[2024-01-24 15:02:18,877] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:18,881] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:18,881] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a3eb340-ee72-4fe3-8be2-0ca6f1ee22b8/dqc_reference
[2024-01-24 15:02:20,843] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:20,846] [INFO] Task started: Prodigal
[2024-01-24 15:02:20,847] [INFO] Running command: gunzip -c /var/lib/cwl/stg2bf46545-6a67-427b-96e1-628d1bdae0c0/GCF_011038655.2_ASM1103865v2_genomic.fna.gz | prodigal -d GCF_011038655.2_ASM1103865v2_genomic.fna/cds.fna -a GCF_011038655.2_ASM1103865v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:30,174] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:30,174] [INFO] Task started: HMMsearch
[2024-01-24 15:02:30,174] [INFO] Running command: hmmsearch --tblout GCF_011038655.2_ASM1103865v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a3eb340-ee72-4fe3-8be2-0ca6f1ee22b8/dqc_reference/reference_markers.hmm GCF_011038655.2_ASM1103865v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:30,411] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:30,412] [INFO] Found 6/6 markers.
[2024-01-24 15:02:30,441] [INFO] Query marker FASTA was written to GCF_011038655.2_ASM1103865v2_genomic.fna/markers.fasta
[2024-01-24 15:02:30,442] [INFO] Task started: Blastn
[2024-01-24 15:02:30,442] [INFO] Running command: blastn -query GCF_011038655.2_ASM1103865v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a3eb340-ee72-4fe3-8be2-0ca6f1ee22b8/dqc_reference/reference_markers.fasta -out GCF_011038655.2_ASM1103865v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:31,434] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:31,437] [INFO] Selected 22 target genomes.
[2024-01-24 15:02:31,437] [INFO] Target genome list was writen to GCF_011038655.2_ASM1103865v2_genomic.fna/target_genomes.txt
[2024-01-24 15:02:31,447] [INFO] Task started: fastANI
[2024-01-24 15:02:31,447] [INFO] Running command: fastANI --query /var/lib/cwl/stg2bf46545-6a67-427b-96e1-628d1bdae0c0/GCF_011038655.2_ASM1103865v2_genomic.fna.gz --refList GCF_011038655.2_ASM1103865v2_genomic.fna/target_genomes.txt --output GCF_011038655.2_ASM1103865v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:42,526] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:42,527] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a3eb340-ee72-4fe3-8be2-0ca6f1ee22b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:42,527] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a3eb340-ee72-4fe3-8be2-0ca6f1ee22b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:42,545] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:02:42,546] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:42,546] [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 lizhenjunii	strain=ZJ-599	GCA_011038655.2	2709394	2709394	type	True	100.0	869	869	95	conclusive
Corynebacterium camporealensis	strain=CIP 105508	GCA_000766885.2	161896	161896	type	True	79.1608	239	869	95	below_threshold
Corynebacterium aurimucosum	strain=FDAARGOS_1109	GCA_016728705.1	169292	169292	suspected-type	True	79.1283	254	869	95	below_threshold
Corynebacterium minutissimum	strain=NCTC10288	GCA_900478045.1	38301	38301	type	True	79.0929	218	869	95	below_threshold
Corynebacterium camporealensis	strain=DSM 44610	GCA_000980815.1	161896	161896	type	True	79.0794	240	869	95	below_threshold
Corynebacterium aurimucosum	strain=DSM 44532	GCA_024138775.1	169292	169292	suspected-type	True	78.8852	254	869	95	below_threshold
Corynebacterium singulare	strain=IBS B52218	GCA_000833575.1	161899	161899	type	True	78.8456	240	869	95	below_threshold
Corynebacterium tuberculostearicum	strain=FDAARGOS_1117	GCA_016728365.1	38304	38304	type	True	78.7442	228	869	95	below_threshold
Corynebacterium endometrii	strain=LMM-1653	GCA_004795735.1	2488819	2488819	type	True	78.7244	203	869	95	below_threshold
Corynebacterium tuberculostearicum	strain=DSM 44922	GCA_013408445.1	38304	38304	type	True	78.5923	231	869	95	below_threshold
Corynebacterium phoceense	strain=MC1	GCA_900092335.1	1686286	1686286	type	True	78.5853	282	869	95	below_threshold
Corynebacterium flavescens	strain=OJ8	GCA_001941465.1	28028	28028	type	True	78.4867	193	869	95	below_threshold
Corynebacterium halotolerans	strain=YIM 70093 = DSM 44683	GCA_000341345.1	225326	225326	type	True	78.4309	187	869	95	below_threshold
Corynebacterium riegelii	strain=FDAARGOS_1114	GCA_016728505.1	156976	156976	type	True	78.2744	151	869	95	below_threshold
Corynebacterium haemomassiliense	strain=Marseille-Q3615	GCA_013978595.1	2754726	2754726	type	True	78.1983	168	869	95	below_threshold
Corynebacterium fournieri	strain=Marseille-P2948	GCA_900176865.1	1852390	1852390	type	True	78.0044	151	869	95	below_threshold
Corynebacterium flavescens	strain=NBRC 14136	GCA_006539465.1	28028	28028	type	True	78.0022	180	869	95	below_threshold
Corynebacterium flavescens	strain=CCUG 28791T	GCA_008693105.1	28028	28028	type	True	77.9677	181	869	95	below_threshold
Corynebacterium halotolerans	strain=DSM 44683	GCA_000688435.1	225326	225326	type	True	77.8555	184	869	95	below_threshold
Corynebacterium hadale	strain=NBT06-6	GCA_002273005.1	2026255	2026255	type	True	77.5419	137	869	95	below_threshold
Corynebacterium godavarianum	strain=LMG 29598	GCA_007559235.1	2054421	2054421	type	True	77.5015	147	869	95	below_threshold
