[2024-01-24 11:06:04,663] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:06:04,664] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:06:04,664] [INFO] DQC Reference Directory: /var/lib/cwl/stg2dc92518-7dcb-41c5-ab50-177f195d5956/dqc_reference
[2024-01-24 11:06:07,010] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:06:07,012] [INFO] Task started: Prodigal
[2024-01-24 11:06:07,012] [INFO] Running command: gunzip -c /var/lib/cwl/stgea66b7a0-9ac4-4afd-b13a-8ec111122408/GCF_030408595.1_ASM3040859v1_genomic.fna.gz | prodigal -d GCF_030408595.1_ASM3040859v1_genomic.fna/cds.fna -a GCF_030408595.1_ASM3040859v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:06:17,750] [INFO] Task succeeded: Prodigal
[2024-01-24 11:06:17,751] [INFO] Task started: HMMsearch
[2024-01-24 11:06:17,751] [INFO] Running command: hmmsearch --tblout GCF_030408595.1_ASM3040859v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2dc92518-7dcb-41c5-ab50-177f195d5956/dqc_reference/reference_markers.hmm GCF_030408595.1_ASM3040859v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:06:17,999] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:06:18,001] [INFO] Found 6/6 markers.
[2024-01-24 11:06:18,028] [INFO] Query marker FASTA was written to GCF_030408595.1_ASM3040859v1_genomic.fna/markers.fasta
[2024-01-24 11:06:18,029] [INFO] Task started: Blastn
[2024-01-24 11:06:18,029] [INFO] Running command: blastn -query GCF_030408595.1_ASM3040859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2dc92518-7dcb-41c5-ab50-177f195d5956/dqc_reference/reference_markers.fasta -out GCF_030408595.1_ASM3040859v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:18,911] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:18,915] [INFO] Selected 22 target genomes.
[2024-01-24 11:06:18,916] [INFO] Target genome list was writen to GCF_030408595.1_ASM3040859v1_genomic.fna/target_genomes.txt
[2024-01-24 11:06:18,929] [INFO] Task started: fastANI
[2024-01-24 11:06:18,929] [INFO] Running command: fastANI --query /var/lib/cwl/stgea66b7a0-9ac4-4afd-b13a-8ec111122408/GCF_030408595.1_ASM3040859v1_genomic.fna.gz --refList GCF_030408595.1_ASM3040859v1_genomic.fna/target_genomes.txt --output GCF_030408595.1_ASM3040859v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:29,165] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:29,165] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2dc92518-7dcb-41c5-ab50-177f195d5956/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:29,166] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2dc92518-7dcb-41c5-ab50-177f195d5956/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:29,195] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:06:29,195] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:29,195] [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 canis	strain=CCUG 58627	GCA_007859215.1	679663	679663	type	True	99.9405	950	1015	95	conclusive
Corynebacterium freiburgense	strain=DSM 45254	GCA_000428805.1	556548	556548	type	True	78.6911	262	1015	95	below_threshold
Corynebacterium aquilae	strain=S-613	GCA_001941445.1	203263	203263	type	True	78.6218	157	1015	95	below_threshold
Corynebacterium marinum	strain=DSM 44953	GCA_000835165.1	349751	349751	type	True	78.2318	136	1015	95	below_threshold
Corynebacterium vitaeruminis	strain=DSM 20294	GCA_000550805.1	38305	38305	type	True	78.2149	162	1015	95	below_threshold
Corynebacterium durum	strain=DSM 45333	GCA_013410305.1	61592	61592	type	True	78.1613	165	1015	95	below_threshold
Corynebacterium freneyi	strain=DSM 44506	GCA_017876455.1	134034	134034	type	True	77.9745	141	1015	95	below_threshold
Corynebacterium pollutisoli	strain=VDS11	GCA_900177745.1	1610489	1610489	type	True	77.9554	142	1015	95	below_threshold
Corynebacterium urealyticum	strain=FDAARGOS_994	GCA_016127975.1	43771	43771	type	True	77.9487	88	1015	95	below_threshold
Corynebacterium fournieri	strain=Marseille-P2948	GCA_900176865.1	1852390	1852390	type	True	77.903	103	1015	95	below_threshold
Corynebacterium urealyticum	strain=DSM 7109	GCA_000069945.1	43771	43771	type	True	77.8809	85	1015	95	below_threshold
Corynebacterium urealyticum	strain=NCTC12011	GCA_900187235.1	43771	43771	type	True	77.8312	87	1015	95	below_threshold
Corynebacterium marinum	strain=CGMCC 1.6998	GCA_014645275.1	349751	349751	type	True	77.6828	135	1015	95	below_threshold
Corynebacterium freneyi	strain=FDAARGOS 1426	GCA_019047805.1	134034	134034	type	True	77.6153	140	1015	95	below_threshold
Corynebacterium humireducens	strain=NBRC 106098	GCA_001571025.1	1223514	1223514	type	True	77.577	136	1015	95	below_threshold
Corynebacterium appendicis	strain=DSM 44531	GCA_900156665.1	163202	163202	type	True	77.479	83	1015	95	below_threshold
Corynebacterium frankenforstense	strain=ST18	GCA_001941485.1	1230998	1230998	type	True	77.4754	149	1015	95	below_threshold
Corynebacterium mastitidis	strain=DSM 44356	GCA_000375365.1	161890	161890	type	True	77.4682	138	1015	95	below_threshold
Corynebacterium ciconiae	strain=DSM 44920	GCA_000372385.1	227319	227319	type	True	77.4513	126	1015	95	below_threshold
Corynebacterium ihumii	strain=GD7	GCA_000403725.2	1232427	1232427	type	True	77.2565	119	1015	95	below_threshold
Corynebacterium afermentans subsp. lipophilum	strain=CCUG 32105	GCA_015351335.1	144184	38286	type	True	77.108	110	1015	95	below_threshold
