[2024-01-24 14:15:33,575] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:15:33,579] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:15:33,579] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f49e606-d00f-4a23-b842-9cbcef4b4060/dqc_reference
[2024-01-24 14:15:34,998] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:15:34,999] [INFO] Task started: Prodigal
[2024-01-24 14:15:34,999] [INFO] Running command: gunzip -c /var/lib/cwl/stg8021d36d-eb93-42ec-a865-97efd6c83f44/GCF_030408455.1_ASM3040845v1_genomic.fna.gz | prodigal -d GCF_030408455.1_ASM3040845v1_genomic.fna/cds.fna -a GCF_030408455.1_ASM3040845v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:44,670] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:44,671] [INFO] Task started: HMMsearch
[2024-01-24 14:15:44,671] [INFO] Running command: hmmsearch --tblout GCF_030408455.1_ASM3040845v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f49e606-d00f-4a23-b842-9cbcef4b4060/dqc_reference/reference_markers.hmm GCF_030408455.1_ASM3040845v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:44,947] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:44,949] [INFO] Found 6/6 markers.
[2024-01-24 14:15:44,979] [INFO] Query marker FASTA was written to GCF_030408455.1_ASM3040845v1_genomic.fna/markers.fasta
[2024-01-24 14:15:44,980] [INFO] Task started: Blastn
[2024-01-24 14:15:44,980] [INFO] Running command: blastn -query GCF_030408455.1_ASM3040845v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f49e606-d00f-4a23-b842-9cbcef4b4060/dqc_reference/reference_markers.fasta -out GCF_030408455.1_ASM3040845v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:46,008] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:46,012] [INFO] Selected 9 target genomes.
[2024-01-24 14:15:46,012] [INFO] Target genome list was writen to GCF_030408455.1_ASM3040845v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:46,017] [INFO] Task started: fastANI
[2024-01-24 14:15:46,017] [INFO] Running command: fastANI --query /var/lib/cwl/stg8021d36d-eb93-42ec-a865-97efd6c83f44/GCF_030408455.1_ASM3040845v1_genomic.fna.gz --refList GCF_030408455.1_ASM3040845v1_genomic.fna/target_genomes.txt --output GCF_030408455.1_ASM3040845v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:51,444] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:51,444] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f49e606-d00f-4a23-b842-9cbcef4b4060/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:51,444] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f49e606-d00f-4a23-b842-9cbcef4b4060/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:51,455] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:15:51,455] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:15:51,455] [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 testudinoris	strain=DSM 44614	GCA_001021045.1	136857	136857	type	True	88.544	777	935	95	below_threshold
Corynebacterium pollutisoli	strain=VDS11	GCA_900177745.1	1610489	1610489	type	True	80.6499	476	935	95	below_threshold
Corynebacterium marinum	strain=DSM 44953	GCA_000835165.1	349751	349751	type	True	80.4988	469	935	95	below_threshold
Corynebacterium humireducens	strain=DSM 45392	GCA_000819445.1	1223514	1223514	type	True	80.4898	479	935	95	below_threshold
Corynebacterium marinum	strain=CGMCC 1.6998	GCA_014645275.1	349751	349751	type	True	80.3511	462	935	95	below_threshold
Corynebacterium humireducens	strain=NBRC 106098	GCA_001571025.1	1223514	1223514	type	True	80.2659	465	935	95	below_threshold
Corynebacterium comes	strain=2019	GCA_009734405.1	2675218	2675218	type	True	79.9222	443	935	95	below_threshold
Corynebacterium halotolerans	strain=YIM 70093 = DSM 44683	GCA_000341345.1	225326	225326	type	True	79.7249	420	935	95	below_threshold
Corynebacterium halotolerans	strain=DSM 44683	GCA_000688435.1	225326	225326	type	True	79.4605	414	935	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:51,461] [INFO] DFAST Taxonomy check result was written to GCF_030408455.1_ASM3040845v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:51,461] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:51,462] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:51,462] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f49e606-d00f-4a23-b842-9cbcef4b4060/dqc_reference/checkm_data
[2024-01-24 14:15:51,464] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:51,496] [INFO] Task started: CheckM
[2024-01-24 14:15:51,496] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030408455.1_ASM3040845v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030408455.1_ASM3040845v1_genomic.fna/checkm_input GCF_030408455.1_ASM3040845v1_genomic.fna/checkm_result
[2024-01-24 14:16:23,125] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:23,126] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:23,145] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:23,146] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:23,146] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030408455.1_ASM3040845v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:23,146] [INFO] Task started: Blastn
[2024-01-24 14:16:23,147] [INFO] Running command: blastn -query GCF_030408455.1_ASM3040845v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f49e606-d00f-4a23-b842-9cbcef4b4060/dqc_reference/reference_markers_gtdb.fasta -out GCF_030408455.1_ASM3040845v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:24,595] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:24,599] [INFO] Selected 8 target genomes.
[2024-01-24 14:16:24,599] [INFO] Target genome list was writen to GCF_030408455.1_ASM3040845v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:24,603] [INFO] Task started: fastANI
[2024-01-24 14:16:24,604] [INFO] Running command: fastANI --query /var/lib/cwl/stg8021d36d-eb93-42ec-a865-97efd6c83f44/GCF_030408455.1_ASM3040845v1_genomic.fna.gz --refList GCF_030408455.1_ASM3040845v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030408455.1_ASM3040845v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:29,375] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:29,383] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:16:29,384] [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_001021045.1	s__Corynebacterium testudinoris	88.5738	776	935	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	80.6632	474	935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.83	98.83	0.98	0.98	2	-
GCF_000819445.1	s__Corynebacterium humireducens	80.5066	478	935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.80	97.60	0.97	0.93	3	-
GCF_000835165.1	s__Corynebacterium marinum	80.4892	469	935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.21	98.42	0.97	0.94	3	-
GCF_003955685.1	s__Corynebacterium sp003955685	80.0817	425	935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009734405.1	s__Corynebacterium sp009734405	79.9403	443	935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012838985.1	s__Corynebacterium sp012838985	79.7461	386	935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341345.1	s__Corynebacterium halotolerans	79.6922	422	935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:29,386] [INFO] GTDB search result was written to GCF_030408455.1_ASM3040845v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:29,386] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:29,398] [INFO] DFAST_QC result json was written to GCF_030408455.1_ASM3040845v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:29,399] [INFO] DFAST_QC completed!
[2024-01-24 14:16:29,399] [INFO] Total running time: 0h0m56s