[2024-01-24 11:43:41,929] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:41,940] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:41,940] [INFO] DQC Reference Directory: /var/lib/cwl/stg2de8aa22-546c-4371-986a-e2ab7deb300b/dqc_reference
[2024-01-24 11:43:43,418] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:43,419] [INFO] Task started: Prodigal
[2024-01-24 11:43:43,419] [INFO] Running command: gunzip -c /var/lib/cwl/stgea81484d-1943-4557-bd5e-de8ffb2253d2/GCF_900155535.1_ASM90015553v1_genomic.fna.gz | prodigal -d GCF_900155535.1_ASM90015553v1_genomic.fna/cds.fna -a GCF_900155535.1_ASM90015553v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:50,880] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:50,881] [INFO] Task started: HMMsearch
[2024-01-24 11:43:50,881] [INFO] Running command: hmmsearch --tblout GCF_900155535.1_ASM90015553v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2de8aa22-546c-4371-986a-e2ab7deb300b/dqc_reference/reference_markers.hmm GCF_900155535.1_ASM90015553v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:51,203] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:51,204] [INFO] Found 6/6 markers.
[2024-01-24 11:43:51,226] [INFO] Query marker FASTA was written to GCF_900155535.1_ASM90015553v1_genomic.fna/markers.fasta
[2024-01-24 11:43:51,226] [INFO] Task started: Blastn
[2024-01-24 11:43:51,226] [INFO] Running command: blastn -query GCF_900155535.1_ASM90015553v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2de8aa22-546c-4371-986a-e2ab7deb300b/dqc_reference/reference_markers.fasta -out GCF_900155535.1_ASM90015553v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:52,329] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:52,332] [INFO] Selected 13 target genomes.
[2024-01-24 11:43:52,332] [INFO] Target genome list was writen to GCF_900155535.1_ASM90015553v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:52,356] [INFO] Task started: fastANI
[2024-01-24 11:43:52,357] [INFO] Running command: fastANI --query /var/lib/cwl/stgea81484d-1943-4557-bd5e-de8ffb2253d2/GCF_900155535.1_ASM90015553v1_genomic.fna.gz --refList GCF_900155535.1_ASM90015553v1_genomic.fna/target_genomes.txt --output GCF_900155535.1_ASM90015553v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:43:59,409] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:59,409] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2de8aa22-546c-4371-986a-e2ab7deb300b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:43:59,410] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2de8aa22-546c-4371-986a-e2ab7deb300b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:43:59,421] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:43:59,421] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:43:59,421] [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 urinipleomorphum	strain=Marseille-P2799	GCA_900155535.1	1852380	1852380	type	True	100.0	749	749	95	conclusive
Corynebacterium appendicis	strain=DSM 44531	GCA_900156665.1	163202	163202	type	True	85.1697	591	749	95	below_threshold
Corynebacterium senegalense	strain=Marseille-P4329	GCA_900411315.1	2080750	2080750	type	True	80.3875	362	749	95	below_threshold
Corynebacterium jeddahense	strain=JCB	GCA_000577555.1	1414719	1414719	type	True	80.2105	319	749	95	below_threshold
Corynebacterium lujinxingii	strain=zg-917	GCA_014267325.1	2763010	2763010	type	True	80.1715	342	749	95	below_threshold
Corynebacterium lujinxingii	strain=zg-917	GCA_014490555.1	2763010	2763010	type	True	80.1528	347	749	95	below_threshold
Corynebacterium bouchesdurhonense	strain=SN14	GCA_900078305.2	1720192	1720192	type	True	80.0225	348	749	95	below_threshold
Corynebacterium haemomassiliense	strain=Marseille-Q3615	GCA_013978595.1	2754726	2754726	type	True	79.9853	372	749	95	below_threshold
Corynebacterium afermentans subsp. lipophilum	strain=CCUG 32105	GCA_015351335.1	144184	38286	type	True	79.8081	339	749	95	below_threshold
Corynebacterium ihumii	strain=GD7	GCA_000403725.2	1232427	1232427	type	True	79.7114	337	749	95	below_threshold
Corynebacterium tuscaniense	strain=CCUG 51321T	GCA_008693065.1	302449	302449	type	True	79.591	350	749	95	below_threshold
Corynebacterium lipophiloflavum	strain=DSM 44291	GCA_000159635.1	161889	161889	type	True	79.2357	305	749	95	below_threshold
Corynebacterium qintianiae	strain=MC1420	GCA_011038645.2	2709392	2709392	type	True	79.1935	309	749	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:43:59,423] [INFO] DFAST Taxonomy check result was written to GCF_900155535.1_ASM90015553v1_genomic.fna/tc_result.tsv
[2024-01-24 11:43:59,424] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:43:59,424] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:43:59,424] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2de8aa22-546c-4371-986a-e2ab7deb300b/dqc_reference/checkm_data
[2024-01-24 11:43:59,425] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:43:59,465] [INFO] Task started: CheckM
[2024-01-24 11:43:59,466] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900155535.1_ASM90015553v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900155535.1_ASM90015553v1_genomic.fna/checkm_input GCF_900155535.1_ASM90015553v1_genomic.fna/checkm_result
[2024-01-24 11:44:26,653] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:26,654] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:26,673] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:26,673] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:26,673] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900155535.1_ASM90015553v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:26,674] [INFO] Task started: Blastn
[2024-01-24 11:44:26,674] [INFO] Running command: blastn -query GCF_900155535.1_ASM90015553v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2de8aa22-546c-4371-986a-e2ab7deb300b/dqc_reference/reference_markers_gtdb.fasta -out GCF_900155535.1_ASM90015553v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:28,231] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:28,235] [INFO] Selected 9 target genomes.
[2024-01-24 11:44:28,236] [INFO] Target genome list was writen to GCF_900155535.1_ASM90015553v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:28,244] [INFO] Task started: fastANI
[2024-01-24 11:44:28,245] [INFO] Running command: fastANI --query /var/lib/cwl/stgea81484d-1943-4557-bd5e-de8ffb2253d2/GCF_900155535.1_ASM90015553v1_genomic.fna.gz --refList GCF_900155535.1_ASM90015553v1_genomic.fna/target_genomes_gtdb.txt --output GCF_900155535.1_ASM90015553v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:33,044] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:33,053] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:33,053] [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_900155535.1	s__Corynebacterium urinipleomorphum	100.0	749	749	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_900156665.1	s__Corynebacterium appendicis	85.1697	591	749	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017942225.1	s__Corynebacterium sp017942225	84.5455	585	749	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000143825.1	s__Corynebacterium genitalium_A	81.1536	466	749	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900618065.1	s__Corynebacterium sp900618065	80.786	452	749	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014490555.1	s__Corynebacterium sp014490555	80.1362	348	749	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	0.99	3	-
GCF_900078305.2	s__Corynebacterium bouchesdurhonense	80.0343	346	749	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_013978595.1	s__Corynebacterium haemomassiliense	79.9825	371	749	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008693065.1	s__Corynebacterium tuscaniense	79.58	352	749	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.42	98.40	0.94	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:33,055] [INFO] GTDB search result was written to GCF_900155535.1_ASM90015553v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:33,055] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:33,058] [INFO] DFAST_QC result json was written to GCF_900155535.1_ASM90015553v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:33,058] [INFO] DFAST_QC completed!
[2024-01-24 11:44:33,059] [INFO] Total running time: 0h0m51s