[2024-01-24 13:28:29,280] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:29,282] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:29,282] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c4d4b3b-36ca-4c88-9c2a-cbc68279a3be/dqc_reference
[2024-01-24 13:28:30,486] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:30,487] [INFO] Task started: Prodigal
[2024-01-24 13:28:30,487] [INFO] Running command: gunzip -c /var/lib/cwl/stg60971c10-fb51-4bb7-82ed-fb3d6992a2df/GCF_014217255.1_ASM1421725v1_genomic.fna.gz | prodigal -d GCF_014217255.1_ASM1421725v1_genomic.fna/cds.fna -a GCF_014217255.1_ASM1421725v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:38,268] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:38,268] [INFO] Task started: HMMsearch
[2024-01-24 13:28:38,269] [INFO] Running command: hmmsearch --tblout GCF_014217255.1_ASM1421725v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c4d4b3b-36ca-4c88-9c2a-cbc68279a3be/dqc_reference/reference_markers.hmm GCF_014217255.1_ASM1421725v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:38,500] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:38,501] [INFO] Found 6/6 markers.
[2024-01-24 13:28:38,533] [INFO] Query marker FASTA was written to GCF_014217255.1_ASM1421725v1_genomic.fna/markers.fasta
[2024-01-24 13:28:38,533] [INFO] Task started: Blastn
[2024-01-24 13:28:38,533] [INFO] Running command: blastn -query GCF_014217255.1_ASM1421725v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c4d4b3b-36ca-4c88-9c2a-cbc68279a3be/dqc_reference/reference_markers.fasta -out GCF_014217255.1_ASM1421725v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:39,479] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:39,481] [INFO] Selected 20 target genomes.
[2024-01-24 13:28:39,482] [INFO] Target genome list was writen to GCF_014217255.1_ASM1421725v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:39,520] [INFO] Task started: fastANI
[2024-01-24 13:28:39,521] [INFO] Running command: fastANI --query /var/lib/cwl/stg60971c10-fb51-4bb7-82ed-fb3d6992a2df/GCF_014217255.1_ASM1421725v1_genomic.fna.gz --refList GCF_014217255.1_ASM1421725v1_genomic.fna/target_genomes.txt --output GCF_014217255.1_ASM1421725v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:48,223] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:48,223] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c4d4b3b-36ca-4c88-9c2a-cbc68279a3be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:48,224] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c4d4b3b-36ca-4c88-9c2a-cbc68279a3be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:48,238] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:48,238] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:48,239] [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 incognita	strain=Marseille-Q3630	GCA_014217255.1	2754725	2754725	type	True	100.0	782	782	95	conclusive
Corynebacterium camporealensis	strain=DSM 44610	GCA_000980815.1	161896	161896	type	True	79.6122	238	782	95	below_threshold
Corynebacterium camporealensis	strain=CIP 105508	GCA_000766885.2	161896	161896	type	True	79.5901	243	782	95	below_threshold
Corynebacterium aurimucosum	strain=FDAARGOS_1109	GCA_016728705.1	169292	169292	suspected-type	True	79.3918	263	782	95	below_threshold
Corynebacterium senegalense	strain=Marseille-P4329	GCA_900411315.1	2080750	2080750	type	True	79.3016	254	782	95	below_threshold
Corynebacterium striatum	strain=NBRC 15291	GCA_006538485.1	43770	43770	type	True	79.2875	270	782	95	below_threshold
Corynebacterium striatum	strain=FDAARGOS_1054	GCA_016403285.1	43770	43770	type	True	79.2744	270	782	95	below_threshold
Corynebacterium striatum	strain=NCTC764	GCA_900447675.1	43770	43770	type	True	79.2171	274	782	95	below_threshold
Corynebacterium massiliense	strain=DSM 45435	GCA_000420605.1	441501	441501	type	True	79.1731	267	782	95	below_threshold
Corynebacterium aurimucosum	strain=DSM 44532	GCA_024138775.1	169292	169292	suspected-type	True	79.1455	256	782	95	below_threshold
Corynebacterium phoceense	strain=MC1	GCA_900092335.1	1686286	1686286	type	True	79.1276	269	782	95	below_threshold
Corynebacterium striatum	strain=ATCC 6940	GCA_000159135.1	43770	43770	type	True	79.1043	257	782	95	below_threshold
Corynebacterium wankanglinii	strain=zg-913	GCA_013601005.1	2735136	2735136	type	True	78.8468	201	782	95	below_threshold
Corynebacterium mycetoides	strain=DSM 20632	GCA_900103625.1	38302	38302	type	True	78.8071	228	782	95	below_threshold
Corynebacterium jeddahense	strain=JCB	GCA_000577555.1	1414719	1414719	type	True	78.7912	215	782	95	below_threshold
Corynebacterium doosanense	strain=CAU 212	GCA_000767055.1	1121358	1121358	type	True	78.7316	267	782	95	below_threshold
Corynebacterium halotolerans	strain=YIM 70093 = DSM 44683	GCA_000341345.1	225326	225326	type	True	78.6981	301	782	95	below_threshold
Corynebacterium doosanense	strain=DSM 45436	GCA_000372245.1	1121358	1121358	type	True	78.4464	266	782	95	below_threshold
