[2024-01-24 10:58:06,470] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:58:06,475] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:58:06,475] [INFO] DQC Reference Directory: /var/lib/cwl/stg4edaedd7-4b51-4156-992c-a50c4807f815/dqc_reference
[2024-01-24 10:58:09,632] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:58:09,633] [INFO] Task started: Prodigal
[2024-01-24 10:58:09,634] [INFO] Running command: gunzip -c /var/lib/cwl/stg963141e0-9e3d-4344-89f5-45f7d3417460/GCF_000767255.1_ASM76725v1_genomic.fna.gz | prodigal -d GCF_000767255.1_ASM76725v1_genomic.fna/cds.fna -a GCF_000767255.1_ASM76725v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:17,876] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:17,877] [INFO] Task started: HMMsearch
[2024-01-24 10:58:17,877] [INFO] Running command: hmmsearch --tblout GCF_000767255.1_ASM76725v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4edaedd7-4b51-4156-992c-a50c4807f815/dqc_reference/reference_markers.hmm GCF_000767255.1_ASM76725v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:18,134] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:18,136] [INFO] Found 6/6 markers.
[2024-01-24 10:58:18,162] [INFO] Query marker FASTA was written to GCF_000767255.1_ASM76725v1_genomic.fna/markers.fasta
[2024-01-24 10:58:18,162] [INFO] Task started: Blastn
[2024-01-24 10:58:18,162] [INFO] Running command: blastn -query GCF_000767255.1_ASM76725v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4edaedd7-4b51-4156-992c-a50c4807f815/dqc_reference/reference_markers.fasta -out GCF_000767255.1_ASM76725v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:18,982] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:18,990] [INFO] Selected 20 target genomes.
[2024-01-24 10:58:18,991] [INFO] Target genome list was writen to GCF_000767255.1_ASM76725v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:19,097] [INFO] Task started: fastANI
[2024-01-24 10:58:19,097] [INFO] Running command: fastANI --query /var/lib/cwl/stg963141e0-9e3d-4344-89f5-45f7d3417460/GCF_000767255.1_ASM76725v1_genomic.fna.gz --refList GCF_000767255.1_ASM76725v1_genomic.fna/target_genomes.txt --output GCF_000767255.1_ASM76725v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:27,983] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:27,983] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4edaedd7-4b51-4156-992c-a50c4807f815/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:27,984] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4edaedd7-4b51-4156-992c-a50c4807f815/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:28,002] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:28,002] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:28,003] [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 auriscanis	strain=CIP 106629	GCA_000767255.1	99807	99807	type	True	100.0	837	840	95	conclusive
Corynebacterium resistens	strain=DSM 45100	GCA_000177535.2	258224	258224	type	True	80.2481	451	840	95	below_threshold
Corynebacterium urogenitale	strain=LMM-1652	GCA_009026825.1	2487892	2487892	type	True	79.228	159	840	95	below_threshold
Corynebacterium dentalis	strain=Marseille-P4122	GCA_900232865.1	2014528	2014528	type	True	78.8764	168	840	95	below_threshold
Corynebacterium jeikeium	strain=ATCC 43734	GCA_000163435.1	38289	38289	suspected-type	True	78.8144	184	840	95	below_threshold
Corynebacterium zhongnanshanii	strain=zg-320	GCA_014490575.1	2768834	2768834	type	True	78.5644	155	840	95	below_threshold
Corynebacterium urealyticum	strain=NCTC12011	GCA_900187235.1	43771	43771	type	True	78.4743	139	840	95	below_threshold
Corynebacterium falsenii	strain=FDAARGOS_1494	GCA_020099275.1	108486	108486	type	True	78.4062	209	840	95	below_threshold
Corynebacterium urealyticum	strain=DSM 7109	GCA_000069945.1	43771	43771	type	True	78.3266	139	840	95	below_threshold
Corynebacterium urealyticum	strain=FDAARGOS_994	GCA_016127975.1	43771	43771	type	True	78.3193	140	840	95	below_threshold
Corynebacterium accolens	strain=DSM 44278	GCA_023520795.1	38284	38284	type	True	77.9805	70	840	95	below_threshold
Corynebacterium lactis	strain=RW2-5	GCA_001274895.1	1231000	1231000	type	True	77.9616	79	840	95	below_threshold
Corynebacterium accolens	strain=ATCC 49725	GCA_000159115.1	38284	38284	type	True	77.7629	69	840	95	below_threshold
Corynebacterium terpenotabidum	strain=Y-11	GCA_000418365.1	89154	89154	type	True	77.6876	103	840	95	below_threshold
Corynebacterium ciconiae	strain=DSM 44920	GCA_000372385.1	227319	227319	type	True	77.3471	80	840	95	below_threshold
Corynebacterium godavarianum	strain=LMG 29598	GCA_007559235.1	2054421	2054421	type	True	77.3449	71	840	95	below_threshold
Corynebacterium glyciniphilum	strain=AJ 3170	GCA_000626675.1	1404244	1404244	type	True	77.1717	97	840	95	below_threshold
