[2023-06-27 18:06:19,494] [INFO] DFAST_QC pipeline started.
[2023-06-27 18:06:19,496] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 18:06:19,496] [INFO] DQC Reference Directory: /var/lib/cwl/stg073920f2-a120-442c-98f9-8341e1bda39b/dqc_reference
[2023-06-27 18:06:20,658] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 18:06:20,659] [INFO] Task started: Prodigal
[2023-06-27 18:06:20,659] [INFO] Running command: gunzip -c /var/lib/cwl/stg61effac4-30bd-4554-8281-c31c745a6cdc/GCA_026705105.1_ASM2670510v1_genomic.fna.gz | prodigal -d GCA_026705105.1_ASM2670510v1_genomic.fna/cds.fna -a GCA_026705105.1_ASM2670510v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 18:06:26,723] [INFO] Task succeeded: Prodigal
[2023-06-27 18:06:26,724] [INFO] Task started: HMMsearch
[2023-06-27 18:06:26,724] [INFO] Running command: hmmsearch --tblout GCA_026705105.1_ASM2670510v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg073920f2-a120-442c-98f9-8341e1bda39b/dqc_reference/reference_markers.hmm GCA_026705105.1_ASM2670510v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 18:06:26,897] [INFO] Task succeeded: HMMsearch
[2023-06-27 18:06:26,898] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg61effac4-30bd-4554-8281-c31c745a6cdc/GCA_026705105.1_ASM2670510v1_genomic.fna.gz]
[2023-06-27 18:06:26,922] [INFO] Query marker FASTA was written to GCA_026705105.1_ASM2670510v1_genomic.fna/markers.fasta
[2023-06-27 18:06:26,922] [INFO] Task started: Blastn
[2023-06-27 18:06:26,922] [INFO] Running command: blastn -query GCA_026705105.1_ASM2670510v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg073920f2-a120-442c-98f9-8341e1bda39b/dqc_reference/reference_markers.fasta -out GCA_026705105.1_ASM2670510v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 18:06:27,488] [INFO] Task succeeded: Blastn
[2023-06-27 18:06:27,492] [INFO] Selected 22 target genomes.
[2023-06-27 18:06:27,492] [INFO] Target genome list was writen to GCA_026705105.1_ASM2670510v1_genomic.fna/target_genomes.txt
[2023-06-27 18:06:27,496] [INFO] Task started: fastANI
[2023-06-27 18:06:27,496] [INFO] Running command: fastANI --query /var/lib/cwl/stg61effac4-30bd-4554-8281-c31c745a6cdc/GCA_026705105.1_ASM2670510v1_genomic.fna.gz --refList GCA_026705105.1_ASM2670510v1_genomic.fna/target_genomes.txt --output GCA_026705105.1_ASM2670510v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 18:06:45,347] [INFO] Task succeeded: fastANI
[2023-06-27 18:06:45,348] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg073920f2-a120-442c-98f9-8341e1bda39b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 18:06:45,348] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg073920f2-a120-442c-98f9-8341e1bda39b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 18:06:45,356] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 18:06:45,357] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 18:06:45,357] [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
Actinoplanes teichomyceticus	strain=NBRC 13999	GCA_016862415.1	1867	1867	type	True	74.8744	55	649	95	below_threshold
Actinoplanes teichomyceticus	strain=ATCC 31121	GCA_003711105.1	1867	1867	type	True	74.868	56	649	95	below_threshold
Actinoplanes teichomyceticus	strain=DSM 43866	GCA_007829915.1	1867	1867	type	True	74.868	56	649	95	below_threshold
Actinomadura roseirufa		GCA_900659635.1	2094049	2094049	type	True	74.8136	63	649	95	below_threshold
Actinomadura meyerae	strain=DSM 44715	GCA_900188445.1	240840	240840	type	True	74.7575	68	649	95	below_threshold
Actinomadura madurae	strain=DSM 43067	GCA_900115095.1	1993	1993	type	True	74.7347	72	649	95	below_threshold
Saccharothrix saharensis	strain=DSM 45456	GCA_006716745.1	571190	571190	type	True	74.7062	59	649	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	74.6772	85	649	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 18:06:45,360] [INFO] DFAST Taxonomy check result was written to GCA_026705105.1_ASM2670510v1_genomic.fna/tc_result.tsv
