[2024-01-25 19:53:36,866] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:53:36,867] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:53:36,868] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f64a6e6-2bb5-4aa0-93b3-ea2f0ac36816/dqc_reference
[2024-01-25 19:53:37,962] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:53:37,963] [INFO] Task started: Prodigal
[2024-01-25 19:53:37,963] [INFO] Running command: gunzip -c /var/lib/cwl/stgfbb6518d-7953-491c-9ebc-302dbbc62fbb/GCF_009707865.1_ASM970786v1_genomic.fna.gz | prodigal -d GCF_009707865.1_ASM970786v1_genomic.fna/cds.fna -a GCF_009707865.1_ASM970786v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:53:59,516] [INFO] Task succeeded: Prodigal
[2024-01-25 19:53:59,517] [INFO] Task started: HMMsearch
[2024-01-25 19:53:59,517] [INFO] Running command: hmmsearch --tblout GCF_009707865.1_ASM970786v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f64a6e6-2bb5-4aa0-93b3-ea2f0ac36816/dqc_reference/reference_markers.hmm GCF_009707865.1_ASM970786v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:53:59,872] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:53:59,873] [INFO] Found 6/6 markers.
[2024-01-25 19:53:59,933] [INFO] Query marker FASTA was written to GCF_009707865.1_ASM970786v1_genomic.fna/markers.fasta
[2024-01-25 19:53:59,934] [INFO] Task started: Blastn
[2024-01-25 19:53:59,934] [INFO] Running command: blastn -query GCF_009707865.1_ASM970786v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f64a6e6-2bb5-4aa0-93b3-ea2f0ac36816/dqc_reference/reference_markers.fasta -out GCF_009707865.1_ASM970786v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:54:01,140] [INFO] Task succeeded: Blastn
[2024-01-25 19:54:01,143] [INFO] Selected 12 target genomes.
[2024-01-25 19:54:01,143] [INFO] Target genome list was writen to GCF_009707865.1_ASM970786v1_genomic.fna/target_genomes.txt
[2024-01-25 19:54:01,155] [INFO] Task started: fastANI
[2024-01-25 19:54:01,155] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbb6518d-7953-491c-9ebc-302dbbc62fbb/GCF_009707865.1_ASM970786v1_genomic.fna.gz --refList GCF_009707865.1_ASM970786v1_genomic.fna/target_genomes.txt --output GCF_009707865.1_ASM970786v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:54:20,982] [INFO] Task succeeded: fastANI
[2024-01-25 19:54:20,982] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f64a6e6-2bb5-4aa0-93b3-ea2f0ac36816/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:54:20,982] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f64a6e6-2bb5-4aa0-93b3-ea2f0ac36816/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:54:20,991] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:54:20,991] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:54:20,991] [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
Amycolatopsis pithecellobii	strain=RM579	GCA_009707865.1	664692	664692	type	True	100.0	2558	2564	95	conclusive
Amycolatopsis acidiphila	strain=JCM 30562	GCA_007713745.1	715473	715473	type	True	83.8969	1230	2564	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	83.8844	1279	2564	95	below_threshold
Amycolatopsis alkalitolerans	strain=SYSUP0005	GCA_006152065.1	2547244	2547244	type	True	83.7388	1206	2564	95	below_threshold
Amycolatopsis bartoniae	strain=DSM 45807	GCA_014191255.1	941986	941986	type	True	82.6193	1242	2564	95	below_threshold
Amycolatopsis bartoniae	strain=DSM 45807	GCA_007713755.1	941986	941986	type	True	82.6142	1200	2564	95	below_threshold
Amycolatopsis sacchari	strain=DSM 44468	GCA_900114035.1	115433	115433	type	True	82.476	1248	2564	95	below_threshold
Amycolatopsis acididurans	strain=K13G38	GCA_012328925.1	2724524	2724524	type	True	81.5241	1133	2564	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	80.7811	1010	2564	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	79.0327	780	2564	95	below_threshold
Prauserella aidingensis	strain=DSM 45266	GCA_024171865.1	387890	387890	type	True	78.5762	628	2564	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	77.6215	619	2564	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:54:20,992] [INFO] DFAST Taxonomy check result was written to GCF_009707865.1_ASM970786v1_genomic.fna/tc_result.tsv
[2024-01-25 19:54:20,993] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:54:20,993] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:54:20,993] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f64a6e6-2bb5-4aa0-93b3-ea2f0ac36816/dqc_reference/checkm_data
[2024-01-25 19:54:20,994] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:54:21,070] [INFO] Task started: CheckM
[2024-01-25 19:54:21,070] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009707865.1_ASM970786v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009707865.1_ASM970786v1_genomic.fna/checkm_input GCF_009707865.1_ASM970786v1_genomic.fna/checkm_result
[2024-01-25 19:55:45,769] [INFO] Task succeeded: CheckM
[2024-01-25 19:55:45,770] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:55:45,824] [INFO] ===== Completeness check finished =====
[2024-01-25 19:55:45,825] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:55:45,826] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009707865.1_ASM970786v1_genomic.fna/markers.fasta)
[2024-01-25 19:55:45,826] [INFO] Task started: Blastn
[2024-01-25 19:55:45,826] [INFO] Running command: blastn -query GCF_009707865.1_ASM970786v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f64a6e6-2bb5-4aa0-93b3-ea2f0ac36816/dqc_reference/reference_markers_gtdb.fasta -out GCF_009707865.1_ASM970786v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:55:47,755] [INFO] Task succeeded: Blastn
[2024-01-25 19:55:47,761] [INFO] Selected 7 target genomes.
[2024-01-25 19:55:47,761] [INFO] Target genome list was writen to GCF_009707865.1_ASM970786v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:55:47,767] [INFO] Task started: fastANI
[2024-01-25 19:55:47,767] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbb6518d-7953-491c-9ebc-302dbbc62fbb/GCF_009707865.1_ASM970786v1_genomic.fna.gz --refList GCF_009707865.1_ASM970786v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009707865.1_ASM970786v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:56:00,530] [INFO] Task succeeded: fastANI
[2024-01-25 19:56:00,538] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:56:00,538] [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_009707865.1	s__Amycolatopsis pithecellobii	100.0	2558	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007713745.1	s__Amycolatopsis acidiphila	83.9065	1228	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	0.99	0.99	2	-
GCF_006152065.1	s__Amycolatopsis alkalitolerans	83.7367	1206	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014191255.1	s__Amycolatopsis bartoniae	82.6139	1243	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.98	99.98	0.99	0.99	3	-
GCF_900114035.1	s__Amycolatopsis sacchari	82.4481	1252	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012328925.1	s__Amycolatopsis acididurans	81.5356	1132	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000519205.1	s__Amycolatopsis taiwanensis	80.0316	896	2564	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:56:00,539] [INFO] GTDB search result was written to GCF_009707865.1_ASM970786v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:56:00,540] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:56:00,543] [INFO] DFAST_QC result json was written to GCF_009707865.1_ASM970786v1_genomic.fna/dqc_result.json
[2024-01-25 19:56:00,543] [INFO] DFAST_QC completed!
[2024-01-25 19:56:00,543] [INFO] Total running time: 0h2m24s