[2024-01-24 13:28:44,563] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:44,565] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:44,565] [INFO] DQC Reference Directory: /var/lib/cwl/stg514f13ab-02e4-4d57-a187-7ee061599655/dqc_reference
[2024-01-24 13:28:45,817] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:45,818] [INFO] Task started: Prodigal
[2024-01-24 13:28:45,819] [INFO] Running command: gunzip -c /var/lib/cwl/stg92fab58e-d7dd-4773-90fe-28fcdee46add/GCF_009707125.1_ASM970712v1_genomic.fna.gz | prodigal -d GCF_009707125.1_ASM970712v1_genomic.fna/cds.fna -a GCF_009707125.1_ASM970712v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:55,706] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:55,706] [INFO] Task started: HMMsearch
[2024-01-24 13:28:55,706] [INFO] Running command: hmmsearch --tblout GCF_009707125.1_ASM970712v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg514f13ab-02e4-4d57-a187-7ee061599655/dqc_reference/reference_markers.hmm GCF_009707125.1_ASM970712v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:55,986] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:55,987] [INFO] Found 6/6 markers.
[2024-01-24 13:28:56,020] [INFO] Query marker FASTA was written to GCF_009707125.1_ASM970712v1_genomic.fna/markers.fasta
[2024-01-24 13:28:56,021] [INFO] Task started: Blastn
[2024-01-24 13:28:56,021] [INFO] Running command: blastn -query GCF_009707125.1_ASM970712v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg514f13ab-02e4-4d57-a187-7ee061599655/dqc_reference/reference_markers.fasta -out GCF_009707125.1_ASM970712v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:57,350] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:57,357] [INFO] Selected 11 target genomes.
[2024-01-24 13:28:57,358] [INFO] Target genome list was writen to GCF_009707125.1_ASM970712v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:57,364] [INFO] Task started: fastANI
[2024-01-24 13:28:57,364] [INFO] Running command: fastANI --query /var/lib/cwl/stg92fab58e-d7dd-4773-90fe-28fcdee46add/GCF_009707125.1_ASM970712v1_genomic.fna.gz --refList GCF_009707125.1_ASM970712v1_genomic.fna/target_genomes.txt --output GCF_009707125.1_ASM970712v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:06,261] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:06,262] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg514f13ab-02e4-4d57-a187-7ee061599655/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:06,263] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg514f13ab-02e4-4d57-a187-7ee061599655/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:06,279] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:29:06,279] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:29:06,279] [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
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	100.0	1114	1116	95	conclusive
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	90.5006	977	1116	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	82.5777	721	1116	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	80.5308	582	1116	95	below_threshold
Pedococcus cremeus	strain=CGMCC 1.6963	GCA_900111375.1	587636	587636	type	True	79.1147	488	1116	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	78.8741	462	1116	95	below_threshold
Luteipulveratus halotolerans	strain=C296001	GCA_001247745.1	1631356	1631356	type	True	78.8329	437	1116	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	78.7412	460	1116	95	below_threshold
Flexivirga aerilata	strain=ID2601S	GCA_013002715.1	1656889	1656889	type	True	78.3774	388	1116	95	below_threshold
Dermacoccus nishinomiyaensis	strain=FDAARGOS_1119	GCA_016766835.1	1274	1274	type	True	78.1018	322	1116	95	below_threshold
Cellulomonas massiliensis	strain=JC225	GCA_000312005.1	1465811	1465811	type	True	77.3306	327	1116	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:06,281] [INFO] DFAST Taxonomy check result was written to GCF_009707125.1_ASM970712v1_genomic.fna/tc_result.tsv
[2024-01-24 13:29:06,282] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:06,282] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:06,282] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg514f13ab-02e4-4d57-a187-7ee061599655/dqc_reference/checkm_data
[2024-01-24 13:29:06,283] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:06,324] [INFO] Task started: CheckM
[2024-01-24 13:29:06,324] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009707125.1_ASM970712v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009707125.1_ASM970712v1_genomic.fna/checkm_input GCF_009707125.1_ASM970712v1_genomic.fna/checkm_result
[2024-01-24 13:29:57,839] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:57,840] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:57,862] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:57,862] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:57,863] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009707125.1_ASM970712v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:57,863] [INFO] Task started: Blastn
[2024-01-24 13:29:57,863] [INFO] Running command: blastn -query GCF_009707125.1_ASM970712v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg514f13ab-02e4-4d57-a187-7ee061599655/dqc_reference/reference_markers_gtdb.fasta -out GCF_009707125.1_ASM970712v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:59,967] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:59,970] [INFO] Selected 13 target genomes.
[2024-01-24 13:29:59,971] [INFO] Target genome list was writen to GCF_009707125.1_ASM970712v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:59,986] [INFO] Task started: fastANI
[2024-01-24 13:29:59,986] [INFO] Running command: fastANI --query /var/lib/cwl/stg92fab58e-d7dd-4773-90fe-28fcdee46add/GCF_009707125.1_ASM970712v1_genomic.fna.gz --refList GCF_009707125.1_ASM970712v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009707125.1_ASM970712v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:11,289] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:11,301] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:30:11,301] [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_009707125.1	s__Arsenicicoccus sp009707125	100.0	1114	1116	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Arsenicicoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000426385.1	s__Arsenicicoccus bolidensis	90.5006	977	1116	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Arsenicicoccus	95.0	98.16	98.06	0.89	0.88	4	-
GCF_001189535.1	s__Arsenicicoccus sp001189535	85.8406	896	1116	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Arsenicicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716205.1	s__Oryzihumus leptocrescens	79.723	468	1116	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Oryzihumus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428025.1	s__Pedococcus sp001428025	79.2148	436	1116	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111375.1	s__Pedococcus cremeus	79.0954	490	1116	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	95.41	95.41	0.91	0.91	2	-
GCF_000720925.1	s__Phycicoccus jejuensis	78.8924	460	1116	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	96.36	95.39	0.88	0.87	4	-
GCF_006717025.1	s__Terrabacter lapilli	78.7862	479	1116	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	95.88	95.88	0.91	0.91	2	-
GCF_009192725.1	s__Segeticoccus rhizosphaerae	78.753	320	1116	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Segeticoccus	95.0	99.13	99.13	0.90	0.90	2	-
GCF_006715875.1	s__Terrabacter sp006715875	78.7525	470	1116	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429185.1	s__Terrabacter sp001429185	78.7272	485	1116	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	99.06	99.06	0.95	0.95	2	-
GCA_014857905.1	s__JACYXE01 sp014857905	78.5361	457	1116	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__JACYXE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715055.1	s__Lapillicoccus jejuensis	78.4152	523	1116	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Lapillicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:30:11,303] [INFO] GTDB search result was written to GCF_009707125.1_ASM970712v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:11,303] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:11,307] [INFO] DFAST_QC result json was written to GCF_009707125.1_ASM970712v1_genomic.fna/dqc_result.json
[2024-01-24 13:30:11,307] [INFO] DFAST_QC completed!
[2024-01-24 13:30:11,307] [INFO] Total running time: 0h1m27s