[2023-06-27 18:06:45,360] [INFO] ===== Taxonomy check completed =====
[2023-06-27 18:06:45,361] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 18:06:45,361] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg073920f2-a120-442c-98f9-8341e1bda39b/dqc_reference/checkm_data
[2023-06-27 18:06:45,362] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 18:06:45,391] [INFO] Task started: CheckM
[2023-06-27 18:06:45,392] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026705105.1_ASM2670510v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026705105.1_ASM2670510v1_genomic.fna/checkm_input GCA_026705105.1_ASM2670510v1_genomic.fna/checkm_result
[2023-06-27 18:07:08,387] [INFO] Task succeeded: CheckM
[2023-06-27 18:07:08,389] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.98%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 18:07:08,408] [INFO] ===== Completeness check finished =====
[2023-06-27 18:07:08,409] [INFO] ===== Start GTDB Search =====
[2023-06-27 18:07:08,409] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026705105.1_ASM2670510v1_genomic.fna/markers.fasta)
[2023-06-27 18:07:08,409] [INFO] Task started: Blastn
[2023-06-27 18:07:08,409] [INFO] Running command: blastn -query GCA_026705105.1_ASM2670510v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg073920f2-a120-442c-98f9-8341e1bda39b/dqc_reference/reference_markers_gtdb.fasta -out GCA_026705105.1_ASM2670510v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 18:07:09,231] [INFO] Task succeeded: Blastn
[2023-06-27 18:07:09,235] [INFO] Selected 20 target genomes.
[2023-06-27 18:07:09,235] [INFO] Target genome list was writen to GCA_026705105.1_ASM2670510v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 18:07:09,240] [INFO] Task started: fastANI
[2023-06-27 18:07:09,240] [INFO] Running command: fastANI --query /var/lib/cwl/stg61effac4-30bd-4554-8281-c31c745a6cdc/GCA_026705105.1_ASM2670510v1_genomic.fna.gz --refList GCA_026705105.1_ASM2670510v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026705105.1_ASM2670510v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 18:07:19,605] [INFO] Task succeeded: fastANI
[2023-06-27 18:07:19,612] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 18:07:19,612] [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
GCA_009838915.1	s__Bin125 sp009838915	88.674	513	649	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Bin125;f__Bin125;g__Bin125	95.0	98.62	97.86	0.96	0.92	7	-
GCA_009838735.1	s__Bin125 sp009838735	80.625	401	649	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Bin125;f__Bin125;g__Bin125	95.0	96.51	95.66	0.92	0.90	7	-
GCA_002239025.1	s__Bin125 sp002239025	79.3355	352	649	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Bin125;f__Bin125;g__Bin125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007571275.1	s__Bin125 sp007571275	78.6536	279	649	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Bin125;f__Bin125;g__Bin125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009840945.1	s__VXMT01 sp009840945	75.8163	61	649	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__VXMT01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115095.1	s__Spirillospora madurae	74.7347	72	649	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.34	99.27	0.95	0.95	3	-
--------------------------------------------------------------------------------
[2023-06-27 18:07:19,614] [INFO] GTDB search result was written to GCA_026705105.1_ASM2670510v1_genomic.fna/result_gtdb.tsv
[2023-06-27 18:07:19,614] [INFO] ===== GTDB Search completed =====
[2023-06-27 18:07:19,617] [INFO] DFAST_QC result json was written to GCA_026705105.1_ASM2670510v1_genomic.fna/dqc_result.json
[2023-06-27 18:07:19,618] [INFO] DFAST_QC completed!
[2023-06-27 18:07:19,618] [INFO] Total running time: 0h1m0s