[2024-01-24 12:05:58,974] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:05:58,977] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:05:58,977] [INFO] DQC Reference Directory: /var/lib/cwl/stg8020bd10-4836-4e0e-9227-b5a5a60c3507/dqc_reference
[2024-01-24 12:06:00,418] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:00,419] [INFO] Task started: Prodigal
[2024-01-24 12:06:00,419] [INFO] Running command: gunzip -c /var/lib/cwl/stg2fb2e625-eb4a-4113-a4c3-187c540408aa/GCF_003352835.1_ASM335283v1_genomic.fna.gz | prodigal -d GCF_003352835.1_ASM335283v1_genomic.fna/cds.fna -a GCF_003352835.1_ASM335283v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:10,785] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:10,786] [INFO] Task started: HMMsearch
[2024-01-24 12:06:10,786] [INFO] Running command: hmmsearch --tblout GCF_003352835.1_ASM335283v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8020bd10-4836-4e0e-9227-b5a5a60c3507/dqc_reference/reference_markers.hmm GCF_003352835.1_ASM335283v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:11,116] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:11,117] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg2fb2e625-eb4a-4113-a4c3-187c540408aa/GCF_003352835.1_ASM335283v1_genomic.fna.gz]
[2024-01-24 12:06:11,157] [INFO] Query marker FASTA was written to GCF_003352835.1_ASM335283v1_genomic.fna/markers.fasta
[2024-01-24 12:06:11,158] [INFO] Task started: Blastn
[2024-01-24 12:06:11,158] [INFO] Running command: blastn -query GCF_003352835.1_ASM335283v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8020bd10-4836-4e0e-9227-b5a5a60c3507/dqc_reference/reference_markers.fasta -out GCF_003352835.1_ASM335283v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:12,010] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:12,013] [INFO] Selected 11 target genomes.
[2024-01-24 12:06:12,014] [INFO] Target genome list was writen to GCF_003352835.1_ASM335283v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:12,018] [INFO] Task started: fastANI
[2024-01-24 12:06:12,018] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fb2e625-eb4a-4113-a4c3-187c540408aa/GCF_003352835.1_ASM335283v1_genomic.fna.gz --refList GCF_003352835.1_ASM335283v1_genomic.fna/target_genomes.txt --output GCF_003352835.1_ASM335283v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:20,218] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:20,218] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8020bd10-4836-4e0e-9227-b5a5a60c3507/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:20,218] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8020bd10-4836-4e0e-9227-b5a5a60c3507/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:20,228] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:20,229] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:20,229] [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
Ornithinimicrobium murale	strain=DSM 22056	GCA_003352835.1	1050153	1050153	type	True	100.0	1077	1078	95	conclusive
Ornithinimicrobium cavernae	strain=KCTC 49018	GCA_003121625.1	2666047	2666047	type	True	83.8945	643	1078	95	below_threshold
Ornithinimicrobium ciconiae	strain=H23M54	GCA_007197575.1	2594265	2594265	type	True	82.1178	569	1078	95	below_threshold
Ornithinicoccus hortensis	strain=DSM 12335	GCA_006716185.1	82346	82346	type	True	79.8615	452	1078	95	below_threshold
Ornithinicoccus hortensis	strain=HKI0125	GCA_009602515.1	82346	82346	type	True	79.842	436	1078	95	below_threshold
Serinicoccus hydrothermalis	strain=JLT9	GCA_001685415.1	1758689	1758689	type	True	79.1569	365	1078	95	below_threshold
Serinicoccus profundi	strain=CGMCC 4.5582	GCA_008001015.1	1078471	1078471	type	True	79.0262	328	1078	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	79.0055	350	1078	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	78.9983	365	1078	95	below_threshold
Serinicoccus marinus	strain=DSM 15273	GCA_008386315.1	247333	247333	type	True	78.8075	327	1078	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	77.6457	242	1078	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:20,230] [INFO] DFAST Taxonomy check result was written to GCF_003352835.1_ASM335283v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:20,231] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:20,231] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:20,231] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8020bd10-4836-4e0e-9227-b5a5a60c3507/dqc_reference/checkm_data
[2024-01-24 12:06:20,233] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:20,272] [INFO] Task started: CheckM
[2024-01-24 12:06:20,272] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003352835.1_ASM335283v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003352835.1_ASM335283v1_genomic.fna/checkm_input GCF_003352835.1_ASM335283v1_genomic.fna/checkm_result
[2024-01-24 12:06:59,027] [INFO] Task succeeded: CheckM
[2024-01-24 12:06:59,028] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:06:59,051] [INFO] ===== Completeness check finished =====
[2024-01-24 12:06:59,052] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:06:59,052] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003352835.1_ASM335283v1_genomic.fna/markers.fasta)
[2024-01-24 12:06:59,053] [INFO] Task started: Blastn
[2024-01-24 12:06:59,053] [INFO] Running command: blastn -query GCF_003352835.1_ASM335283v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8020bd10-4836-4e0e-9227-b5a5a60c3507/dqc_reference/reference_markers_gtdb.fasta -out GCF_003352835.1_ASM335283v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:00,256] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:00,261] [INFO] Selected 7 target genomes.
[2024-01-24 12:07:00,261] [INFO] Target genome list was writen to GCF_003352835.1_ASM335283v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:00,268] [INFO] Task started: fastANI
[2024-01-24 12:07:00,269] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fb2e625-eb4a-4113-a4c3-187c540408aa/GCF_003352835.1_ASM335283v1_genomic.fna.gz --refList GCF_003352835.1_ASM335283v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003352835.1_ASM335283v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:05,861] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:05,876] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:05,876] [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_003352835.1	s__Ornithinicoccus muralis	100.0	1077	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003121625.1	s__Ornithinicoccus cavernae	83.9021	642	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007197575.1	s__Ornithinicoccus sp007197575	82.1043	570	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012515595.1	s__Ornithinicoccus sp012515595	82.0096	458	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716185.1	s__Ornithinicoccus hortensis	79.8529	452	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000421185.1	s__Ornithinimicrobium pekingense	79.2593	396	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004322775.1	s__Serinicoccus sp004322775	79.1902	397	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:05,878] [INFO] GTDB search result was written to GCF_003352835.1_ASM335283v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:05,879] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:05,884] [INFO] DFAST_QC result json was written to GCF_003352835.1_ASM335283v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:05,884] [INFO] DFAST_QC completed!
[2024-01-24 12:07:05,884] [INFO] Total running time: 0h1m7s