[2024-01-24 12:06:24,792] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:24,794] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:24,794] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d9e26fc-542c-4b07-9f67-a0ec3dfa1fec/dqc_reference
[2024-01-24 12:06:26,138] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:26,145] [INFO] Task started: Prodigal
[2024-01-24 12:06:26,145] [INFO] Running command: gunzip -c /var/lib/cwl/stg71f6288a-b503-4156-9d3f-233648cb2e01/GCF_030408855.1_ASM3040885v1_genomic.fna.gz | prodigal -d GCF_030408855.1_ASM3040885v1_genomic.fna/cds.fna -a GCF_030408855.1_ASM3040885v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:34,364] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:34,365] [INFO] Task started: HMMsearch
[2024-01-24 12:06:34,365] [INFO] Running command: hmmsearch --tblout GCF_030408855.1_ASM3040885v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d9e26fc-542c-4b07-9f67-a0ec3dfa1fec/dqc_reference/reference_markers.hmm GCF_030408855.1_ASM3040885v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:34,565] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:34,567] [INFO] Found 6/6 markers.
[2024-01-24 12:06:34,601] [INFO] Query marker FASTA was written to GCF_030408855.1_ASM3040885v1_genomic.fna/markers.fasta
[2024-01-24 12:06:34,601] [INFO] Task started: Blastn
[2024-01-24 12:06:34,601] [INFO] Running command: blastn -query GCF_030408855.1_ASM3040885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d9e26fc-542c-4b07-9f67-a0ec3dfa1fec/dqc_reference/reference_markers.fasta -out GCF_030408855.1_ASM3040885v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:35,703] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:35,706] [INFO] Selected 13 target genomes.
[2024-01-24 12:06:35,707] [INFO] Target genome list was writen to GCF_030408855.1_ASM3040885v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:35,727] [INFO] Task started: fastANI
[2024-01-24 12:06:35,727] [INFO] Running command: fastANI --query /var/lib/cwl/stg71f6288a-b503-4156-9d3f-233648cb2e01/GCF_030408855.1_ASM3040885v1_genomic.fna.gz --refList GCF_030408855.1_ASM3040885v1_genomic.fna/target_genomes.txt --output GCF_030408855.1_ASM3040885v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:41,758] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:41,759] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d9e26fc-542c-4b07-9f67-a0ec3dfa1fec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:41,759] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d9e26fc-542c-4b07-9f67-a0ec3dfa1fec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:41,770] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:06:41,771] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:06:41,771] [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 jeddahense	strain=JCB	GCA_000577555.1	1414719	1414719	type	True	80.9878	387	843	95	below_threshold
Corynebacterium haemomassiliense	strain=Marseille-Q3615	GCA_013978595.1	2754726	2754726	type	True	80.9769	479	843	95	below_threshold
Corynebacterium bouchesdurhonense	strain=SN14	GCA_900078305.2	1720192	1720192	type	True	80.9751	452	843	95	below_threshold
Corynebacterium afermentans subsp. lipophilum	strain=CCUG 32105	GCA_015351335.1	144184	38286	type	True	80.6981	437	843	95	below_threshold
Corynebacterium lujinxingii	strain=zg-917	GCA_014490555.1	2763010	2763010	type	True	80.5555	409	843	95	below_threshold
Corynebacterium lujinxingii	strain=zg-917	GCA_014267325.1	2763010	2763010	type	True	80.5375	396	843	95	below_threshold
Corynebacterium ihumii	strain=GD7	GCA_000403725.2	1232427	1232427	type	True	80.4202	427	843	95	below_threshold
Corynebacterium imitans	strain=DSM 44264	GCA_000739455.1	156978	156978	type	True	80.2979	399	843	95	below_threshold
Corynebacterium imitans	strain=NCTC13015	GCA_900187215.1	156978	156978	type	True	80.2461	411	843	95	below_threshold
Corynebacterium senegalense	strain=Marseille-P4329	GCA_900411315.1	2080750	2080750	type	True	80.1924	418	843	95	below_threshold
Corynebacterium wankanglinii	strain=zg-913	GCA_013601005.1	2735136	2735136	type	True	80.1348	384	843	95	below_threshold
Corynebacterium gottingense	strain=DSM 103494	GCA_003693265.1	2041036	2041036	type	True	80.0864	404	843	95	below_threshold
