[2024-01-24 12:46:49,453] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:46:49,455] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:46:49,455] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d5ed11d-8b10-46f5-bbe9-b250d2ca8ba9/dqc_reference
[2024-01-24 12:46:50,622] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:46:50,623] [INFO] Task started: Prodigal
[2024-01-24 12:46:50,623] [INFO] Running command: gunzip -c /var/lib/cwl/stg07558b46-0211-450c-a375-f34644b45310/GCF_000159635.1_ASM15963v1_genomic.fna.gz | prodigal -d GCF_000159635.1_ASM15963v1_genomic.fna/cds.fna -a GCF_000159635.1_ASM15963v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:46:57,553] [INFO] Task succeeded: Prodigal
[2024-01-24 12:46:57,554] [INFO] Task started: HMMsearch
[2024-01-24 12:46:57,554] [INFO] Running command: hmmsearch --tblout GCF_000159635.1_ASM15963v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d5ed11d-8b10-46f5-bbe9-b250d2ca8ba9/dqc_reference/reference_markers.hmm GCF_000159635.1_ASM15963v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:46:57,716] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:46:57,717] [INFO] Found 6/6 markers.
[2024-01-24 12:46:57,741] [INFO] Query marker FASTA was written to GCF_000159635.1_ASM15963v1_genomic.fna/markers.fasta
[2024-01-24 12:46:57,742] [INFO] Task started: Blastn
[2024-01-24 12:46:57,742] [INFO] Running command: blastn -query GCF_000159635.1_ASM15963v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d5ed11d-8b10-46f5-bbe9-b250d2ca8ba9/dqc_reference/reference_markers.fasta -out GCF_000159635.1_ASM15963v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:58,698] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:58,702] [INFO] Selected 12 target genomes.
[2024-01-24 12:46:58,702] [INFO] Target genome list was writen to GCF_000159635.1_ASM15963v1_genomic.fna/target_genomes.txt
[2024-01-24 12:46:58,708] [INFO] Task started: fastANI
[2024-01-24 12:46:58,708] [INFO] Running command: fastANI --query /var/lib/cwl/stg07558b46-0211-450c-a375-f34644b45310/GCF_000159635.1_ASM15963v1_genomic.fna.gz --refList GCF_000159635.1_ASM15963v1_genomic.fna/target_genomes.txt --output GCF_000159635.1_ASM15963v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:04,868] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:04,869] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d5ed11d-8b10-46f5-bbe9-b250d2ca8ba9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:04,869] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d5ed11d-8b10-46f5-bbe9-b250d2ca8ba9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:04,879] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:04,879] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:04,879] [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 lipophiloflavum	strain=DSM 44291	GCA_000159635.1	161889	161889	type	True	99.9994	768	778	95	conclusive
Corynebacterium sanguinis	strain=CCUG 58655	GCA_007641235.1	2594913	2594913	type	True	92.4945	667	778	95	below_threshold
Corynebacterium mycetoides	strain=DSM 20632	GCA_900103625.1	38302	38302	type	True	84.3398	561	778	95	below_threshold
Corynebacterium qintianiae	strain=MC1420	GCA_011038645.2	2709392	2709392	type	True	82.6283	540	778	95	below_threshold
Corynebacterium senegalense	strain=Marseille-P4329	GCA_900411315.1	2080750	2080750	type	True	81.554	490	778	95	below_threshold
Corynebacterium liangguodongii	strain=2184	GCA_003070865.1	2079535	2079535	type	True	81.3162	491	778	95	below_threshold
Corynebacterium timonense	strain=DSM 45434	GCA_900105305.1	441500	441500	type	True	80.7285	449	778	95	below_threshold
Corynebacterium jeddahense	strain=JCB	GCA_000577555.1	1414719	1414719	type	True	80.6967	382	778	95	below_threshold
Corynebacterium timonense	strain=5401744	GCA_000312345.1	441500	441500	type	True	80.6496	453	778	95	below_threshold
Corynebacterium lujinxingii	strain=zg-917	GCA_014490555.1	2763010	2763010	type	True	79.9839	374	778	95	below_threshold
Corynebacterium godavarianum	strain=LMG 29598	GCA_007559235.1	2054421	2054421	type	True	79.6369	386	778	95	below_threshold
Corynebacterium hadale	strain=NBT06-6	GCA_002273005.1	2026255	2026255	type	True	79.3741	377	778	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:05,027] [INFO] DFAST Taxonomy check result was written to GCF_000159635.1_ASM15963v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:05,028] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:05,029] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:05,029] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d5ed11d-8b10-46f5-bbe9-b250d2ca8ba9/dqc_reference/checkm_data
[2024-01-24 12:47:05,030] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:05,057] [INFO] Task started: CheckM
[2024-01-24 12:47:05,057] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000159635.1_ASM15963v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000159635.1_ASM15963v1_genomic.fna/checkm_input GCF_000159635.1_ASM15963v1_genomic.fna/checkm_result
[2024-01-24 12:47:29,380] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:29,381] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.37%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:29,400] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:29,401] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:29,401] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000159635.1_ASM15963v1_genomic.fna/markers.fasta)
[2024-01-24 12:47:29,401] [INFO] Task started: Blastn
[2024-01-24 12:47:29,402] [INFO] Running command: blastn -query GCF_000159635.1_ASM15963v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d5ed11d-8b10-46f5-bbe9-b250d2ca8ba9/dqc_reference/reference_markers_gtdb.fasta -out GCF_000159635.1_ASM15963v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:30,911] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:30,915] [INFO] Selected 11 target genomes.
[2024-01-24 12:47:30,915] [INFO] Target genome list was writen to GCF_000159635.1_ASM15963v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:30,922] [INFO] Task started: fastANI
[2024-01-24 12:47:30,922] [INFO] Running command: fastANI --query /var/lib/cwl/stg07558b46-0211-450c-a375-f34644b45310/GCF_000159635.1_ASM15963v1_genomic.fna.gz --refList GCF_000159635.1_ASM15963v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000159635.1_ASM15963v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:37,212] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:37,222] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:47:37,222] [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_000159635.1	s__Corynebacterium lipophiloflavum	99.9994	768	778	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_007641235.1	s__Corynebacterium sanguinis	92.4739	667	778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.27	97.90	0.92	0.90	7	-
GCF_900103625.1	s__Corynebacterium mycetoides	84.3628	559	778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011038645.2	s__Corynebacterium qintianiae	82.6573	537	778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.90	98.90	0.92	0.92	2	-
GCF_900411315.1	s__Corynebacterium senegalense	81.554	490	778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003070865.1	s__Corynebacterium liangguodongii	81.3106	491	778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900105305.1	s__Corynebacterium timonense	80.7846	445	778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.93	99.93	0.99	0.99	2	-
GCF_000577555.1	s__Corynebacterium jeddahense	80.7136	381	778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002339505.1	s__Corynebacterium sp002339505	80.3328	429	778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014490555.1	s__Corynebacterium sp014490555	79.9838	374	778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	0.99	3	-
GCF_003693265.1	s__Corynebacterium gottingense	79.4631	362	778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.52	97.05	0.92	0.90	11	-
--------------------------------------------------------------------------------
[2024-01-24 12:47:37,225] [INFO] GTDB search result was written to GCF_000159635.1_ASM15963v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:37,225] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:37,229] [INFO] DFAST_QC result json was written to GCF_000159635.1_ASM15963v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:37,229] [INFO] DFAST_QC completed!
[2024-01-24 12:47:37,229] [INFO] Total running time: 0h0m48s