Corynebacterium lipophiloflavum	strain=DSM 44291	GCA_000159635.1	161889	161889	type	True	77.0811	92	1015	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:29,197] [INFO] DFAST Taxonomy check result was written to GCF_030408595.1_ASM3040859v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:29,201] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:29,202] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:29,202] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2dc92518-7dcb-41c5-ab50-177f195d5956/dqc_reference/checkm_data
[2024-01-24 11:06:29,203] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:29,238] [INFO] Task started: CheckM
[2024-01-24 11:06:29,239] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030408595.1_ASM3040859v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030408595.1_ASM3040859v1_genomic.fna/checkm_input GCF_030408595.1_ASM3040859v1_genomic.fna/checkm_result
[2024-01-24 11:07:02,833] [INFO] Task succeeded: CheckM
[2024-01-24 11:07:02,835] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:07:02,851] [INFO] ===== Completeness check finished =====
[2024-01-24 11:07:02,852] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:07:02,852] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030408595.1_ASM3040859v1_genomic.fna/markers.fasta)
[2024-01-24 11:07:02,852] [INFO] Task started: Blastn
[2024-01-24 11:07:02,853] [INFO] Running command: blastn -query GCF_030408595.1_ASM3040859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2dc92518-7dcb-41c5-ab50-177f195d5956/dqc_reference/reference_markers_gtdb.fasta -out GCF_030408595.1_ASM3040859v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:07:04,053] [INFO] Task succeeded: Blastn
[2024-01-24 11:07:04,056] [INFO] Selected 22 target genomes.
[2024-01-24 11:07:04,057] [INFO] Target genome list was writen to GCF_030408595.1_ASM3040859v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:07:04,074] [INFO] Task started: fastANI
[2024-01-24 11:07:04,074] [INFO] Running command: fastANI --query /var/lib/cwl/stgea66b7a0-9ac4-4afd-b13a-8ec111122408/GCF_030408595.1_ASM3040859v1_genomic.fna.gz --refList GCF_030408595.1_ASM3040859v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030408595.1_ASM3040859v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:14,440] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:14,460] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:07:14,460] [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_007859215.1	s__Corynebacterium canis	99.9405	950	1015	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_000428805.1	s__Corynebacterium freiburgense	78.6762	263	1015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001941445.1	s__Corynebacterium aquilae	78.525	156	1015	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	78.2284	136	1015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.21	98.42	0.97	0.94	3	-
GCF_013410305.1	s__Corynebacterium durum	78.1633	165	1015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.07	97.26	0.97	0.94	4	-
GCF_000550805.1	s__Corynebacterium vitaeruminis	78.1191	161	1015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.86	98.60	0.94	0.94	3	-
GCF_900177745.1	s__Corynebacterium pollutisoli	77.9554	142	1015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.83	98.83	0.98	0.98	2	-
GCF_000069945.1	s__Corynebacterium urealyticum	77.8895	84	1015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.66	97.50	0.94	0.89	9	-
GCF_002994655.1	s__Corynebacterium sp002994655	77.8304	165	1015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595275.1	s__Corynebacterium sp016595275	77.7638	126	1015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002861385.1	s__Corynebacterium aurimucosum_C	77.6136	100	1015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.04	96.50	0.91	0.89	28	-
GCF_900156665.1	s__Corynebacterium appendicis	77.479	83	1015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000372385.1	s__Corynebacterium ciconiae	77.4513	126	1015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001941485.1	s__Corynebacterium frankenforstense	77.4316	146	1015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001807485.1	s__Corynebacterium sp001807485	77.247	96	1015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.83	97.75	0.93	0.93	3	-
GCA_019120635.1	s__Corynebacterium intestinavium	77.192	74	1015	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	77.1245	116	1015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.96	97.96	0.92	0.92	2	-
GCF_015351335.1	s__Corynebacterium lipophilum	77.108	110	1015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900156035.1	s__Corynebacterium afermentans	77.0889	113	1015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.27	97.60	0.93	0.89	5	-
GCF_000159635.1	s__Corynebacterium lipophiloflavum	77.0811	92	1015	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	76.4944	99	1015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:07:14,461] [INFO] GTDB search result was written to GCF_030408595.1_ASM3040859v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:14,462] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:14,466] [INFO] DFAST_QC result json was written to GCF_030408595.1_ASM3040859v1_genomic.fna/dqc_result.json
[2024-01-24 11:07:14,466] [INFO] DFAST_QC completed!
[2024-01-24 11:07:14,466] [INFO] Total running time: 0h1m10s