[2024-01-24 11:22:49,480] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:22:49,482] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:22:49,482] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b53aa8e-caa7-4a64-b0e8-959c019b3687/dqc_reference
[2024-01-24 11:22:50,658] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:22:50,659] [INFO] Task started: Prodigal
[2024-01-24 11:22:50,659] [INFO] Running command: gunzip -c /var/lib/cwl/stg37e2f855-0a26-4cac-8da3-0b7081cd6f43/GCF_007970465.1_ASM797046v1_genomic.fna.gz | prodigal -d GCF_007970465.1_ASM797046v1_genomic.fna/cds.fna -a GCF_007970465.1_ASM797046v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:23:00,002] [INFO] Task succeeded: Prodigal
[2024-01-24 11:23:00,002] [INFO] Task started: HMMsearch
[2024-01-24 11:23:00,002] [INFO] Running command: hmmsearch --tblout GCF_007970465.1_ASM797046v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b53aa8e-caa7-4a64-b0e8-959c019b3687/dqc_reference/reference_markers.hmm GCF_007970465.1_ASM797046v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:23:00,225] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:23:00,226] [INFO] Found 6/6 markers.
[2024-01-24 11:23:00,258] [INFO] Query marker FASTA was written to GCF_007970465.1_ASM797046v1_genomic.fna/markers.fasta
[2024-01-24 11:23:00,258] [INFO] Task started: Blastn
[2024-01-24 11:23:00,258] [INFO] Running command: blastn -query GCF_007970465.1_ASM797046v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b53aa8e-caa7-4a64-b0e8-959c019b3687/dqc_reference/reference_markers.fasta -out GCF_007970465.1_ASM797046v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:23:01,379] [INFO] Task succeeded: Blastn
[2024-01-24 11:23:01,383] [INFO] Selected 11 target genomes.
[2024-01-24 11:23:01,383] [INFO] Target genome list was writen to GCF_007970465.1_ASM797046v1_genomic.fna/target_genomes.txt
[2024-01-24 11:23:01,389] [INFO] Task started: fastANI
[2024-01-24 11:23:01,389] [INFO] Running command: fastANI --query /var/lib/cwl/stg37e2f855-0a26-4cac-8da3-0b7081cd6f43/GCF_007970465.1_ASM797046v1_genomic.fna.gz --refList GCF_007970465.1_ASM797046v1_genomic.fna/target_genomes.txt --output GCF_007970465.1_ASM797046v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:23:08,018] [INFO] Task succeeded: fastANI
[2024-01-24 11:23:08,019] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b53aa8e-caa7-4a64-b0e8-959c019b3687/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:23:08,019] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b53aa8e-caa7-4a64-b0e8-959c019b3687/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:23:08,028] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:23:08,028] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:23:08,028] [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 nuruki	strain=S6-4	GCA_007970465.1	1032851	1032851	type	True	100.0	1057	1057	95	conclusive
Corynebacterium nuruki	strain=S6-4	GCA_000213935.2	1032851	1032851	type	True	99.9574	999	1057	95	conclusive
Corynebacterium variabile	strain=NBRC 15286	GCA_006539825.1	1727	1727	type	True	82.9152	692	1057	95	below_threshold
Corynebacterium terpenotabidum	strain=Y-11	GCA_000418365.1	89154	89154	type	True	82.0037	600	1057	95	below_threshold
Corynebacterium neomassiliense	strain=Marseille-P3888	GCA_900626215.1	2079482	2079482	type	True	80.5539	556	1057	95	below_threshold
Corynebacterium bovis	strain=DSM 20582	GCA_000183325.2	36808	36808	type	True	80.0212	348	1057	95	below_threshold
Corynebacterium bovis	strain=DSM 20582	GCA_014191555.1	36808	36808	type	True	79.8106	433	1057	95	below_threshold
Corynebacterium bovis	strain=FDAARGOS_1052	GCA_016128075.1	36808	36808	type	True	79.7758	430	1057	95	below_threshold
Corynebacterium urealyticum	strain=FDAARGOS_994	GCA_016127975.1	43771	43771	type	True	78.8825	260	1057	95	below_threshold
Corynebacterium afermentans subsp. lipophilum	strain=CCUG 32105	GCA_015351335.1	144184	38286	type	True	78.0847	186	1057	95	below_threshold
