain=2183	GCA_003065405.1	2080740	2080740	type	True	77.798	166	861	95	below_threshold
Corynebacterium gottingense	strain=DSM 103494	GCA_003693265.1	2041036	2041036	type	True	77.7411	143	861	95	below_threshold
Corynebacterium mucifaciens	strain=ATCC 700355	GCA_012396315.1	57171	57171	type	True	77.6735	135	861	95	below_threshold
Corynebacterium godavarianum	strain=LMG 29598	GCA_007559235.1	2054421	2054421	type	True	77.6637	141	861	95	below_threshold
Corynebacterium hadale	strain=NBT06-6	GCA_002273005.1	2026255	2026255	type	True	77.6404	142	861	95	below_threshold
Corynebacterium pilosum	strain=DSM 20521	GCA_000373805.1	35756	35756	type	True	77.5401	113	861	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:01:10,429] [INFO] DFAST Taxonomy check result was written to GCF_030440575.1_ASM3044057v1_genomic.fna/tc_result.tsv
[2024-01-25 19:01:10,430] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:01:10,430] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:01:10,430] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge494aa32-1393-4d7f-b629-0b2358e0e79d/dqc_reference/checkm_data
[2024-01-25 19:01:10,431] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:01:10,459] [INFO] Task started: CheckM
[2024-01-25 19:01:10,459] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030440575.1_ASM3044057v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030440575.1_ASM3044057v1_genomic.fna/checkm_input GCF_030440575.1_ASM3044057v1_genomic.fna/checkm_result
[2024-01-25 19:01:36,714] [INFO] Task succeeded: CheckM
[2024-01-25 19:01:36,716] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:01:36,796] [INFO] ===== Completeness check finished =====
[2024-01-25 19:01:36,796] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:01:36,797] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030440575.1_ASM3044057v1_genomic.fna/markers.fasta)
[2024-01-25 19:01:36,797] [INFO] Task started: Blastn
[2024-01-25 19:01:36,797] [INFO] Running command: blastn -query GCF_030440575.1_ASM3044057v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge494aa32-1393-4d7f-b629-0b2358e0e79d/dqc_reference/reference_markers_gtdb.fasta -out GCF_030440575.1_ASM3044057v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:01:38,017] [INFO] Task succeeded: Blastn
[2024-01-25 19:01:38,020] [INFO] Selected 19 target genomes.
[2024-01-25 19:01:38,020] [INFO] Target genome list was writen to GCF_030440575.1_ASM3044057v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:01:38,046] [INFO] Task started: fastANI
[2024-01-25 19:01:38,046] [INFO] Running command: fastANI --query /var/lib/cwl/stga9f9dd1c-966a-4b71-87ae-eea86d68215a/GCF_030440575.1_ASM3044057v1_genomic.fna.gz --refList GCF_030440575.1_ASM3044057v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030440575.1_ASM3044057v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:01:46,885] [INFO] Task succeeded: fastANI
[2024-01-25 19:01:46,897] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:01:46,897] [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_000372385.1	s__Corynebacterium ciconiae	99.9847	835	861	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_008930665.1	s__Corynebacterium sp008930665	84.4728	690	861	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.86	95.30	0.97	0.95	18	-
GCF_001941445.1	s__Corynebacterium aquilae	78.7319	177	861	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000418365.1	s__Corynebacterium terpenotabidum	78.7281	121	861	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000550805.1	s__Corynebacterium vitaeruminis	78.5903	212	861	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.86	98.60	0.94	0.94	3	-
GCF_000341345.1	s__Corynebacterium halotolerans	78.588	203	861	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006334925.1	s__Corynebacterium tapiri	78.5168	120	861	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	78.5026	183	861	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001021025.1	s__Corynebacterium epidermidicanis	78.3998	117	861	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001941485.1	s__Corynebacterium frankenforstense	78.3739	201	861	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000835165.1	s__Corynebacterium marinum	78.3578	185	861	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.21	98.42	0.97	0.94	3	-
GCF_001021045.1	s__Corynebacterium testudinoris	78.1188	170	861	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	77.9089	161	861	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003065405.1	s__Corynebacterium yudongzhengii	77.871	168	861	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013978595.1	s__Corynebacterium haemomassiliense	77.8352	167	861	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003693265.1	s__Corynebacterium gottingense	77.6915	144	861	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.52	97.05	0.92	0.90	11	-
GCF_012396315.1	s__Corynebacterium mucifaciens	77.6735	135	861	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	95.74	95.74	0.89	0.89	2	-
GCA_900539985.1	s__Corynebacterium sp900539985	77.6081	118	861	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.98	99.98	0.92	0.92	2	-
GCF_007859215.1	s__Corynebacterium canis	77.3825	124	861	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:01:46,899] [INFO] GTDB search result was written to GCF_030440575.1_ASM3044057v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:01:46,900] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:01:46,904] [INFO] DFAST_QC result json was written to GCF_030440575.1_ASM3044057v1_genomic.fna/dqc_result.json
[2024-01-25 19:01:46,904] [INFO] DFAST_QC completed!
[2024-01-25 19:01:46,904] [INFO] Total running time: 0h0m56s