Corynebacterium frankenforstense	strain=ST18	GCA_001941485.1	1230998	1230998	type	True	78.2885	265	782	95	below_threshold
Sanguibacter keddieii	strain=DSM 10542	GCA_000024925.1	60920	60920	type	True	76.3386	81	782	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:48,240] [INFO] DFAST Taxonomy check result was written to GCF_014217255.1_ASM1421725v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:48,241] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:48,241] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:48,241] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c4d4b3b-36ca-4c88-9c2a-cbc68279a3be/dqc_reference/checkm_data
[2024-01-24 13:28:48,242] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:48,270] [INFO] Task started: CheckM
[2024-01-24 13:28:48,270] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014217255.1_ASM1421725v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014217255.1_ASM1421725v1_genomic.fna/checkm_input GCF_014217255.1_ASM1421725v1_genomic.fna/checkm_result
[2024-01-24 13:29:15,350] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:15,352] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:15,365] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:15,366] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:15,366] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014217255.1_ASM1421725v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:15,366] [INFO] Task started: Blastn
[2024-01-24 13:29:15,367] [INFO] Running command: blastn -query GCF_014217255.1_ASM1421725v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c4d4b3b-36ca-4c88-9c2a-cbc68279a3be/dqc_reference/reference_markers_gtdb.fasta -out GCF_014217255.1_ASM1421725v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:16,750] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:16,753] [INFO] Selected 18 target genomes.
[2024-01-24 13:29:16,753] [INFO] Target genome list was writen to GCF_014217255.1_ASM1421725v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:16,779] [INFO] Task started: fastANI
[2024-01-24 13:29:16,779] [INFO] Running command: fastANI --query /var/lib/cwl/stg60971c10-fb51-4bb7-82ed-fb3d6992a2df/GCF_014217255.1_ASM1421725v1_genomic.fna.gz --refList GCF_014217255.1_ASM1421725v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014217255.1_ASM1421725v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:25,876] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:25,891] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:25,892] [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_014217255.1	s__Corynebacterium incognitum	100.0	782	782	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_000980815.1	s__Corynebacterium camporealensis	79.6353	236	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.96	99.96	1.00	1.00	2	-
GCF_001815935.1	s__Corynebacterium sp001815935	79.6004	314	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002861385.1	s__Corynebacterium aurimucosum_C	79.5106	272	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.04	96.50	0.91	0.89	28	-
GCF_001812805.1	s__Corynebacterium sp001812805	79.4292	237	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016728705.1	s__Corynebacterium sp001807205	79.3297	262	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.15	96.83	0.93	0.90	8	-
GCA_014490595.1	s__Corynebacterium sp014490595	79.2137	167	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.54	97.13	0.94	0.90	3	-
GCF_001586215.1	s__Corynebacterium simulans	79.1988	237	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.78	97.47	0.94	0.92	11	-
GCF_000420605.1	s__Corynebacterium massiliense	79.1733	267	782	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	79.1451	268	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.96	96.08	0.95	0.92	11	-
GCF_000159135.1	s__Corynebacterium striatum	79.1315	255	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.44	95.19	0.92	0.85	41	-
GCF_900103625.1	s__Corynebacterium mycetoides	78.8148	226	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000577555.1	s__Corynebacterium jeddahense	78.7912	215	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000767055.1	s__Corynebacterium doosanense	78.6895	265	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001941485.1	s__Corynebacterium frankenforstense	78.2871	267	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024925.1	s__Sanguibacter keddieii	76.5072	82	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001722485.1	s__Cellulosimicrobium cellulans_A	76.2348	67	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:25,893] [INFO] GTDB search result was written to GCF_014217255.1_ASM1421725v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:25,895] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:25,899] [INFO] DFAST_QC result json was written to GCF_014217255.1_ASM1421725v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:25,900] [INFO] DFAST_QC completed!
[2024-01-24 13:29:25,900] [INFO] Total running time: 0h0m57s