Catellatospora vulcania	strain=NEAU-JM1	GCA_009720385.1	1460450	1460450	type	True	75.5168	52	869	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:42,547] [INFO] DFAST Taxonomy check result was written to GCF_011038655.2_ASM1103865v2_genomic.fna/tc_result.tsv
[2024-01-24 15:02:42,548] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:42,548] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:42,548] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a3eb340-ee72-4fe3-8be2-0ca6f1ee22b8/dqc_reference/checkm_data
[2024-01-24 15:02:42,550] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:42,577] [INFO] Task started: CheckM
[2024-01-24 15:02:42,577] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011038655.2_ASM1103865v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011038655.2_ASM1103865v2_genomic.fna/checkm_input GCF_011038655.2_ASM1103865v2_genomic.fna/checkm_result
[2024-01-24 15:03:14,171] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:14,173] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:14,195] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:14,195] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:14,195] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011038655.2_ASM1103865v2_genomic.fna/markers.fasta)
[2024-01-24 15:03:14,196] [INFO] Task started: Blastn
[2024-01-24 15:03:14,196] [INFO] Running command: blastn -query GCF_011038655.2_ASM1103865v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a3eb340-ee72-4fe3-8be2-0ca6f1ee22b8/dqc_reference/reference_markers_gtdb.fasta -out GCF_011038655.2_ASM1103865v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:15,542] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:15,545] [INFO] Selected 20 target genomes.
[2024-01-24 15:03:15,546] [INFO] Target genome list was writen to GCF_011038655.2_ASM1103865v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:15,562] [INFO] Task started: fastANI
[2024-01-24 15:03:15,562] [INFO] Running command: fastANI --query /var/lib/cwl/stg2bf46545-6a67-427b-96e1-628d1bdae0c0/GCF_011038655.2_ASM1103865v2_genomic.fna.gz --refList GCF_011038655.2_ASM1103865v2_genomic.fna/target_genomes_gtdb.txt --output GCF_011038655.2_ASM1103865v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:26,009] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:26,030] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:26,031] [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_011038655.2	s__Corynebacterium lizhenjunii	100.0	869	869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.69	98.69	0.97	0.97	2	conclusive
GCF_002861385.1	s__Corynebacterium aurimucosum_C	79.3908	231	869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.04	96.50	0.91	0.89	28	-
GCF_000988205.1	s__Corynebacterium minutissimum_A	79.3774	251	869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.53	96.09	0.91	0.89	16	-
GCF_016728705.1	s__Corynebacterium sp001807205	79.2029	256	869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.15	96.83	0.93	0.90	8	-
GCF_000980815.1	s__Corynebacterium camporealensis	79.0673	239	869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.96	99.96	1.00	1.00	2	-
GCF_016889765.1	s__Corynebacterium minutissimum_B	79.0364	227	869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.10	96.19	0.95	0.91	3	-
GCF_000805675.1	s__Corynebacterium minutissimum	78.8581	211	869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.99	99.99	1.00	1.00	6	-
GCF_001586215.1	s__Corynebacterium simulans	78.7977	207	869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.78	97.47	0.94	0.92	11	-
GCF_013408445.1	s__Corynebacterium tuberculostearicum	78.7367	234	869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	96.3332	98.29	96.59	0.96	0.92	3	-
GCF_001815935.1	s__Corynebacterium sp001815935	78.7287	260	869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900092335.1	s__Corynebacterium phoceense	78.5714	283	869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.96	96.08	0.95	0.92	11	-
GCF_016894265.1	s__Corynebacterium tuberculostearicum_D	78.3722	220	869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.1108	N/A	N/A	N/A	N/A	1	-
GCA_900539985.1	s__Corynebacterium sp900539985	78.3234	187	869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.98	99.98	0.92	0.92	2	-
GCF_016728505.1	s__Corynebacterium riegelii	78.2126	150	869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.34	97.30	0.92	0.92	4	-
GCF_000341345.1	s__Corynebacterium halotolerans	78.1861	184	869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013978595.1	s__Corynebacterium haemomassiliense	78.1578	167	869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019114925.1	s__Corynebacterium faecipullorum	77.9838	191	869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008693105.1	s__Corynebacterium flavescens	77.9636	182	869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.46	98.96	0.96	0.94	6	-
GCF_001831515.1	s__Corynebacterium sp001831515	77.8035	156	869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.57	96.57	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:03:26,033] [INFO] GTDB search result was written to GCF_011038655.2_ASM1103865v2_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:26,033] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:26,043] [INFO] DFAST_QC result json was written to GCF_011038655.2_ASM1103865v2_genomic.fna/dqc_result.json
[2024-01-24 15:03:26,043] [INFO] DFAST_QC completed!
[2024-01-24 15:03:26,044] [INFO] Total running time: 0h1m7s