[2024-01-24 13:17:34,746] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:34,754] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:34,755] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ef5f061-2a54-4d73-999e-713c0ba77bd3/dqc_reference
[2024-01-24 13:17:36,164] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:36,165] [INFO] Task started: Prodigal
[2024-01-24 13:17:36,165] [INFO] Running command: gunzip -c /var/lib/cwl/stg7294987b-6ea4-4f06-acfc-43f3e3af14b8/GCF_022869005.1_ASM2286900v1_genomic.fna.gz | prodigal -d GCF_022869005.1_ASM2286900v1_genomic.fna/cds.fna -a GCF_022869005.1_ASM2286900v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:45,235] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:45,236] [INFO] Task started: HMMsearch
[2024-01-24 13:17:45,236] [INFO] Running command: hmmsearch --tblout GCF_022869005.1_ASM2286900v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ef5f061-2a54-4d73-999e-713c0ba77bd3/dqc_reference/reference_markers.hmm GCF_022869005.1_ASM2286900v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:45,513] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:45,514] [INFO] Found 6/6 markers.
[2024-01-24 13:17:45,540] [INFO] Query marker FASTA was written to GCF_022869005.1_ASM2286900v1_genomic.fna/markers.fasta
[2024-01-24 13:17:45,541] [INFO] Task started: Blastn
[2024-01-24 13:17:45,541] [INFO] Running command: blastn -query GCF_022869005.1_ASM2286900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ef5f061-2a54-4d73-999e-713c0ba77bd3/dqc_reference/reference_markers.fasta -out GCF_022869005.1_ASM2286900v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:46,636] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:46,639] [INFO] Selected 10 target genomes.
[2024-01-24 13:17:46,640] [INFO] Target genome list was writen to GCF_022869005.1_ASM2286900v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:46,644] [INFO] Task started: fastANI
[2024-01-24 13:17:46,644] [INFO] Running command: fastANI --query /var/lib/cwl/stg7294987b-6ea4-4f06-acfc-43f3e3af14b8/GCF_022869005.1_ASM2286900v1_genomic.fna.gz --refList GCF_022869005.1_ASM2286900v1_genomic.fna/target_genomes.txt --output GCF_022869005.1_ASM2286900v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:53,492] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:53,492] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ef5f061-2a54-4d73-999e-713c0ba77bd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:53,493] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ef5f061-2a54-4d73-999e-713c0ba77bd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:53,502] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:17:53,503] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:17:53,503] [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 glyciniphilum	strain=AJ 3170	GCA_000626675.1	1404244	1404244	type	True	84.3777	799	999	95	below_threshold
Corynebacterium nuruki	strain=S6-4	GCA_000213935.2	1032851	1032851	type	True	81.0135	558	999	95	below_threshold
Corynebacterium nuruki	strain=S6-4	GCA_007970465.1	1032851	1032851	type	True	80.9712	579	999	95	below_threshold
Corynebacterium variabile	strain=NBRC 15286	GCA_006539825.1	1727	1727	type	True	80.7252	562	999	95	below_threshold
Corynebacterium terpenotabidum	strain=Y-11	GCA_000418365.1	89154	89154	type	True	80.181	491	999	95	below_threshold
Corynebacterium bovis	strain=DSM 20582	GCA_000183325.2	36808	36808	type	True	79.6053	333	999	95	below_threshold
Corynebacterium neomassiliense	strain=Marseille-P3888	GCA_900626215.1	2079482	2079482	type	True	79.5734	465	999	95	below_threshold
Corynebacterium bovis	strain=FDAARGOS_1052	GCA_016128075.1	36808	36808	type	True	79.382	414	999	95	below_threshold
Corynebacterium bovis	strain=DSM 20582	GCA_014191555.1	36808	36808	type	True	79.3723	413	999	95	below_threshold
Corynebacterium halotolerans	strain=YIM 70093 = DSM 44683	GCA_000341345.1	225326	225326	type	True	78.8359	334	999	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:53,504] [INFO] DFAST Taxonomy check result was written to GCF_022869005.1_ASM2286900v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:53,505] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:53,505] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:53,505] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ef5f061-2a54-4d73-999e-713c0ba77bd3/dqc_reference/checkm_data
[2024-01-24 13:17:53,506] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:53,558] [INFO] Task started: CheckM
[2024-01-24 13:17:53,559] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022869005.1_ASM2286900v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022869005.1_ASM2286900v1_genomic.fna/checkm_input GCF_022869005.1_ASM2286900v1_genomic.fna/checkm_result
[2024-01-24 13:18:25,273] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:25,274] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:25,293] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:25,294] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:25,295] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022869005.1_ASM2286900v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:25,295] [INFO] Task started: Blastn
[2024-01-24 13:18:25,295] [INFO] Running command: blastn -query GCF_022869005.1_ASM2286900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ef5f061-2a54-4d73-999e-713c0ba77bd3/dqc_reference/reference_markers_gtdb.fasta -out GCF_022869005.1_ASM2286900v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:26,827] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:26,832] [INFO] Selected 7 target genomes.
[2024-01-24 13:18:26,833] [INFO] Target genome list was writen to GCF_022869005.1_ASM2286900v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:26,840] [INFO] Task started: fastANI
[2024-01-24 13:18:26,840] [INFO] Running command: fastANI --query /var/lib/cwl/stg7294987b-6ea4-4f06-acfc-43f3e3af14b8/GCF_022869005.1_ASM2286900v1_genomic.fna.gz --refList GCF_022869005.1_ASM2286900v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022869005.1_ASM2286900v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:31,951] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:31,962] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:18:31,962] [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_007673095.1	s__Corynebacterium sp002363255	85.2289	802	999	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.44	97.44	0.87	0.87	2	-
GCF_001942345.1	s__Corynebacterium sp001942345	85.0906	791	999	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000626675.1	s__Corynebacterium glyciniphilum	84.3875	798	999	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	82.0607	617	999	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	82.0517	601	999	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902782855.1	s__Corynebacterium sp902782855	80.3916	463	999	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	80.2812	490	999	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 13:18:31,964] [INFO] GTDB search result was written to GCF_022869005.1_ASM2286900v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:31,965] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:31,968] [INFO] DFAST_QC result json was written to GCF_022869005.1_ASM2286900v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:31,968] [INFO] DFAST_QC completed!
[2024-01-24 13:18:31,968] [INFO] Total running time: 0h0m57s