[2024-01-25 19:48:51,326] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:48:51,328] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:48:51,328] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c7c1d1b-4a07-4055-b3ab-1aa0f20ac512/dqc_reference
[2024-01-25 19:48:52,451] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:48:52,452] [INFO] Task started: Prodigal
[2024-01-25 19:48:52,452] [INFO] Running command: gunzip -c /var/lib/cwl/stgbec79158-1147-454a-b336-3e0f9f0af60b/GCF_001044155.1_ASM104415v1_genomic.fna.gz | prodigal -d GCF_001044155.1_ASM104415v1_genomic.fna/cds.fna -a GCF_001044155.1_ASM104415v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:48:59,583] [INFO] Task succeeded: Prodigal
[2024-01-25 19:48:59,583] [INFO] Task started: HMMsearch
[2024-01-25 19:48:59,583] [INFO] Running command: hmmsearch --tblout GCF_001044155.1_ASM104415v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c7c1d1b-4a07-4055-b3ab-1aa0f20ac512/dqc_reference/reference_markers.hmm GCF_001044155.1_ASM104415v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:48:59,765] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:48:59,766] [INFO] Found 6/6 markers.
[2024-01-25 19:48:59,790] [INFO] Query marker FASTA was written to GCF_001044155.1_ASM104415v1_genomic.fna/markers.fasta
[2024-01-25 19:48:59,791] [INFO] Task started: Blastn
[2024-01-25 19:48:59,791] [INFO] Running command: blastn -query GCF_001044155.1_ASM104415v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c7c1d1b-4a07-4055-b3ab-1aa0f20ac512/dqc_reference/reference_markers.fasta -out GCF_001044155.1_ASM104415v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:49:00,583] [INFO] Task succeeded: Blastn
[2024-01-25 19:49:00,586] [INFO] Selected 7 target genomes.
[2024-01-25 19:49:00,587] [INFO] Target genome list was writen to GCF_001044155.1_ASM104415v1_genomic.fna/target_genomes.txt
[2024-01-25 19:49:00,594] [INFO] Task started: fastANI
[2024-01-25 19:49:00,594] [INFO] Running command: fastANI --query /var/lib/cwl/stgbec79158-1147-454a-b336-3e0f9f0af60b/GCF_001044155.1_ASM104415v1_genomic.fna.gz --refList GCF_001044155.1_ASM104415v1_genomic.fna/target_genomes.txt --output GCF_001044155.1_ASM104415v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:49:04,607] [INFO] Task succeeded: fastANI
[2024-01-25 19:49:04,608] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c7c1d1b-4a07-4055-b3ab-1aa0f20ac512/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:49:04,608] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c7c1d1b-4a07-4055-b3ab-1aa0f20ac512/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:49:04,614] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 19:49:04,614] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:49:04,614] [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 pilosum	strain=CIP103422	GCA_001044155.1	35756	35756	type	True	100.0	842	842	95	conclusive
Corynebacterium pilosum	strain=NCTC11862	GCA_900447205.1	35756	35756	type	True	99.9495	839	842	95	conclusive
Corynebacterium pilosum	strain=DSM 20521	GCA_000373805.1	35756	35756	type	True	99.9393	826	842	95	conclusive
Corynebacterium cystitidis	strain=NCTC11863	GCA_900187295.1	35757	35757	type	True	80.668	513	842	95	below_threshold
Corynebacterium cystitidis	strain=DSM 20524	GCA_900111265.1	35757	35757	type	True	80.6678	513	842	95	below_threshold
Corynebacterium mycetoides	strain=DSM 20632	GCA_900103625.1	38302	38302	type	True	78.3803	257	842	95	below_threshold
Corynebacterium singulare	strain=IBS B52218	GCA_000833575.1	161899	161899	type	True	77.5001	142	842	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:49:04,616] [INFO] DFAST Taxonomy check result was written to GCF_001044155.1_ASM104415v1_genomic.fna/tc_result.tsv
[2024-01-25 19:49:04,616] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:49:04,616] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:49:04,617] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c7c1d1b-4a07-4055-b3ab-1aa0f20ac512/dqc_reference/checkm_data
[2024-01-25 19:49:04,617] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:49:04,646] [INFO] Task started: CheckM
