[2024-01-24 14:06:18,044] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:18,047] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:18,048] [INFO] DQC Reference Directory: /var/lib/cwl/stge30e52d3-57f2-4960-a6dd-8e49839c9f98/dqc_reference
[2024-01-24 14:06:19,395] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:19,396] [INFO] Task started: Prodigal
[2024-01-24 14:06:19,396] [INFO] Running command: gunzip -c /var/lib/cwl/stgf29366e3-83a1-4aa1-87bf-a947a56b9097/GCF_008693065.1_ASM869306v1_genomic.fna.gz | prodigal -d GCF_008693065.1_ASM869306v1_genomic.fna/cds.fna -a GCF_008693065.1_ASM869306v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:26,913] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:26,914] [INFO] Task started: HMMsearch
[2024-01-24 14:06:26,914] [INFO] Running command: hmmsearch --tblout GCF_008693065.1_ASM869306v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge30e52d3-57f2-4960-a6dd-8e49839c9f98/dqc_reference/reference_markers.hmm GCF_008693065.1_ASM869306v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:27,202] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:27,203] [INFO] Found 6/6 markers.
[2024-01-24 14:06:27,229] [INFO] Query marker FASTA was written to GCF_008693065.1_ASM869306v1_genomic.fna/markers.fasta
[2024-01-24 14:06:27,230] [INFO] Task started: Blastn
[2024-01-24 14:06:27,230] [INFO] Running command: blastn -query GCF_008693065.1_ASM869306v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge30e52d3-57f2-4960-a6dd-8e49839c9f98/dqc_reference/reference_markers.fasta -out GCF_008693065.1_ASM869306v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:28,123] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:28,126] [INFO] Selected 17 target genomes.
[2024-01-24 14:06:28,127] [INFO] Target genome list was writen to GCF_008693065.1_ASM869306v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:28,212] [INFO] Task started: fastANI
[2024-01-24 14:06:28,212] [INFO] Running command: fastANI --query /var/lib/cwl/stgf29366e3-83a1-4aa1-87bf-a947a56b9097/GCF_008693065.1_ASM869306v1_genomic.fna.gz --refList GCF_008693065.1_ASM869306v1_genomic.fna/target_genomes.txt --output GCF_008693065.1_ASM869306v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:37,682] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:37,682] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge30e52d3-57f2-4960-a6dd-8e49839c9f98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:37,683] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge30e52d3-57f2-4960-a6dd-8e49839c9f98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:37,699] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:37,699] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:37,700] [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 tuscaniense	strain=CCUG 51321T	GCA_008693065.1	302449	302449	type	True	100.0	665	669	95	conclusive
Corynebacterium appendicis	strain=DSM 44531	GCA_900156665.1	163202	163202	type	True	79.7693	335	669	95	below_threshold
Corynebacterium urinipleomorphum	strain=Marseille-P2799	GCA_900155535.1	1852380	1852380	type	True	79.6916	346	669	95	below_threshold
Corynebacterium imitans	strain=NCTC13015	GCA_900187215.1	156978	156978	type	True	79.5666	217	669	95	below_threshold
Corynebacterium afermentans subsp. lipophilum	strain=CCUG 32105	GCA_015351335.1	144184	38286	type	True	79.4332	192	669	95	below_threshold
Corynebacterium haemomassiliense	strain=Marseille-Q3615	GCA_013978595.1	2754726	2754726	type	True	79.3525	207	669	95	below_threshold
Corynebacterium jeddahense	strain=JCB	GCA_000577555.1	1414719	1414719	type	True	79.2746	192	669	95	below_threshold
Corynebacterium riegelii	strain=FDAARGOS_1114	GCA_016728505.1	156976	156976	type	True	79.2149	192	669	95	below_threshold
Corynebacterium lujinxingii	strain=zg-917	GCA_014267325.1	2763010	2763010	type	True	79.0775	199	669	95	below_threshold
Corynebacterium lujinxingii	strain=zg-917	GCA_014490555.1	2763010	2763010	type	True	79.0161	200	669	95	below_threshold
Corynebacterium coyleae	strain=DSM 44184	GCA_900105505.1	53374	53374	type	True	79.0013	206	669	95	below_threshold
Corynebacterium coyleae	strain=FDAARGOS 1425	GCA_019048165.1	53374	53374	type	True	78.9119	204	669	95	below_threshold
Corynebacterium fournieri	strain=Marseille-P2948	GCA_900176865.1	1852390	1852390	type	True	78.7802	210	669	95	below_threshold
Corynebacterium aquatimens	strain=DSM 45632	GCA_015752125.1	1190508	1190508	type	True	78.63	232	669	95	below_threshold
Corynebacterium cystitidis	strain=NCTC11863	GCA_900187295.1	35757	35757	type	True	77.512	100	669	95	below_threshold
Corynebacterium cystitidis	strain=DSM 20524	GCA_900111265.1	35757	35757	type	True	77.4896	100	669	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:37,701] [INFO] DFAST Taxonomy check result was written to GCF_008693065.1_ASM869306v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:37,702] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:37,702] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:37,702] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge30e52d3-57f2-4960-a6dd-8e49839c9f98/dqc_reference/checkm_data
[2024-01-24 14:06:37,704] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:37,729] [INFO] Task started: CheckM
[2024-01-24 14:06:37,730] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008693065.1_ASM869306v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008693065.1_ASM869306v1_genomic.fna/checkm_input GCF_008693065.1_ASM869306v1_genomic.fna/checkm_result
[2024-01-24 14:07:05,861] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:05,862] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:05,882] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:05,882] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:05,883] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008693065.1_ASM869306v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:05,883] [INFO] Task started: Blastn
[2024-01-24 14:07:05,883] [INFO] Running command: blastn -query GCF_008693065.1_ASM869306v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge30e52d3-57f2-4960-a6dd-8e49839c9f98/dqc_reference/reference_markers_gtdb.fasta -out GCF_008693065.1_ASM869306v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:07,119] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:07,123] [INFO] Selected 13 target genomes.
[2024-01-24 14:07:07,123] [INFO] Target genome list was writen to GCF_008693065.1_ASM869306v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:07,151] [INFO] Task started: fastANI
[2024-01-24 14:07:07,152] [INFO] Running command: fastANI --query /var/lib/cwl/stgf29366e3-83a1-4aa1-87bf-a947a56b9097/GCF_008693065.1_ASM869306v1_genomic.fna.gz --refList GCF_008693065.1_ASM869306v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008693065.1_ASM869306v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:14,156] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:14,174] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:14,174] [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_008693065.1	s__Corynebacterium tuscaniense	100.0	665	669	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.42	98.40	0.94	0.94	3	conclusive
GCF_017942225.1	s__Corynebacterium sp017942225	80.0398	341	669	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156665.1	s__Corynebacterium appendicis	79.7454	337	669	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155535.1	s__Corynebacterium urinipleomorphum	79.6916	346	669	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	79.6232	319	669	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015351335.1	s__Corynebacterium lipophilum	79.4077	193	669	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	79.3646	207	669	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	79.2797	318	669	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	79.2494	193	669	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176865.1	s__Corynebacterium fournieri	78.8011	209	669	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015752125.1	s__Corynebacterium aquatimens	78.6255	231	669	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187295.1	s__Corynebacterium cystitidis	77.511	100	669	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:14,176] [INFO] GTDB search result was written to GCF_008693065.1_ASM869306v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:14,176] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:14,180] [INFO] DFAST_QC result json was written to GCF_008693065.1_ASM869306v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:14,180] [INFO] DFAST_QC completed!
[2024-01-24 14:07:14,180] [INFO] Total running time: 0h0m56s