[2024-01-24 14:37:46,909] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:37:46,913] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:37:46,913] [INFO] DQC Reference Directory: /var/lib/cwl/stg709a3538-6486-48fc-ab6f-c4b97a506be4/dqc_reference
[2024-01-24 14:37:50,273] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:37:50,274] [INFO] Task started: Prodigal
[2024-01-24 14:37:50,274] [INFO] Running command: gunzip -c /var/lib/cwl/stg48e9a30d-1adb-4b33-9bb3-b0f49cfbf62e/GCF_003065405.1_ASM306540v1_genomic.fna.gz | prodigal -d GCF_003065405.1_ASM306540v1_genomic.fna/cds.fna -a GCF_003065405.1_ASM306540v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:37:58,148] [INFO] Task succeeded: Prodigal
[2024-01-24 14:37:58,149] [INFO] Task started: HMMsearch
[2024-01-24 14:37:58,149] [INFO] Running command: hmmsearch --tblout GCF_003065405.1_ASM306540v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg709a3538-6486-48fc-ab6f-c4b97a506be4/dqc_reference/reference_markers.hmm GCF_003065405.1_ASM306540v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:37:58,385] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:37:58,387] [INFO] Found 6/6 markers.
[2024-01-24 14:37:58,412] [INFO] Query marker FASTA was written to GCF_003065405.1_ASM306540v1_genomic.fna/markers.fasta
[2024-01-24 14:37:58,413] [INFO] Task started: Blastn
[2024-01-24 14:37:58,413] [INFO] Running command: blastn -query GCF_003065405.1_ASM306540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg709a3538-6486-48fc-ab6f-c4b97a506be4/dqc_reference/reference_markers.fasta -out GCF_003065405.1_ASM306540v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:37:59,606] [INFO] Task succeeded: Blastn
[2024-01-24 14:37:59,610] [INFO] Selected 12 target genomes.
[2024-01-24 14:37:59,610] [INFO] Target genome list was writen to GCF_003065405.1_ASM306540v1_genomic.fna/target_genomes.txt
[2024-01-24 14:37:59,619] [INFO] Task started: fastANI
[2024-01-24 14:37:59,619] [INFO] Running command: fastANI --query /var/lib/cwl/stg48e9a30d-1adb-4b33-9bb3-b0f49cfbf62e/GCF_003065405.1_ASM306540v1_genomic.fna.gz --refList GCF_003065405.1_ASM306540v1_genomic.fna/target_genomes.txt --output GCF_003065405.1_ASM306540v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:38:06,649] [INFO] Task succeeded: fastANI
[2024-01-24 14:38:06,650] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg709a3538-6486-48fc-ab6f-c4b97a506be4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:38:06,650] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg709a3538-6486-48fc-ab6f-c4b97a506be4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:38:06,661] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:38:06,661] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:38:06,661] [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 yudongzhengii	strain=2183	GCA_003065405.1	2080740	2080740	type	True	100.0	835	837	95	conclusive
Corynebacterium doosanense	strain=CAU 212	GCA_000767055.1	1121358	1121358	type	True	79.8158	439	837	95	below_threshold
Corynebacterium maris	strain=DSM 45190	GCA_000442645.1	575200	575200	type	True	79.8107	365	837	95	below_threshold
Corynebacterium halotolerans	strain=YIM 70093 = DSM 44683	GCA_000341345.1	225326	225326	type	True	79.7787	420	837	95	below_threshold
Corynebacterium halotolerans	strain=DSM 44683	GCA_000688435.1	225326	225326	type	True	79.6533	404	837	95	below_threshold
Corynebacterium frankenforstense	strain=ST18	GCA_001941485.1	1230998	1230998	type	True	79.6457	406	837	95	below_threshold
Corynebacterium doosanense	strain=DSM 45436	GCA_000372245.1	1121358	1121358	type	True	79.6263	429	837	95	below_threshold
Corynebacterium senegalense	strain=Marseille-P4329	GCA_900411315.1	2080750	2080750	type	True	79.3746	353	837	95	below_threshold
Corynebacterium uterequi	strain=DSM 45634	GCA_001021065.1	1072256	1072256	type	True	79.0384	320	837	95	below_threshold
Corynebacterium tapiri	strain=LMG 28165	GCA_006334925.1	1448266	1448266	type	True	78.9217	273	837	95	below_threshold
Corynebacterium pilosum	strain=NCTC11862	GCA_900447205.1	35756	35756	type	True	78.1149	242	837	95	below_threshold
Corynebacterium pilosum	strain=DSM 20521	GCA_000373805.1	35756	35756	type	True	77.7436	235	837	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:38:06,664] [INFO] DFAST Taxonomy check result was written to GCF_003065405.1_ASM306540v1_genomic.fna/tc_result.tsv
