[2024-01-24 13:57:57,794] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:57,796] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:57,796] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a973b8c-5db3-4490-9e65-a4ad6be55636/dqc_reference
[2024-01-24 13:57:59,071] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:59,072] [INFO] Task started: Prodigal
[2024-01-24 13:57:59,072] [INFO] Running command: gunzip -c /var/lib/cwl/stg90e792a6-61ca-4c28-b2fc-ceb26d801bf7/GCF_003574315.2_ASM357431v2_genomic.fna.gz | prodigal -d GCF_003574315.2_ASM357431v2_genomic.fna/cds.fna -a GCF_003574315.2_ASM357431v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:21,644] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:21,644] [INFO] Task started: HMMsearch
[2024-01-24 13:58:21,644] [INFO] Running command: hmmsearch --tblout GCF_003574315.2_ASM357431v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a973b8c-5db3-4490-9e65-a4ad6be55636/dqc_reference/reference_markers.hmm GCF_003574315.2_ASM357431v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:22,023] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:22,024] [INFO] Found 6/6 markers.
[2024-01-24 13:58:22,095] [INFO] Query marker FASTA was written to GCF_003574315.2_ASM357431v2_genomic.fna/markers.fasta
[2024-01-24 13:58:22,096] [INFO] Task started: Blastn
[2024-01-24 13:58:22,096] [INFO] Running command: blastn -query GCF_003574315.2_ASM357431v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a973b8c-5db3-4490-9e65-a4ad6be55636/dqc_reference/reference_markers.fasta -out GCF_003574315.2_ASM357431v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:22,787] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:22,790] [INFO] Selected 23 target genomes.
[2024-01-24 13:58:22,791] [INFO] Target genome list was writen to GCF_003574315.2_ASM357431v2_genomic.fna/target_genomes.txt
[2024-01-24 13:58:22,849] [INFO] Task started: fastANI
[2024-01-24 13:58:22,849] [INFO] Running command: fastANI --query /var/lib/cwl/stg90e792a6-61ca-4c28-b2fc-ceb26d801bf7/GCF_003574315.2_ASM357431v2_genomic.fna.gz --refList GCF_003574315.2_ASM357431v2_genomic.fna/target_genomes.txt --output GCF_003574315.2_ASM357431v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:45,185] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:45,186] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a973b8c-5db3-4490-9e65-a4ad6be55636/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:45,186] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a973b8c-5db3-4490-9e65-a4ad6be55636/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:45,198] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:58:45,198] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:58:45,198] [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
Nocardioides humi	strain=DCY24	GCA_006494775.1	449461	449461	type	True	75.1764	104	2548	95	below_threshold
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	75.0472	93	2548	95	below_threshold
Stigmatella hybrida	strain=DSM 14722	GCA_020103775.1	394097	394097	type	True	74.9999	76	2548	95	below_threshold
Stigmatella aurantiaca	strain=DSM 17044	GCA_900109545.1	41	41	type	True	74.9929	84	2548	95	below_threshold
Actinomadura montaniterrae	strain=CYP1-1B	GCA_008923365.1	1803903	1803903	type	True	74.8456	183	2548	95	below_threshold
Actinomadura darangshiensis	strain=DSM 45941	GCA_004349235.1	705336	705336	type	True	74.8443	154	2548	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	74.8008	69	2548	95	below_threshold
Humisphaera borealis	strain=M1803	GCA_015169395.1	2807512	2807512	type	True	74.7494	67	2548	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	74.7465	188	2548	95	below_threshold
Actinomadura litoris	strain=NEAU-AAG5	GCA_009733595.1	2678616	2678616	type	True	74.7337	154	2548	95	below_threshold
Paraburkholderia kirstenboschensis	strain=LMG 28727	GCA_904848585.1	1245436	1245436	type	True	74.6298	55	2548	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:45,200] [INFO] DFAST Taxonomy check result was written to GCF_003574315.2_ASM357431v2_genomic.fna/tc_result.tsv
[2024-01-24 13:58:45,201] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:45,201] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:45,201] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a973b8c-5db3-4490-9e65-a4ad6be55636/dqc_reference/checkm_data
[2024-01-24 13:58:45,203] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:45,279] [INFO] Task started: CheckM
[2024-01-24 13:58:45,280] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003574315.2_ASM357431v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003574315.2_ASM357431v2_genomic.fna/checkm_input GCF_003574315.2_ASM357431v2_genomic.fna/checkm_result
[2024-01-24 13:59:46,309] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:46,310] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.93%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:46,333] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:46,334] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:46,334] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003574315.2_ASM357431v2_genomic.fna/markers.fasta)
[2024-01-24 13:59:46,334] [INFO] Task started: Blastn
[2024-01-24 13:59:46,335] [INFO] Running command: blastn -query GCF_003574315.2_ASM357431v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a973b8c-5db3-4490-9e65-a4ad6be55636/dqc_reference/reference_markers_gtdb.fasta -out GCF_003574315.2_ASM357431v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:47,444] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:47,448] [INFO] Selected 19 target genomes.
