[2024-01-24 14:39:15,170] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:15,177] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:15,178] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb6eb9f6-88c8-410d-a57e-981513f592b3/dqc_reference
[2024-01-24 14:39:16,594] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:16,595] [INFO] Task started: Prodigal
[2024-01-24 14:39:16,595] [INFO] Running command: gunzip -c /var/lib/cwl/stgd32be4ce-f2a3-40c1-89db-be6a5863264d/GCF_002846475.1_ASM284647v1_genomic.fna.gz | prodigal -d GCF_002846475.1_ASM284647v1_genomic.fna/cds.fna -a GCF_002846475.1_ASM284647v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:42:46,088] [INFO] Task succeeded: Prodigal
[2024-01-24 14:42:46,088] [INFO] Task started: HMMsearch
[2024-01-24 14:42:46,088] [INFO] Running command: hmmsearch --tblout GCF_002846475.1_ASM284647v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb6eb9f6-88c8-410d-a57e-981513f592b3/dqc_reference/reference_markers.hmm GCF_002846475.1_ASM284647v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:42:46,575] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:42:46,576] [INFO] Found 6/6 markers.
[2024-01-24 14:42:46,649] [INFO] Query marker FASTA was written to GCF_002846475.1_ASM284647v1_genomic.fna/markers.fasta
[2024-01-24 14:42:46,649] [INFO] Task started: Blastn
[2024-01-24 14:42:46,649] [INFO] Running command: blastn -query GCF_002846475.1_ASM284647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb6eb9f6-88c8-410d-a57e-981513f592b3/dqc_reference/reference_markers.fasta -out GCF_002846475.1_ASM284647v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:42:48,041] [INFO] Task succeeded: Blastn
[2024-01-24 14:42:48,045] [INFO] Selected 7 target genomes.
[2024-01-24 14:42:48,046] [INFO] Target genome list was writen to GCF_002846475.1_ASM284647v1_genomic.fna/target_genomes.txt
[2024-01-24 14:42:48,056] [INFO] Task started: fastANI
[2024-01-24 14:42:48,056] [INFO] Running command: fastANI --query /var/lib/cwl/stgd32be4ce-f2a3-40c1-89db-be6a5863264d/GCF_002846475.1_ASM284647v1_genomic.fna.gz --refList GCF_002846475.1_ASM284647v1_genomic.fna/target_genomes.txt --output GCF_002846475.1_ASM284647v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:43:08,305] [INFO] Task succeeded: fastANI
[2024-01-24 14:43:08,306] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb6eb9f6-88c8-410d-a57e-981513f592b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:43:08,306] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb6eb9f6-88c8-410d-a57e-981513f592b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:43:08,316] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:43:08,316] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:43:08,316] [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
Saccharopolyspora spinosa	strain=DSM 44228	GCA_002846475.1	60894	60894	type	True	100.0	3006	3006	95	conclusive
Saccharopolyspora spinosa	strain=NRRL 18395	GCA_000194155.1	60894	60894	type	True	99.7732	2818	3006	95	conclusive
Saccharopolyspora shandongensis	strain=CGMCC 4.3530	GCA_900106995.1	418495	418495	type	True	88.3077	1767	3006	95	below_threshold
Saccharopolyspora elongata	strain=7K502	GCA_004348985.1	2530387	2530387	type	True	88.2476	1776	3006	95	below_threshold
Saccharopolyspora phatthalungensis	strain=DSM 45584	GCA_014203395.1	664693	664693	type	True	86.4505	1566	3006	95	below_threshold
Saccharopolyspora hirsuta	strain=VKM Ac-666	GCA_008630535.1	1837	1837	type	True	85.0689	1450	3006	95	below_threshold
Saccharopolyspora hordei	strain=DSM 44065	GCA_013410345.1	1838	1838	type	True	84.3508	1292	3006	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:43:08,318] [INFO] DFAST Taxonomy check result was written to GCF_002846475.1_ASM284647v1_genomic.fna/tc_result.tsv
[2024-01-24 14:43:08,319] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:43:08,319] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:43:08,319] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb6eb9f6-88c8-410d-a57e-981513f592b3/dqc_reference/checkm_data
[2024-01-24 14:43:08,320] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:43:08,407] [INFO] Task started: CheckM
[2024-01-24 14:43:08,407] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002846475.1_ASM284647v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002846475.1_ASM284647v1_genomic.fna/checkm_input GCF_002846475.1_ASM284647v1_genomic.fna/checkm_result
[2024-01-24 14:50:51,516] [INFO] Task succeeded: CheckM
[2024-01-24 14:50:51,519] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:50:51,546] [INFO] ===== Completeness check finished =====
[2024-01-24 14:50:51,547] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:50:51,548] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002846475.1_ASM284647v1_genomic.fna/markers.fasta)
[2024-01-24 14:50:51,549] [INFO] Task started: Blastn
[2024-01-24 14:50:51,549] [INFO] Running command: blastn -query GCF_002846475.1_ASM284647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb6eb9f6-88c8-410d-a57e-981513f592b3/dqc_reference/reference_markers_gtdb.fasta -out GCF_002846475.1_ASM284647v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:50:53,472] [INFO] Task succeeded: Blastn
[2024-01-24 14:50:53,477] [INFO] Selected 7 target genomes.
[2024-01-24 14:50:53,477] [INFO] Target genome list was writen to GCF_002846475.1_ASM284647v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:50:53,507] [INFO] Task started: fastANI
[2024-01-24 14:50:53,508] [INFO] Running command: fastANI --query /var/lib/cwl/stgd32be4ce-f2a3-40c1-89db-be6a5863264d/GCF_002846475.1_ASM284647v1_genomic.fna.gz --refList GCF_002846475.1_ASM284647v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002846475.1_ASM284647v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:51:12,496] [INFO] Task succeeded: fastANI
[2024-01-24 14:51:12,504] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:51:12,504] [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_000194155.1	s__Saccharopolyspora spinosa	99.7747	2817	3006	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	99.78	99.78	0.99	0.98	3	conclusive
GCF_014697215.1	s__Saccharopolyspora pogona	93.7826	2157	3006	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	95.67	95.67	0.80	0.80	2	-
GCF_900106995.1	s__Saccharopolyspora shandongensis	88.2977	1769	3006	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348985.1	s__Saccharopolyspora sp004348985	88.2252	1778	3006	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203395.1	s__Saccharopolyspora phatthalungensis	86.4424	1562	3006	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	99.57	99.57	0.93	0.93	2	-
GCF_008630535.1	s__Saccharopolyspora hirsuta	85.0395	1454	3006	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018141105.1	s__Saccharopolyspora_D erythraea_A	81.831	1269	3006	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:51:12,506] [INFO] GTDB search result was written to GCF_002846475.1_ASM284647v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:51:12,507] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:51:12,510] [INFO] DFAST_QC result json was written to GCF_002846475.1_ASM284647v1_genomic.fna/dqc_result.json
[2024-01-24 14:51:12,510] [INFO] DFAST_QC completed!
[2024-01-24 14:51:12,510] [INFO] Total running time: 0h11m57s