[2024-01-24 14:47:04,808] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:04,810] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:04,810] [INFO] DQC Reference Directory: /var/lib/cwl/stg12e114e4-a151-47ed-a442-f6a6cbdec6f2/dqc_reference
[2024-01-24 14:47:06,077] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:06,078] [INFO] Task started: Prodigal
[2024-01-24 14:47:06,078] [INFO] Running command: gunzip -c /var/lib/cwl/stg952e6829-3c76-4047-bfd3-a1906aba8858/GCF_011038645.2_ASM1103864v2_genomic.fna.gz | prodigal -d GCF_011038645.2_ASM1103864v2_genomic.fna/cds.fna -a GCF_011038645.2_ASM1103864v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:12,992] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:12,992] [INFO] Task started: HMMsearch
[2024-01-24 14:47:12,992] [INFO] Running command: hmmsearch --tblout GCF_011038645.2_ASM1103864v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg12e114e4-a151-47ed-a442-f6a6cbdec6f2/dqc_reference/reference_markers.hmm GCF_011038645.2_ASM1103864v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:13,224] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:13,226] [INFO] Found 6/6 markers.
[2024-01-24 14:47:13,277] [INFO] Query marker FASTA was written to GCF_011038645.2_ASM1103864v2_genomic.fna/markers.fasta
[2024-01-24 14:47:13,277] [INFO] Task started: Blastn
[2024-01-24 14:47:13,278] [INFO] Running command: blastn -query GCF_011038645.2_ASM1103864v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg12e114e4-a151-47ed-a442-f6a6cbdec6f2/dqc_reference/reference_markers.fasta -out GCF_011038645.2_ASM1103864v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:14,294] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:14,298] [INFO] Selected 14 target genomes.
[2024-01-24 14:47:14,298] [INFO] Target genome list was writen to GCF_011038645.2_ASM1103864v2_genomic.fna/target_genomes.txt
[2024-01-24 14:47:14,319] [INFO] Task started: fastANI
[2024-01-24 14:47:14,320] [INFO] Running command: fastANI --query /var/lib/cwl/stg952e6829-3c76-4047-bfd3-a1906aba8858/GCF_011038645.2_ASM1103864v2_genomic.fna.gz --refList GCF_011038645.2_ASM1103864v2_genomic.fna/target_genomes.txt --output GCF_011038645.2_ASM1103864v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:21,404] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:21,404] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg12e114e4-a151-47ed-a442-f6a6cbdec6f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:21,405] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg12e114e4-a151-47ed-a442-f6a6cbdec6f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:21,416] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:21,417] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:21,417] [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 qintianiae	strain=MC1420	GCA_011038645.2	2709392	2709392	type	True	100.0	739	739	95	conclusive
Corynebacterium sanguinis	strain=CCUG 58655	GCA_007641235.1	2594913	2594913	type	True	83.7592	537	739	95	below_threshold
Corynebacterium mycetoides	strain=DSM 20632	GCA_900103625.1	38302	38302	type	True	83.1622	557	739	95	below_threshold
Corynebacterium lipophiloflavum	strain=DSM 44291	GCA_000159635.1	161889	161889	type	True	82.7737	521	739	95	below_threshold
Corynebacterium senegalense	strain=Marseille-P4329	GCA_900411315.1	2080750	2080750	type	True	81.4492	489	739	95	below_threshold
Corynebacterium timonense	strain=DSM 45434	GCA_900105305.1	441500	441500	type	True	80.6166	430	739	95	below_threshold
Corynebacterium timonense	strain=5401744	GCA_000312345.1	441500	441500	type	True	80.4904	420	739	95	below_threshold
Corynebacterium jeddahense	strain=JCB	GCA_000577555.1	1414719	1414719	type	True	80.4779	359	739	95	below_threshold
Corynebacterium haemomassiliense	strain=Marseille-Q3615	GCA_013978595.1	2754726	2754726	type	True	80.2604	405	739	95	below_threshold
Corynebacterium lujinxingii	strain=zg-917	GCA_014490555.1	2763010	2763010	type	True	80.1081	363	739	95	below_threshold
Corynebacterium bouchesdurhonense	strain=SN14	GCA_900078305.2	1720192	1720192	type	True	80.0874	377	739	95	below_threshold
Corynebacterium lujinxingii	strain=zg-917	GCA_014267325.1	2763010	2763010	type	True	79.9931	359	739	95	below_threshold
Corynebacterium godavarianum	strain=LMG 29598	GCA_007559235.1	2054421	2054421	type	True	79.9575	370	739	95	below_threshold
