[2024-01-24 13:54:10,884] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:54:10,887] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:54:10,888] [INFO] DQC Reference Directory: /var/lib/cwl/stgef95dd2c-789b-42eb-9ba5-707dfc8ce55b/dqc_reference
[2024-01-24 13:54:12,262] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:54:12,263] [INFO] Task started: Prodigal
[2024-01-24 13:54:12,263] [INFO] Running command: gunzip -c /var/lib/cwl/stgae102a6d-d8f9-415b-ae9c-aeecdd8f1690/GCF_000418365.1_ASM41836v1_genomic.fna.gz | prodigal -d GCF_000418365.1_ASM41836v1_genomic.fna/cds.fna -a GCF_000418365.1_ASM41836v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:54:20,698] [INFO] Task succeeded: Prodigal
[2024-01-24 13:54:20,698] [INFO] Task started: HMMsearch
[2024-01-24 13:54:20,698] [INFO] Running command: hmmsearch --tblout GCF_000418365.1_ASM41836v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef95dd2c-789b-42eb-9ba5-707dfc8ce55b/dqc_reference/reference_markers.hmm GCF_000418365.1_ASM41836v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:54:20,974] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:54:20,976] [INFO] Found 6/6 markers.
[2024-01-24 13:54:21,002] [INFO] Query marker FASTA was written to GCF_000418365.1_ASM41836v1_genomic.fna/markers.fasta
[2024-01-24 13:54:21,002] [INFO] Task started: Blastn
[2024-01-24 13:54:21,003] [INFO] Running command: blastn -query GCF_000418365.1_ASM41836v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef95dd2c-789b-42eb-9ba5-707dfc8ce55b/dqc_reference/reference_markers.fasta -out GCF_000418365.1_ASM41836v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:54:21,999] [INFO] Task succeeded: Blastn
[2024-01-24 13:54:22,004] [INFO] Selected 7 target genomes.
[2024-01-24 13:54:22,005] [INFO] Target genome list was writen to GCF_000418365.1_ASM41836v1_genomic.fna/target_genomes.txt
[2024-01-24 13:54:22,008] [INFO] Task started: fastANI
[2024-01-24 13:54:22,009] [INFO] Running command: fastANI --query /var/lib/cwl/stgae102a6d-d8f9-415b-ae9c-aeecdd8f1690/GCF_000418365.1_ASM41836v1_genomic.fna.gz --refList GCF_000418365.1_ASM41836v1_genomic.fna/target_genomes.txt --output GCF_000418365.1_ASM41836v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:54:27,410] [INFO] Task succeeded: fastANI
[2024-01-24 13:54:27,411] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef95dd2c-789b-42eb-9ba5-707dfc8ce55b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:54:27,412] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef95dd2c-789b-42eb-9ba5-707dfc8ce55b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:54:27,419] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:54:27,419] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:54:27,420] [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 terpenotabidum	strain=Y-11	GCA_000418365.1	89154	89154	type	True	100.0	916	917	95	conclusive
Corynebacterium variabile	strain=NBRC 15286	GCA_006539825.1	1727	1727	type	True	83.8999	694	917	95	below_threshold
Corynebacterium nuruki	strain=S6-4	GCA_007970465.1	1032851	1032851	type	True	81.9656	602	917	95	below_threshold
Corynebacterium nuruki	strain=S6-4	GCA_000213935.2	1032851	1032851	type	True	81.8184	589	917	95	below_threshold
Corynebacterium neomassiliense	strain=Marseille-P3888	GCA_900626215.1	2079482	2079482	type	True	80.9749	598	917	95	below_threshold
Corynebacterium bovis	strain=FDAARGOS_1052	GCA_016128075.1	36808	36808	type	True	79.2874	331	917	95	below_threshold
Actinocatenispora comari	strain=NUM-2625	GCA_017312725.1	2807577	2807577	type	True	75.6988	136	917	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:54:27,421] [INFO] DFAST Taxonomy check result was written to GCF_000418365.1_ASM41836v1_genomic.fna/tc_result.tsv
[2024-01-24 13:54:27,422] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:54:27,422] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:54:27,422] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef95dd2c-789b-42eb-9ba5-707dfc8ce55b/dqc_reference/checkm_data
[2024-01-24 13:54:27,423] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:54:27,451] [INFO] Task started: CheckM
[2024-01-24 13:54:27,452] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000418365.1_ASM41836v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000418365.1_ASM41836v1_genomic.fna/checkm_input GCF_000418365.1_ASM41836v1_genomic.fna/checkm_result
[2024-01-24 13:54:59,869] [INFO] Task succeeded: CheckM
[2024-01-24 13:54:59,871] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:54:59,902] [INFO] ===== Completeness check finished =====
[2024-01-24 13:54:59,903] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:54:59,903] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000418365.1_ASM41836v1_genomic.fna/markers.fasta)
[2024-01-24 13:54:59,904] [INFO] Task started: Blastn
[2024-01-24 13:54:59,904] [INFO] Running command: blastn -query GCF_000418365.1_ASM41836v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef95dd2c-789b-42eb-9ba5-707dfc8ce55b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000418365.1_ASM41836v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:01,540] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:01,650] [INFO] Selected 7 target genomes.
[2024-01-24 13:55:01,650] [INFO] Target genome list was writen to GCF_000418365.1_ASM41836v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:55:01,668] [INFO] Task started: fastANI
[2024-01-24 13:55:01,669] [INFO] Running command: fastANI --query /var/lib/cwl/stgae102a6d-d8f9-415b-ae9c-aeecdd8f1690/GCF_000418365.1_ASM41836v1_genomic.fna.gz --refList GCF_000418365.1_ASM41836v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000418365.1_ASM41836v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:55:06,667] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:06,679] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:55:06,679] [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_000418365.1	s__Corynebacterium terpenotabidum	100.0	916	917	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006539825.1	s__Corynebacterium variabile	83.9134	693	917	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	83.0819	569	917	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007970465.1	s__Corynebacterium nuruki	82.0018	603	917	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.35	98.70	0.99	0.98	3	-
GCA_900049755.1	s__Corynebacterium provencense	81.0901	581	917	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.28	98.82	0.94	0.91	4	-
GCA_019114135.1	s__Corynebacterium avicola	80.7456	493	917	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	79.9076	427	917	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.44	97.44	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:55:06,681] [INFO] GTDB search result was written to GCF_000418365.1_ASM41836v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:55:06,681] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:55:06,684] [INFO] DFAST_QC result json was written to GCF_000418365.1_ASM41836v1_genomic.fna/dqc_result.json
[2024-01-24 13:55:06,684] [INFO] DFAST_QC completed!
[2024-01-24 13:55:06,684] [INFO] Total running time: 0h0m56s