Corynebacterium fournieri	strain=Marseille-P2948	GCA_900176865.1	1852390	1852390	type	True	77.9593	193	1057	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:23:08,030] [INFO] DFAST Taxonomy check result was written to GCF_007970465.1_ASM797046v1_genomic.fna/tc_result.tsv
[2024-01-24 11:23:08,030] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:23:08,031] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:23:08,031] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b53aa8e-caa7-4a64-b0e8-959c019b3687/dqc_reference/checkm_data
[2024-01-24 11:23:08,032] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:23:08,076] [INFO] Task started: CheckM
[2024-01-24 11:23:08,077] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007970465.1_ASM797046v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007970465.1_ASM797046v1_genomic.fna/checkm_input GCF_007970465.1_ASM797046v1_genomic.fna/checkm_result
[2024-01-24 11:23:54,768] [INFO] Task succeeded: CheckM
[2024-01-24 11:23:54,769] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:23:54,788] [INFO] ===== Completeness check finished =====
[2024-01-24 11:23:54,788] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:23:54,789] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007970465.1_ASM797046v1_genomic.fna/markers.fasta)
[2024-01-24 11:23:54,789] [INFO] Task started: Blastn
[2024-01-24 11:23:54,789] [INFO] Running command: blastn -query GCF_007970465.1_ASM797046v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b53aa8e-caa7-4a64-b0e8-959c019b3687/dqc_reference/reference_markers_gtdb.fasta -out GCF_007970465.1_ASM797046v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:23:56,445] [INFO] Task succeeded: Blastn
[2024-01-24 11:23:56,448] [INFO] Selected 11 target genomes.
[2024-01-24 11:23:56,448] [INFO] Target genome list was writen to GCF_007970465.1_ASM797046v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:23:56,456] [INFO] Task started: fastANI
[2024-01-24 11:23:56,456] [INFO] Running command: fastANI --query /var/lib/cwl/stg37e2f855-0a26-4cac-8da3-0b7081cd6f43/GCF_007970465.1_ASM797046v1_genomic.fna.gz --refList GCF_007970465.1_ASM797046v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007970465.1_ASM797046v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:24:04,023] [INFO] Task succeeded: fastANI
[2024-01-24 11:24:04,035] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:24:04,035] [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_007970465.1	s__Corynebacterium nuruki	100.0	1057	1057	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.35	98.70	0.99	0.98	3	conclusive
GCF_006539825.1	s__Corynebacterium variabile	82.9605	688	1057	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.53	98.15	0.92	0.86	8	-
GCA_902782855.1	s__Corynebacterium sp902782855	82.5031	542	1057	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000418365.1	s__Corynebacterium terpenotabidum	81.9384	600	1057	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019120175.1	s__Corynebacterium faecigallinarum	81.1129	569	1057	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019114135.1	s__Corynebacterium avicola	81.0122	581	1057	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	80.6884	548	1057	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.28	98.82	0.94	0.91	4	-
GCF_000183325.1	s__Corynebacterium bovis	79.9911	350	1057	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.01	98.42	0.92	0.83	23	-
GCF_001942345.1	s__Corynebacterium sp001942345	79.9909	523	1057	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007673095.1	s__Corynebacterium sp002363255	79.9832	504	1057	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.44	97.44	0.87	0.87	2	-
GCF_015351335.1	s__Corynebacterium lipophilum	78.0847	186	1057	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 11:24:04,036] [INFO] GTDB search result was written to GCF_007970465.1_ASM797046v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:24:04,037] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:24:04,040] [INFO] DFAST_QC result json was written to GCF_007970465.1_ASM797046v1_genomic.fna/dqc_result.json
[2024-01-24 11:24:04,040] [INFO] DFAST_QC completed!
[2024-01-24 11:24:04,040] [INFO] Total running time: 0h1m15s