[2024-01-24 13:59:47,449] [INFO] Target genome list was writen to GCF_003574315.2_ASM357431v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:47,550] [INFO] Task started: fastANI
[2024-01-24 13:59:47,550] [INFO] Running command: fastANI --query /var/lib/cwl/stg90e792a6-61ca-4c28-b2fc-ceb26d801bf7/GCF_003574315.2_ASM357431v2_genomic.fna.gz --refList GCF_003574315.2_ASM357431v2_genomic.fna/target_genomes_gtdb.txt --output GCF_003574315.2_ASM357431v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:05,388] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:05,398] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:05,399] [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_003574315.1	s__Capsulimonas corticalis	99.979	2494	2548	d__Bacteria;p__Armatimonadota;c__Armatimonadia;o__Armatimonadales;f__Capsulimonadaceae;g__Capsulimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_019239955.1	s__JAFAZD01 sp019239955	76.5539	302	2548	d__Bacteria;p__Armatimonadota;c__Armatimonadia;o__Armatimonadales;f__Capsulimonadaceae;g__JAFAZD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903951425.1	s__CAJBBX01 sp903951425	75.2257	73	2548	d__Bacteria;p__Armatimonadota;c__Chthonomonadetes;o__Chthonomonadales;f__CAJBBX01;g__CAJBBX01	95.0	99.93	99.86	0.97	0.95	8	-
GCA_903885605.1	s__CAJBBX01 sp903885605	75.0331	91	2548	d__Bacteria;p__Armatimonadota;c__Chthonomonadetes;o__Chthonomonadales;f__CAJBBX01;g__CAJBBX01	95.0	99.86	99.85	0.97	0.97	5	-
GCF_008312895.1	s__Luteimonas sp008312895	74.9697	96	2548	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011046675.1	s__AWTP1-13 sp011046675	74.8692	92	2548	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__AWTP1-13	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007556775.1	s__Thermomonas lycopersici	74.8692	63	2548	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008327685.1	s__Spirillospora sp008327685	74.808	135	2548	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015489145.1	s__S143-5 sp015489145	74.8015	64	2548	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__S143-5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348735.1	s__Spirillospora sp004348735	74.7037	123	2548	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806325.1	s__CADCWE01 sp902806325	74.7004	64	2548	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermomicrobiales;f__UBA6265;g__CADCWE01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:05,401] [INFO] GTDB search result was written to GCF_003574315.2_ASM357431v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:05,401] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:05,404] [INFO] DFAST_QC result json was written to GCF_003574315.2_ASM357431v2_genomic.fna/dqc_result.json
[2024-01-24 14:00:05,404] [INFO] DFAST_QC completed!
[2024-01-24 14:00:05,404] [INFO] Total running time: 0h2m8s