Corynebacterium riegelii	strain=FDAARGOS_1114	GCA_016728505.1	156976	156976	type	True	79.6048	348	843	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:41,773] [INFO] DFAST Taxonomy check result was written to GCF_030408855.1_ASM3040885v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:41,773] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:41,773] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:41,773] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d9e26fc-542c-4b07-9f67-a0ec3dfa1fec/dqc_reference/checkm_data
[2024-01-24 12:06:41,775] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:41,803] [INFO] Task started: CheckM
[2024-01-24 12:06:41,804] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030408855.1_ASM3040885v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030408855.1_ASM3040885v1_genomic.fna/checkm_input GCF_030408855.1_ASM3040885v1_genomic.fna/checkm_result
[2024-01-24 12:07:09,070] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:09,071] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:09,093] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:09,093] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:09,094] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030408855.1_ASM3040885v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:09,094] [INFO] Task started: Blastn
[2024-01-24 12:07:09,094] [INFO] Running command: blastn -query GCF_030408855.1_ASM3040885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d9e26fc-542c-4b07-9f67-a0ec3dfa1fec/dqc_reference/reference_markers_gtdb.fasta -out GCF_030408855.1_ASM3040885v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:10,623] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:10,626] [INFO] Selected 13 target genomes.
[2024-01-24 12:07:10,626] [INFO] Target genome list was writen to GCF_030408855.1_ASM3040885v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:10,674] [INFO] Task started: fastANI
[2024-01-24 12:07:10,674] [INFO] Running command: fastANI --query /var/lib/cwl/stg71f6288a-b503-4156-9d3f-233648cb2e01/GCF_030408855.1_ASM3040885v1_genomic.fna.gz --refList GCF_030408855.1_ASM3040885v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030408855.1_ASM3040885v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:16,941] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:16,952] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:16,952] [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_002287505.1	s__Corynebacterium glaucum_A	96.7962	790	843	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_013978595.1	s__Corynebacterium haemomassiliense	80.9916	480	843	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	80.988	387	843	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	80.9765	452	843	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001807265.1	s__Corynebacterium sp001807265	80.7297	433	843	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.96	97.96	0.92	0.92	2	-
GCF_903645305.1	s__Corynebacterium sp001764565	80.7003	412	843	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.10	98.10	0.96	0.96	2	-
GCF_015351335.1	s__Corynebacterium lipophilum	80.6981	437	843	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900156035.1	s__Corynebacterium afermentans	80.6567	421	843	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.27	97.60	0.93	0.89	5	-
GCF_014490555.1	s__Corynebacterium sp014490555	80.5543	409	843	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	0.99	3	-
GCA_014490595.1	s__Corynebacterium sp014490595	80.2564	326	843	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.54	97.13	0.94	0.90	3	-
GCF_900411315.1	s__Corynebacterium senegalense	80.1562	417	843	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016728505.1	s__Corynebacterium riegelii	79.6538	348	843	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.34	97.30	0.92	0.92	4	-
GCF_001806875.1	s__Corynebacterium sp001806875	78.984	334	843	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 12:07:16,954] [INFO] GTDB search result was written to GCF_030408855.1_ASM3040885v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:16,954] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:16,959] [INFO] DFAST_QC result json was written to GCF_030408855.1_ASM3040885v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:16,959] [INFO] DFAST_QC completed!
[2024-01-24 12:07:16,959] [INFO] Total running time: 0h0m52s