[2024-01-24 11:12:39,480] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:39,483] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:39,484] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d43682e-0e9d-4151-8a0c-c3e328157c6f/dqc_reference
[2024-01-24 11:12:40,827] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:40,828] [INFO] Task started: Prodigal
[2024-01-24 11:12:40,828] [INFO] Running command: gunzip -c /var/lib/cwl/stg294963ba-7179-4827-93a0-e4e1f3711f5c/GCF_016862995.1_ASM1686299v1_genomic.fna.gz | prodigal -d GCF_016862995.1_ASM1686299v1_genomic.fna/cds.fna -a GCF_016862995.1_ASM1686299v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:05,135] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:05,136] [INFO] Task started: HMMsearch
[2024-01-24 11:13:05,136] [INFO] Running command: hmmsearch --tblout GCF_016862995.1_ASM1686299v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d43682e-0e9d-4151-8a0c-c3e328157c6f/dqc_reference/reference_markers.hmm GCF_016862995.1_ASM1686299v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:05,589] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:05,590] [INFO] Found 6/6 markers.
[2024-01-24 11:13:05,680] [INFO] Query marker FASTA was written to GCF_016862995.1_ASM1686299v1_genomic.fna/markers.fasta
[2024-01-24 11:13:05,680] [INFO] Task started: Blastn
[2024-01-24 11:13:05,680] [INFO] Running command: blastn -query GCF_016862995.1_ASM1686299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d43682e-0e9d-4151-8a0c-c3e328157c6f/dqc_reference/reference_markers.fasta -out GCF_016862995.1_ASM1686299v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:06,980] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:06,984] [INFO] Selected 16 target genomes.
[2024-01-24 11:13:06,985] [INFO] Target genome list was writen to GCF_016862995.1_ASM1686299v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:06,992] [INFO] Task started: fastANI
[2024-01-24 11:13:06,992] [INFO] Running command: fastANI --query /var/lib/cwl/stg294963ba-7179-4827-93a0-e4e1f3711f5c/GCF_016862995.1_ASM1686299v1_genomic.fna.gz --refList GCF_016862995.1_ASM1686299v1_genomic.fna/target_genomes.txt --output GCF_016862995.1_ASM1686299v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:36,021] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:36,022] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d43682e-0e9d-4151-8a0c-c3e328157c6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:36,022] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d43682e-0e9d-4151-8a0c-c3e328157c6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:36,042] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:36,042] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:36,042] [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
Acrocarpospora phusangensis	strain=NBRC 108782	GCA_016862995.1	1070424	1070424	type	True	100.0	2924	2934	95	conclusive
Acrocarpospora macrocephala	strain=NBRC 16266	GCA_009687865.1	150177	150177	type	True	87.6437	2097	2934	95	below_threshold
Acrocarpospora pleiomorpha	strain=NBRC 16267	GCA_009687885.1	90975	90975	type	True	87.6028	2049	2934	95	below_threshold
Acrocarpospora corrugata	strain=NBRC 13972	GCA_009687845.1	35763	35763	type	True	87.6008	2052	2934	95	below_threshold
Acrocarpospora catenulata	strain=H8750	GCA_018476525.1	2836182	2836182	type	True	84.4176	1772	2934	95	below_threshold
Microbispora rosea subsp. aerata	strain=NBRC 14624	GCA_016863075.1	147065	58117	type	True	80.0594	1104	2934	95	below_threshold
Microbispora oryzae	strain=RL4-1S	GCA_017896165.1	2806554	2806554	type	True	79.951	1098	2934	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	79.7646	853	2934	95	below_threshold
Sphaerisporangium corydalis	strain=NEAU-YHS15	GCA_025506355.1	1441875	1441875	type	True	79.7581	1261	2934	95	below_threshold
Nonomuraea mesophila	strain=6K102	GCA_004352805.1	2530382	2530382	type	True	79.0365	1150	2934	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	79.0359	1267	2934	95	below_threshold
Nonomuraea longispora	strain=KC201	GCA_004348345.1	1848320	1848320	type	True	78.9005	1114	2934	95	below_threshold
Marmoricola scoriae	strain=DSM 22127	GCA_900104965.1	642780	642780	type	True	76.5832	429	2934	95	below_threshold
Marmoricola aequoreus	strain=NRRL B-24464	GCA_000720335.1	397278	397278	type	True	76.5164	418	2934	95	below_threshold
Cellulomonas humilata	strain=ATCC 25174	GCA_013359775.1	144055	144055	type	True	75.9402	401	2934	95	below_threshold
