[2024-01-24 11:51:07,028] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:07,031] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:07,031] [INFO] DQC Reference Directory: /var/lib/cwl/stg13d90994-29a5-4300-931e-37c5cf83c432/dqc_reference
[2024-01-24 11:51:08,273] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:08,274] [INFO] Task started: Prodigal
[2024-01-24 11:51:08,274] [INFO] Running command: gunzip -c /var/lib/cwl/stg135657f7-43af-4817-a583-0294c8fc3b7b/GCF_000576595.1_genome_genomic.fna.gz | prodigal -d GCF_000576595.1_genome_genomic.fna/cds.fna -a GCF_000576595.1_genome_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:20,315] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:20,316] [INFO] Task started: HMMsearch
[2024-01-24 11:51:20,316] [INFO] Running command: hmmsearch --tblout GCF_000576595.1_genome_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13d90994-29a5-4300-931e-37c5cf83c432/dqc_reference/reference_markers.hmm GCF_000576595.1_genome_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:20,684] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:20,686] [INFO] Found 6/6 markers.
[2024-01-24 11:51:20,731] [INFO] Query marker FASTA was written to GCF_000576595.1_genome_genomic.fna/markers.fasta
[2024-01-24 11:51:20,732] [INFO] Task started: Blastn
[2024-01-24 11:51:20,732] [INFO] Running command: blastn -query GCF_000576595.1_genome_genomic.fna/markers.fasta -db /var/lib/cwl/stg13d90994-29a5-4300-931e-37c5cf83c432/dqc_reference/reference_markers.fasta -out GCF_000576595.1_genome_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:21,950] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:21,955] [INFO] Selected 22 target genomes.
[2024-01-24 11:51:21,955] [INFO] Target genome list was writen to GCF_000576595.1_genome_genomic.fna/target_genomes.txt
[2024-01-24 11:51:21,966] [INFO] Task started: fastANI
[2024-01-24 11:51:21,967] [INFO] Running command: fastANI --query /var/lib/cwl/stg135657f7-43af-4817-a583-0294c8fc3b7b/GCF_000576595.1_genome_genomic.fna.gz --refList GCF_000576595.1_genome_genomic.fna/target_genomes.txt --output GCF_000576595.1_genome_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:37,650] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:37,650] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13d90994-29a5-4300-931e-37c5cf83c432/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:37,651] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13d90994-29a5-4300-931e-37c5cf83c432/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:37,672] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:51:37,672] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:51:37,673] [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
Intrasporangium calvum	strain=DSM 43043	GCA_000184685.1	53358	53358	type	True	81.4014	743	1486	95	below_threshold
Intrasporangium chromatireducens	strain=Q5-1	GCA_000576575.1	1386088	1386088	type	True	81.1614	648	1486	95	below_threshold
Knoellia flava	strain=CGMCC 1.10749	GCA_014636255.1	913969	913969	type	True	79.9702	558	1486	95	below_threshold
Knoellia flava	strain=TL1	GCA_000768675.1	913969	913969	type	True	79.9132	550	1486	95	below_threshold
Knoellia remsis	strain=ATCC BAA-1496	GCA_003002895.1	407159	407159	type	True	79.6545	506	1486	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	79.6263	593	1486	95	below_threshold
Pedococcus cremeus	strain=CGMCC 1.6963	GCA_900111375.1	587636	587636	type	True	79.4828	621	1486	95	below_threshold
Janibacter indicus	strain=CGMCC 1.12511	GCA_900176385.1	857417	857417	type	True	79.2806	467	1486	95	below_threshold
Janibacter endophyticus	strain=YIM B02568	GCA_016888335.1	2806261	2806261	type	True	79.2316	459	1486	95	below_threshold
Janibacter terrae	strain=NBRC 107853	GCA_001591405.1	103817	103817	type	True	79.1736	459	1486	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	79.1002	502	1486	95	below_threshold
Janibacter massiliensis	strain=Marseille-P4121	GCA_900289115.1	2058291	2058291	type	True	79.0075	379	1486	95	below_threshold
Janibacter hoylei	strain=PVAS-1	GCA_004025845.1	364298	364298	type	True	78.8463	459	1486	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	78.6947	463	1486	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	78.529	445	1486	95	below_threshold
Luteipulveratus halotolerans	strain=C296001	GCA_001247745.1	1631356	1631356	type	True	78.3569	498	1486	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	77.9827	354	1486	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	77.2663	429	1486	95	below_threshold
Pseudokineococcus lusitanus	strain=CECT 7306	GCA_003751265.1	763993	763993	type	True	77.0827	440	1486	95	below_threshold