Corynebacterium hadale	strain=NBT06-6	GCA_002273005.1	2026255	2026255	type	True	77.1498	76	840	95	below_threshold
Corynebacterium atypicum	strain=R2070	GCA_000732945.1	191610	191610	type	True	76.9739	52	840	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:28,005] [INFO] DFAST Taxonomy check result was written to GCF_000767255.1_ASM76725v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:28,005] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:28,005] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:28,006] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4edaedd7-4b51-4156-992c-a50c4807f815/dqc_reference/checkm_data
[2024-01-24 10:58:28,007] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:28,038] [INFO] Task started: CheckM
[2024-01-24 10:58:28,038] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000767255.1_ASM76725v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000767255.1_ASM76725v1_genomic.fna/checkm_input GCF_000767255.1_ASM76725v1_genomic.fna/checkm_result
[2024-01-24 10:58:57,218] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:57,220] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.16%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:57,238] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:57,239] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:57,239] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000767255.1_ASM76725v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:57,240] [INFO] Task started: Blastn
[2024-01-24 10:58:57,240] [INFO] Running command: blastn -query GCF_000767255.1_ASM76725v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4edaedd7-4b51-4156-992c-a50c4807f815/dqc_reference/reference_markers_gtdb.fasta -out GCF_000767255.1_ASM76725v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:58,280] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:58,285] [INFO] Selected 16 target genomes.
[2024-01-24 10:58:58,285] [INFO] Target genome list was writen to GCF_000767255.1_ASM76725v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:58,333] [INFO] Task started: fastANI
[2024-01-24 10:58:58,333] [INFO] Running command: fastANI --query /var/lib/cwl/stg963141e0-9e3d-4344-89f5-45f7d3417460/GCF_000767255.1_ASM76725v1_genomic.fna.gz --refList GCF_000767255.1_ASM76725v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000767255.1_ASM76725v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:06,536] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:06,548] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:06,548] [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_000767255.1	s__Corynebacterium auriscanis	100.0	837	840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.87	97.87	0.94	0.94	2	conclusive
GCF_000177535.2	s__Corynebacterium resistens	80.2401	452	840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009026825.1	s__Corynebacterium sp009026825	79.228	159	840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900232865.1	s__Corynebacterium dentalis	78.8764	168	840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.56	98.56	0.96	0.96	2	-
GCF_000738265.1	s__Corynebacterium jeikeium_A	78.5991	203	840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.92	97.52	0.95	0.93	11	-
GCF_000738175.1	s__Corynebacterium jeikeium_C	78.59	206	840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014490575.1	s__Corynebacterium sp014490575	78.5644	155	840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.40	97.50	0.99	0.97	7	-
GCF_000069945.1	s__Corynebacterium urealyticum	78.3828	137	840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.66	97.50	0.94	0.89	9	-
GCF_001807485.1	s__Corynebacterium sp001807485	78.17	208	840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.83	97.75	0.93	0.93	3	-
GCA_019114175.1	s__Corynebacterium gallistercoris	78.024	155	840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000159115.1	s__Corynebacterium accolens	77.7629	69	840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.20	96.99	0.95	0.94	10	-
GCF_000418365.1	s__Corynebacterium terpenotabidum	77.6876	103	840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900049755.1	s__Corynebacterium provencense	77.4657	76	840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.28	98.82	0.94	0.91	4	-
GCF_000626675.1	s__Corynebacterium glyciniphilum	77.1717	97	840	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 10:59:06,550] [INFO] GTDB search result was written to GCF_000767255.1_ASM76725v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:06,551] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:06,558] [INFO] DFAST_QC result json was written to GCF_000767255.1_ASM76725v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:06,558] [INFO] DFAST_QC completed!
[2024-01-24 10:59:06,558] [INFO] Total running time: 0h1m0s