Microbacterium radiodurans	strain=DSM 25564	GCA_008710705.1	661398	661398	type	True	75.3162	212	2934	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:36,044] [INFO] DFAST Taxonomy check result was written to GCF_016862995.1_ASM1686299v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:36,049] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:36,050] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:36,050] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d43682e-0e9d-4151-8a0c-c3e328157c6f/dqc_reference/checkm_data
[2024-01-24 11:13:36,052] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:36,141] [INFO] Task started: CheckM
[2024-01-24 11:13:36,142] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862995.1_ASM1686299v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862995.1_ASM1686299v1_genomic.fna/checkm_input GCF_016862995.1_ASM1686299v1_genomic.fna/checkm_result
[2024-01-24 11:14:45,405] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:45,407] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:45,432] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:45,432] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:45,432] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862995.1_ASM1686299v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:45,433] [INFO] Task started: Blastn
[2024-01-24 11:14:45,433] [INFO] Running command: blastn -query GCF_016862995.1_ASM1686299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d43682e-0e9d-4151-8a0c-c3e328157c6f/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862995.1_ASM1686299v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:47,409] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:47,413] [INFO] Selected 11 target genomes.
[2024-01-24 11:14:47,413] [INFO] Target genome list was writen to GCF_016862995.1_ASM1686299v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:47,422] [INFO] Task started: fastANI
[2024-01-24 11:14:47,423] [INFO] Running command: fastANI --query /var/lib/cwl/stg294963ba-7179-4827-93a0-e4e1f3711f5c/GCF_016862995.1_ASM1686299v1_genomic.fna.gz --refList GCF_016862995.1_ASM1686299v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862995.1_ASM1686299v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:15:08,654] [INFO] Task succeeded: fastANI
[2024-01-24 11:15:08,674] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:15:08,674] [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_016862995.1	s__Acrocarpospora phusangensis	100.0	2924	2934	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Acrocarpospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009687865.1	s__Acrocarpospora macrocephala	87.6406	2097	2934	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Acrocarpospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009687845.1	s__Acrocarpospora corrugata	87.6295	2048	2934	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Acrocarpospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009687885.1	s__Acrocarpospora pleiomorpha	87.624	2045	2934	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Acrocarpospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018476525.1	s__Acrocarpospora sp018476525	84.4022	1774	2934	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Acrocarpospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647835.1	s__Microbispora aerata	80.1415	1092	2934	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001552515.1	s__Sphaerimonospora mesophila	79.7032	976	2934	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerimonospora	95.0	99.25	99.25	0.94	0.94	2	-
GCF_004348345.1	s__Nonomuraea longispora	78.9143	1110	2934	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	97.23	95.05	0.88	0.87	4	-
GCF_000701325.1	s__Streptomyces sp000701325	76.5759	634	2934	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720335.1	s__Marmoricola aequoreus	76.5253	415	2934	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007988785.1	s__Agrococcus baldri_A	75.5435	260	2934	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:15:08,676] [INFO] GTDB search result was written to GCF_016862995.1_ASM1686299v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:15:08,677] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:15:08,682] [INFO] DFAST_QC result json was written to GCF_016862995.1_ASM1686299v1_genomic.fna/dqc_result.json
[2024-01-24 11:15:08,683] [INFO] DFAST_QC completed!
[2024-01-24 11:15:08,683] [INFO] Total running time: 0h2m29s