Cellulomonas telluris	strain=CPCC 204705	GCA_004886325.1	2306636	2306636	type	True	76.8525	383	1486	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	76.7863	380	1486	95	below_threshold
Cellulomonas hominis	strain=NBRC 16055	GCA_007989225.1	156981	156981	suspected-type	True	76.7862	373	1486	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:37,818] [INFO] DFAST Taxonomy check result was written to GCF_000576595.1_genome_genomic.fna/tc_result.tsv
[2024-01-24 11:51:37,820] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:37,820] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:37,820] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13d90994-29a5-4300-931e-37c5cf83c432/dqc_reference/checkm_data
[2024-01-24 11:51:37,822] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:37,874] [INFO] Task started: CheckM
[2024-01-24 11:51:37,874] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000576595.1_genome_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000576595.1_genome_genomic.fna/checkm_input GCF_000576595.1_genome_genomic.fna/checkm_result
[2024-01-24 11:52:37,896] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:37,897] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:37,926] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:37,927] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:37,927] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000576595.1_genome_genomic.fna/markers.fasta)
[2024-01-24 11:52:37,927] [INFO] Task started: Blastn
[2024-01-24 11:52:37,928] [INFO] Running command: blastn -query GCF_000576595.1_genome_genomic.fna/markers.fasta -db /var/lib/cwl/stg13d90994-29a5-4300-931e-37c5cf83c432/dqc_reference/reference_markers_gtdb.fasta -out GCF_000576595.1_genome_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:39,817] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:39,820] [INFO] Selected 12 target genomes.
[2024-01-24 11:52:39,820] [INFO] Target genome list was writen to GCF_000576595.1_genome_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:39,830] [INFO] Task started: fastANI
[2024-01-24 11:52:39,830] [INFO] Running command: fastANI --query /var/lib/cwl/stg135657f7-43af-4817-a583-0294c8fc3b7b/GCF_000576595.1_genome_genomic.fna.gz --refList GCF_000576595.1_genome_genomic.fna/target_genomes_gtdb.txt --output GCF_000576595.1_genome_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:52,276] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:52,296] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:52,296] [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_000576595.1	s__Humihabitans oryzae	100.0	1481	1486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Humihabitans	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001429185.1	s__Terrabacter sp001429185	83.3896	961	1486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	99.06	99.06	0.95	0.95	2	-
GCF_014646815.1	s__Terrabacter tumescens	83.3634	952	1486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007991735.1	s__Terrabacter aerolatus	83.2534	935	1486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428505.1	s__Terrabacter sp001428505	83.2421	963	1486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	99.23	99.23	0.97	0.97	2	-
GCF_000383675.1	s__Terrabacter sp000383675	83.238	974	1486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006717145.1	s__Humibacillus xanthopallidus_A	83.118	996	1486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Humibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716915.1	s__Terrabacter sp006716915	82.9905	965	1486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000955875.1	s__Terrabacter sp000955875	82.9851	933	1486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001956915.1	s__Monashia flava	82.6333	785	1486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Monashia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361975.1	s__Terrabacter sp013361975	82.4496	547	1486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	98.22	98.02	0.74	0.70	4	-
GCF_003635045.1	s__Terracoccus luteus	81.7908	784	1486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terracoccus	95.0	98.59	98.59	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:52,298] [INFO] GTDB search result was written to GCF_000576595.1_genome_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:52,298] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:52,303] [INFO] DFAST_QC result json was written to GCF_000576595.1_genome_genomic.fna/dqc_result.json
[2024-01-24 11:52:52,303] [INFO] DFAST_QC completed!
[2024-01-24 11:52:52,303] [INFO] Total running time: 0h1m45s