[2024-01-25 19:49:04,646] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001044155.1_ASM104415v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001044155.1_ASM104415v1_genomic.fna/checkm_input GCF_001044155.1_ASM104415v1_genomic.fna/checkm_result
[2024-01-25 19:49:29,658] [INFO] Task succeeded: CheckM
[2024-01-25 19:49:29,659] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:49:29,684] [INFO] ===== Completeness check finished =====
[2024-01-25 19:49:29,684] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:49:29,684] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001044155.1_ASM104415v1_genomic.fna/markers.fasta)
[2024-01-25 19:49:29,684] [INFO] Task started: Blastn
[2024-01-25 19:49:29,685] [INFO] Running command: blastn -query GCF_001044155.1_ASM104415v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c7c1d1b-4a07-4055-b3ab-1aa0f20ac512/dqc_reference/reference_markers_gtdb.fasta -out GCF_001044155.1_ASM104415v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:49:30,871] [INFO] Task succeeded: Blastn
[2024-01-25 19:49:30,876] [INFO] Selected 17 target genomes.
[2024-01-25 19:49:30,877] [INFO] Target genome list was writen to GCF_001044155.1_ASM104415v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:49:30,904] [INFO] Task started: fastANI
[2024-01-25 19:49:30,904] [INFO] Running command: fastANI --query /var/lib/cwl/stgbec79158-1147-454a-b336-3e0f9f0af60b/GCF_001044155.1_ASM104415v1_genomic.fna.gz --refList GCF_001044155.1_ASM104415v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001044155.1_ASM104415v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:49:39,364] [INFO] Task succeeded: fastANI
[2024-01-25 19:49:39,373] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:49:39,374] [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_000373805.1	s__Corynebacterium pilosum	99.9393	826	842	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.98	99.96	0.99	0.99	3	conclusive
GCF_900187295.1	s__Corynebacterium cystitidis	80.6719	511	842	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000379425.1	s__Corynebacterium lubricantis	78.7906	321	842	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001807265.1	s__Corynebacterium sp001807265	78.5324	246	842	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.96	97.96	0.92	0.92	2	-
GCF_900103625.1	s__Corynebacterium mycetoides	78.4378	257	842	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903645305.1	s__Corynebacterium sp001764565	78.3652	228	842	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.10	98.10	0.96	0.96	2	-
GCF_900176865.1	s__Corynebacterium fournieri	78.2586	244	842	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739455.1	s__Corynebacterium imitans	78.2224	268	842	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007641235.1	s__Corynebacterium sanguinis	78.2171	249	842	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.27	97.90	0.92	0.90	7	-
GCF_900105505.1	s__Corynebacterium coyleae	78.1987	214	842	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.88	97.68	0.93	0.91	16	-
GCF_014490555.1	s__Corynebacterium sp014490555	78.1572	249	842	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	0.99	3	-
GCA_900156035.1	s__Corynebacterium afermentans	78.1392	247	842	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.27	97.60	0.93	0.89	5	-
GCF_900105305.1	s__Corynebacterium timonense	77.9605	234	842	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.93	99.93	0.99	0.99	2	-
GCF_012396315.1	s__Corynebacterium mucifaciens	77.8305	235	842	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	95.74	95.74	0.89	0.89	2	-
GCF_000833575.1	s__Corynebacterium singulare	77.5216	141	842	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.05	96.95	0.89	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:49:39,375] [INFO] GTDB search result was written to GCF_001044155.1_ASM104415v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:49:39,376] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:49:39,378] [INFO] DFAST_QC result json was written to GCF_001044155.1_ASM104415v1_genomic.fna/dqc_result.json
[2024-01-25 19:49:39,378] [INFO] DFAST_QC completed!
[2024-01-25 19:49:39,378] [INFO] Total running time: 0h0m48s