[2024-01-24 12:44:11,198] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:11,200] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:11,200] [INFO] DQC Reference Directory: /var/lib/cwl/stg95506d61-2b6b-4bbb-9aae-eee953bc2d5d/dqc_reference
[2024-01-24 12:44:12,509] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:12,510] [INFO] Task started: Prodigal
[2024-01-24 12:44:12,510] [INFO] Running command: gunzip -c /var/lib/cwl/stgf7cfb180-14c8-47f0-9c72-c990043bbd32/GCF_030408555.1_ASM3040855v1_genomic.fna.gz | prodigal -d GCF_030408555.1_ASM3040855v1_genomic.fna/cds.fna -a GCF_030408555.1_ASM3040855v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:21,351] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:21,351] [INFO] Task started: HMMsearch
[2024-01-24 12:44:21,351] [INFO] Running command: hmmsearch --tblout GCF_030408555.1_ASM3040855v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95506d61-2b6b-4bbb-9aae-eee953bc2d5d/dqc_reference/reference_markers.hmm GCF_030408555.1_ASM3040855v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:21,650] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:21,652] [INFO] Found 6/6 markers.
[2024-01-24 12:44:21,676] [INFO] Query marker FASTA was written to GCF_030408555.1_ASM3040855v1_genomic.fna/markers.fasta
[2024-01-24 12:44:21,677] [INFO] Task started: Blastn
[2024-01-24 12:44:21,677] [INFO] Running command: blastn -query GCF_030408555.1_ASM3040855v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95506d61-2b6b-4bbb-9aae-eee953bc2d5d/dqc_reference/reference_markers.fasta -out GCF_030408555.1_ASM3040855v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:22,523] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:22,527] [INFO] Selected 8 target genomes.
[2024-01-24 12:44:22,528] [INFO] Target genome list was writen to GCF_030408555.1_ASM3040855v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:22,534] [INFO] Task started: fastANI
[2024-01-24 12:44:22,534] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7cfb180-14c8-47f0-9c72-c990043bbd32/GCF_030408555.1_ASM3040855v1_genomic.fna.gz --refList GCF_030408555.1_ASM3040855v1_genomic.fna/target_genomes.txt --output GCF_030408555.1_ASM3040855v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:27,656] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:27,657] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95506d61-2b6b-4bbb-9aae-eee953bc2d5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:27,657] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95506d61-2b6b-4bbb-9aae-eee953bc2d5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:27,667] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:44:27,667] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:27,667] [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 aurimucosum	strain=FDAARGOS_1109	GCA_016728705.1	169292	169292	suspected-type	True	99.9929	908	912	95	conclusive
Corynebacterium aurimucosum	strain=DSM 44532	GCA_024138775.1	169292	169292	suspected-type	True	99.8713	893	912	95	conclusive
Corynebacterium minutissimum	strain=NCTC10288	GCA_900478045.1	38301	38301	type	True	84.4886	663	912	95	below_threshold
Corynebacterium minutissimum	strain=NBRC 15361	GCA_001552395.1	38301	38301	type	True	84.2898	640	912	95	below_threshold
Corynebacterium minutissimum	strain=ATCC 23348	GCA_000805675.1	38301	38301	type	True	84.2502	640	912	95	below_threshold
Corynebacterium singulare	strain=IBS B52218	GCA_000833575.1	161899	161899	type	True	83.6348	652	912	95	below_threshold
Corynebacterium tuberculostearicum	strain=FDAARGOS_1117	GCA_016728365.1	38304	38304	type	True	80.2754	368	912	95	below_threshold
Corynebacterium tuberculostearicum	strain=DSM 44922	GCA_013408445.1	38304	38304	type	True	80.2011	371	912	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:27,669] [INFO] DFAST Taxonomy check result was written to GCF_030408555.1_ASM3040855v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:27,670] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:27,671] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:27,671] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95506d61-2b6b-4bbb-9aae-eee953bc2d5d/dqc_reference/checkm_data
[2024-01-24 12:44:27,673] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:27,705] [INFO] Task started: CheckM
[2024-01-24 12:44:27,705] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030408555.1_ASM3040855v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030408555.1_ASM3040855v1_genomic.fna/checkm_input GCF_030408555.1_ASM3040855v1_genomic.fna/checkm_result
[2024-01-24 12:44:58,624] [INFO] Task succeeded: CheckM
[2024-01-24 12:44:58,625] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:44:58,646] [INFO] ===== Completeness check finished =====
[2024-01-24 12:44:58,646] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:44:58,646] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030408555.1_ASM3040855v1_genomic.fna/markers.fasta)
[2024-01-24 12:44:58,647] [INFO] Task started: Blastn
[2024-01-24 12:44:58,647] [INFO] Running command: blastn -query GCF_030408555.1_ASM3040855v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95506d61-2b6b-4bbb-9aae-eee953bc2d5d/dqc_reference/reference_markers_gtdb.fasta -out GCF_030408555.1_ASM3040855v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:59,982] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:59,986] [INFO] Selected 6 target genomes.
[2024-01-24 12:44:59,987] [INFO] Target genome list was writen to GCF_030408555.1_ASM3040855v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:44:59,996] [INFO] Task started: fastANI
[2024-01-24 12:44:59,997] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7cfb180-14c8-47f0-9c72-c990043bbd32/GCF_030408555.1_ASM3040855v1_genomic.fna.gz --refList GCF_030408555.1_ASM3040855v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030408555.1_ASM3040855v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:04,480] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:04,492] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:04,492] [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_016728705.1	s__Corynebacterium sp001807205	99.9929	910	912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.15	96.83	0.93	0.90	8	conclusive
GCF_000022905.1	s__Corynebacterium aurimucosum	93.3294	812	912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCF_001836165.1	s__Corynebacterium sp001836165	92.4167	759	912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.96	97.92	0.93	0.93	3	-
GCA_019114925.1	s__Corynebacterium faecipullorum	92.1972	553	912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000988205.1	s__Corynebacterium minutissimum_A	89.6548	756	912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.53	96.09	0.91	0.89	16	-
GCF_002861385.1	s__Corynebacterium aurimucosum_C	89.0122	746	912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.04	96.50	0.91	0.89	28	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:04,494] [INFO] GTDB search result was written to GCF_030408555.1_ASM3040855v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:04,494] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:04,497] [INFO] DFAST_QC result json was written to GCF_030408555.1_ASM3040855v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:04,497] [INFO] DFAST_QC completed!
[2024-01-24 12:45:04,497] [INFO] Total running time: 0h0m53s