[2024-01-25 20:13:50,785] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:13:50,787] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:13:50,787] [INFO] DQC Reference Directory: /var/lib/cwl/stg796ae8d4-af80-47ae-a833-ccd9441c6574/dqc_reference
[2024-01-25 20:13:51,889] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:13:51,889] [INFO] Task started: Prodigal
[2024-01-25 20:13:51,890] [INFO] Running command: gunzip -c /var/lib/cwl/stgd4f4f2c8-a060-4fcb-8e3e-9584b663b914/GCF_003337235.1_ASM333723v1_genomic.fna.gz | prodigal -d GCF_003337235.1_ASM333723v1_genomic.fna/cds.fna -a GCF_003337235.1_ASM333723v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:14:05,186] [INFO] Task succeeded: Prodigal
[2024-01-25 20:14:05,186] [INFO] Task started: HMMsearch
[2024-01-25 20:14:05,186] [INFO] Running command: hmmsearch --tblout GCF_003337235.1_ASM333723v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg796ae8d4-af80-47ae-a833-ccd9441c6574/dqc_reference/reference_markers.hmm GCF_003337235.1_ASM333723v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:14:05,496] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:14:05,497] [INFO] Found 6/6 markers.
[2024-01-25 20:14:05,538] [INFO] Query marker FASTA was written to GCF_003337235.1_ASM333723v1_genomic.fna/markers.fasta
[2024-01-25 20:14:05,538] [INFO] Task started: Blastn
[2024-01-25 20:14:05,538] [INFO] Running command: blastn -query GCF_003337235.1_ASM333723v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg796ae8d4-af80-47ae-a833-ccd9441c6574/dqc_reference/reference_markers.fasta -out GCF_003337235.1_ASM333723v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:06,762] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:06,765] [INFO] Selected 13 target genomes.
[2024-01-25 20:14:06,766] [INFO] Target genome list was writen to GCF_003337235.1_ASM333723v1_genomic.fna/target_genomes.txt
[2024-01-25 20:14:06,776] [INFO] Task started: fastANI
[2024-01-25 20:14:06,776] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4f4f2c8-a060-4fcb-8e3e-9584b663b914/GCF_003337235.1_ASM333723v1_genomic.fna.gz --refList GCF_003337235.1_ASM333723v1_genomic.fna/target_genomes.txt --output GCF_003337235.1_ASM333723v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:14:23,465] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:23,466] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg796ae8d4-af80-47ae-a833-ccd9441c6574/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:14:23,466] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg796ae8d4-af80-47ae-a833-ccd9441c6574/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:14:23,475] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:14:23,475] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:14:23,475] [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
Halopolyspora algeriensis	strain=CECT 8575	GCA_003337235.1	1500506	1500506	type	True	100.0	1502	1503	95	conclusive
Halopolyspora algeriensis	strain=DSM 46680	GCA_006716575.1	1500506	1500506	type	True	99.994	1466	1503	95	conclusive
Saccharopolyspora erythraea	strain=DSM 40517	GCA_002564065.1	1836	1836	type	True	79.7522	768	1503	95	below_threshold
Saccharopolyspora erythraea	strain=NRRL 2338	GCA_000062885.1	1836	1836	type	True	79.7182	761	1503	95	below_threshold
Saccharopolyspora erythraea	strain=NRRL 2338	GCA_000171635.1	1836	1836	type	True	79.6646	767	1503	95	below_threshold
Saccharopolyspora subtropica	strain=CGMCC 4.7206	GCA_014646075.1	1530170	1530170	type	True	79.602	656	1503	95	below_threshold
Saccharopolyspora hordei	strain=DSM 44065	GCA_013410345.1	1838	1838	type	True	79.5511	713	1503	95	below_threshold
Saccharopolyspora flava	strain=DSM 44771	GCA_900116135.1	95161	95161	type	True	79.3847	682	1503	95	below_threshold
Saccharopolyspora shandongensis	strain=CGMCC 4.3530	GCA_900106995.1	418495	418495	type	True	79.3785	740	1503	95	below_threshold
Saccharopolyspora gloriosae	strain=DSM 45582	GCA_014203325.1	455344	455344	type	True	79.3656	695	1503	95	below_threshold
Actinopolyspora biskrensis	strain=CECT 8576	GCA_013408175.1	1470178	1470178	type	True	79.1768	607	1503	95	below_threshold
Actinopolyspora halophila	strain=DSM 43834	GCA_000371785.1	1850	1850	type	True	79.1543	625	1503	95	below_threshold
Kutzneria buriramensis	strain=DSM 45791	GCA_003387475.1	1045776	1045776	type	True	77.4936	485	1503	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:14:23,477] [INFO] DFAST Taxonomy check result was written to GCF_003337235.1_ASM333723v1_genomic.fna/tc_result.tsv