Corynebacterium ihumii	strain=GD7	GCA_000403725.2	1232427	1232427	type	True	79.7003	377	739	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:21,418] [INFO] DFAST Taxonomy check result was written to GCF_011038645.2_ASM1103864v2_genomic.fna/tc_result.tsv
[2024-01-24 14:47:21,419] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:21,419] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:21,419] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg12e114e4-a151-47ed-a442-f6a6cbdec6f2/dqc_reference/checkm_data
[2024-01-24 14:47:21,420] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:21,444] [INFO] Task started: CheckM
[2024-01-24 14:47:21,445] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011038645.2_ASM1103864v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011038645.2_ASM1103864v2_genomic.fna/checkm_input GCF_011038645.2_ASM1103864v2_genomic.fna/checkm_result
[2024-01-24 14:47:51,168] [INFO] Task succeeded: CheckM
[2024-01-24 14:47:51,169] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:47:51,201] [INFO] ===== Completeness check finished =====
[2024-01-24 14:47:51,202] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:47:51,203] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011038645.2_ASM1103864v2_genomic.fna/markers.fasta)
[2024-01-24 14:47:51,203] [INFO] Task started: Blastn
[2024-01-24 14:47:51,203] [INFO] Running command: blastn -query GCF_011038645.2_ASM1103864v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg12e114e4-a151-47ed-a442-f6a6cbdec6f2/dqc_reference/reference_markers_gtdb.fasta -out GCF_011038645.2_ASM1103864v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:52,791] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:52,794] [INFO] Selected 14 target genomes.
[2024-01-24 14:47:52,795] [INFO] Target genome list was writen to GCF_011038645.2_ASM1103864v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:47:52,805] [INFO] Task started: fastANI
[2024-01-24 14:47:52,805] [INFO] Running command: fastANI --query /var/lib/cwl/stg952e6829-3c76-4047-bfd3-a1906aba8858/GCF_011038645.2_ASM1103864v2_genomic.fna.gz --refList GCF_011038645.2_ASM1103864v2_genomic.fna/target_genomes_gtdb.txt --output GCF_011038645.2_ASM1103864v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:00,475] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:00,487] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:00,488] [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_011038645.2	s__Corynebacterium qintianiae	100.0	739	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.90	98.90	0.92	0.92	2	conclusive
GCF_007641235.1	s__Corynebacterium sanguinis	83.769	536	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.27	97.90	0.92	0.90	7	-
GCF_900103625.1	s__Corynebacterium mycetoides	83.1372	556	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000159635.1	s__Corynebacterium lipophiloflavum	82.768	522	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900411315.1	s__Corynebacterium senegalense	81.4728	490	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002339505.1	s__Corynebacterium sp002339505	80.6128	439	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105305.1	s__Corynebacterium timonense	80.6034	431	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.93	99.93	0.99	0.99	2	-
GCF_000577555.1	s__Corynebacterium jeddahense	80.4365	362	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013978595.1	s__Corynebacterium haemomassiliense	80.2992	405	739	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	80.0871	377	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014490555.1	s__Corynebacterium sp014490555	80.0695	365	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	0.99	3	-
GCF_001807265.1	s__Corynebacterium sp001807265	80.0391	379	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.96	97.96	0.92	0.92	2	-
GCA_900156035.1	s__Corynebacterium afermentans	79.7497	370	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.27	97.60	0.93	0.89	5	-
GCF_012396315.1	s__Corynebacterium mucifaciens	79.734	352	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	95.74	95.74	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:00,489] [INFO] GTDB search result was written to GCF_011038645.2_ASM1103864v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:00,490] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:00,493] [INFO] DFAST_QC result json was written to GCF_011038645.2_ASM1103864v2_genomic.fna/dqc_result.json
[2024-01-24 14:48:00,494] [INFO] DFAST_QC completed!
[2024-01-24 14:48:00,494] [INFO] Total running time: 0h0m56s