[2024-01-24 14:38:06,665] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:38:06,665] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:38:06,665] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg709a3538-6486-48fc-ab6f-c4b97a506be4/dqc_reference/checkm_data
[2024-01-24 14:38:06,666] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:38:06,703] [INFO] Task started: CheckM
[2024-01-24 14:38:06,703] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003065405.1_ASM306540v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003065405.1_ASM306540v1_genomic.fna/checkm_input GCF_003065405.1_ASM306540v1_genomic.fna/checkm_result
[2024-01-24 14:38:34,095] [INFO] Task succeeded: CheckM
[2024-01-24 14:38:34,096] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:38:34,114] [INFO] ===== Completeness check finished =====
[2024-01-24 14:38:34,114] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:38:34,115] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003065405.1_ASM306540v1_genomic.fna/markers.fasta)
[2024-01-24 14:38:34,115] [INFO] Task started: Blastn
[2024-01-24 14:38:34,115] [INFO] Running command: blastn -query GCF_003065405.1_ASM306540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg709a3538-6486-48fc-ab6f-c4b97a506be4/dqc_reference/reference_markers_gtdb.fasta -out GCF_003065405.1_ASM306540v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:38:35,804] [INFO] Task succeeded: Blastn
[2024-01-24 14:38:35,809] [INFO] Selected 15 target genomes.
[2024-01-24 14:38:35,809] [INFO] Target genome list was writen to GCF_003065405.1_ASM306540v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:38:35,821] [INFO] Task started: fastANI
[2024-01-24 14:38:35,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg48e9a30d-1adb-4b33-9bb3-b0f49cfbf62e/GCF_003065405.1_ASM306540v1_genomic.fna.gz --refList GCF_003065405.1_ASM306540v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003065405.1_ASM306540v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:38:44,743] [INFO] Task succeeded: fastANI
[2024-01-24 14:38:44,756] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:38:44,756] [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_003065405.1	s__Corynebacterium yudongzhengii	100.0	836	837	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000819445.1	s__Corynebacterium humireducens	79.8511	402	837	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.80	97.60	0.97	0.93	3	-
GCF_000767055.1	s__Corynebacterium doosanense	79.7926	440	837	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000341345.1	s__Corynebacterium halotolerans	79.7543	420	837	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000442645.1	s__Corynebacterium maris	79.7419	365	837	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177745.1	s__Corynebacterium pollutisoli	79.6956	403	837	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.83	98.83	0.98	0.98	2	-
GCF_001941485.1	s__Corynebacterium frankenforstense	79.5985	407	837	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000835165.1	s__Corynebacterium marinum	79.5672	365	837	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.21	98.42	0.97	0.94	3	-
GCF_900411315.1	s__Corynebacterium senegalense	79.3651	351	837	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001021065.1	s__Corynebacterium uterequi	79.0759	321	837	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013978595.1	s__Corynebacterium haemomassiliense	79.0492	328	837	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006334925.1	s__Corynebacterium tapiri	78.9217	273	837	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015351335.1	s__Corynebacterium lipophilum	78.8837	284	837	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420605.1	s__Corynebacterium massiliense	78.4681	270	837	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000373805.1	s__Corynebacterium pilosum	77.7547	236	837	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.98	99.96	0.99	0.99	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:38:44,761] [INFO] GTDB search result was written to GCF_003065405.1_ASM306540v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:38:44,765] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:38:44,771] [INFO] DFAST_QC result json was written to GCF_003065405.1_ASM306540v1_genomic.fna/dqc_result.json
[2024-01-24 14:38:44,771] [INFO] DFAST_QC completed!
[2024-01-24 14:38:44,772] [INFO] Total running time: 0h0m58s