[2024-01-25 20:14:23,477] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:14:23,477] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:14:23,478] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg796ae8d4-af80-47ae-a833-ccd9441c6574/dqc_reference/checkm_data
[2024-01-25 20:14:23,478] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:14:23,522] [INFO] Task started: CheckM
[2024-01-25 20:14:23,522] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003337235.1_ASM333723v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003337235.1_ASM333723v1_genomic.fna/checkm_input GCF_003337235.1_ASM333723v1_genomic.fna/checkm_result
[2024-01-25 20:15:52,562] [INFO] Task succeeded: CheckM
[2024-01-25 20:15:52,563] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:15:52,632] [INFO] ===== Completeness check finished =====
[2024-01-25 20:15:52,632] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:15:52,633] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003337235.1_ASM333723v1_genomic.fna/markers.fasta)
[2024-01-25 20:15:52,633] [INFO] Task started: Blastn
[2024-01-25 20:15:52,633] [INFO] Running command: blastn -query GCF_003337235.1_ASM333723v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg796ae8d4-af80-47ae-a833-ccd9441c6574/dqc_reference/reference_markers_gtdb.fasta -out GCF_003337235.1_ASM333723v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:54,386] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:54,389] [INFO] Selected 16 target genomes.
[2024-01-25 20:15:54,389] [INFO] Target genome list was writen to GCF_003337235.1_ASM333723v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:15:54,397] [INFO] Task started: fastANI
[2024-01-25 20:15:54,397] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4f4f2c8-a060-4fcb-8e3e-9584b663b914/GCF_003337235.1_ASM333723v1_genomic.fna.gz --refList GCF_003337235.1_ASM333723v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003337235.1_ASM333723v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:16:13,531] [INFO] Task succeeded: fastANI
[2024-01-25 20:16:13,541] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:16:13,541] [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_003337235.1	s__Halopolyspora algeriensis	100.0	1502	1503	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Halopolyspora	95.0	99.99	99.99	0.98	0.98	2	conclusive
GCF_014137975.1	s__Halosaccharopolyspora lacisalsi	81.0301	828	1503	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Halosaccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018141105.1	s__Saccharopolyspora_D erythraea_A	79.8167	734	1503	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000062885.1	s__Saccharopolyspora_D erythraea	79.7184	761	1503	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora_D	95.0	99.99	99.99	1.00	1.00	5	-
GCF_014646075.1	s__Saccharopolyspora subtropica	79.6066	655	1503	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410345.1	s__Saccharopolyspora hordei	79.5443	714	1503	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116135.1	s__Saccharopolyspora flava	79.3963	681	1503	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106995.1	s__Saccharopolyspora shandongensis	79.3644	743	1503	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630535.1	s__Saccharopolyspora hirsuta	79.3546	752	1503	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016526145.1	s__Saccharopolyspora_C sp016526145	79.3393	718	1503	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000384035.1	s__Actinopolyspora mortivallis	79.2281	562	1503	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	95.34	95.34	0.86	0.86	2	-
GCF_006716775.1	s__Actinopolyspora sp006716775	79.171	646	1503	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408175.1	s__Actinopolyspora biskrensis	79.1692	608	1503	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000371785.1	s__Actinopolyspora halophila	79.1467	626	1503	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645795.1	s__Longimycelium tulufanense	77.7735	402	1503	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Longimycelium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386585.1	s__AN110305 sp008386585	77.5502	461	1503	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__AN110305	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:16:13,543] [INFO] GTDB search result was written to GCF_003337235.1_ASM333723v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:16:13,544] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:16:13,546] [INFO] DFAST_QC result json was written to GCF_003337235.1_ASM333723v1_genomic.fna/dqc_result.json
[2024-01-25 20:16:13,547] [INFO] DFAST_QC completed!
[2024-01-25 20:16:13,547] [INFO] Total running time: 0h2m23s