[2024-01-25 17:41:05,554] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:41:05,558] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:41:05,559] [INFO] DQC Reference Directory: /var/lib/cwl/stgbaa26b81-ac22-46c5-9018-c598943ccef7/dqc_reference
[2024-01-25 17:41:06,736] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:41:06,737] [INFO] Task started: Prodigal
[2024-01-25 17:41:06,737] [INFO] Running command: gunzip -c /var/lib/cwl/stg1c6e32c6-6e3d-4dd1-9282-44a04bf84944/GCF_021391495.1_ASM2139149v1_genomic.fna.gz | prodigal -d GCF_021391495.1_ASM2139149v1_genomic.fna/cds.fna -a GCF_021391495.1_ASM2139149v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:41:28,034] [INFO] Task succeeded: Prodigal
[2024-01-25 17:41:28,035] [INFO] Task started: HMMsearch
[2024-01-25 17:41:28,035] [INFO] Running command: hmmsearch --tblout GCF_021391495.1_ASM2139149v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbaa26b81-ac22-46c5-9018-c598943ccef7/dqc_reference/reference_markers.hmm GCF_021391495.1_ASM2139149v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:41:28,348] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:41:28,349] [INFO] Found 6/6 markers.
[2024-01-25 17:41:28,414] [INFO] Query marker FASTA was written to GCF_021391495.1_ASM2139149v1_genomic.fna/markers.fasta
[2024-01-25 17:41:28,415] [INFO] Task started: Blastn
[2024-01-25 17:41:28,415] [INFO] Running command: blastn -query GCF_021391495.1_ASM2139149v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbaa26b81-ac22-46c5-9018-c598943ccef7/dqc_reference/reference_markers.fasta -out GCF_021391495.1_ASM2139149v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:29,723] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:29,725] [INFO] Selected 13 target genomes.
[2024-01-25 17:41:29,726] [INFO] Target genome list was writen to GCF_021391495.1_ASM2139149v1_genomic.fna/target_genomes.txt
[2024-01-25 17:41:29,745] [INFO] Task started: fastANI
[2024-01-25 17:41:29,745] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c6e32c6-6e3d-4dd1-9282-44a04bf84944/GCF_021391495.1_ASM2139149v1_genomic.fna.gz --refList GCF_021391495.1_ASM2139149v1_genomic.fna/target_genomes.txt --output GCF_021391495.1_ASM2139149v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:41:54,010] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:54,010] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbaa26b81-ac22-46c5-9018-c598943ccef7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:41:54,010] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbaa26b81-ac22-46c5-9018-c598943ccef7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:41:54,019] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:41:54,019] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:41:54,019] [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 acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	100.0	2722	2727	95	conclusive
Amycolatopsis acidiphila	strain=JCM 30562	GCA_007713745.1	715473	715473	type	True	99.9428	2567	2727	95	conclusive
Amycolatopsis bartoniae	strain=DSM 45807	GCA_014191255.1	941986	941986	type	True	85.3789	1662	2727	95	below_threshold
Amycolatopsis alkalitolerans	strain=SYSUP0005	GCA_006152065.1	2547244	2547244	type	True	85.3238	1481	2727	95	below_threshold
Amycolatopsis bartoniae	strain=DSM 45807	GCA_007713755.1	941986	941986	type	True	85.2803	1601	2727	95	below_threshold
Amycolatopsis sacchari	strain=DSM 44468	GCA_900114035.1	115433	115433	type	True	85.1235	1594	2727	95	below_threshold
Amycolatopsis pithecellobii	strain=RM579	GCA_009707865.1	664692	664692	type	True	83.8779	1272	2727	95	below_threshold
Amycolatopsis acididurans	strain=K13G38	GCA_012328925.1	2724524	2724524	type	True	82.7852	1425	2727	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	82.3187	1351	2727	95	below_threshold
Amycolatopsis rhizosphaerae	strain=TBRC 6029	GCA_007713715.1	2053003	2053003	type	True	82.2055	1081	2727	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	79.9268	1048	2727	95	below_threshold
Prauserella aidingensis	strain=DSM 45266	GCA_024171865.1	387890	387890	type	True	79.0426	831	2727	95	below_threshold
Lentzea californiensis	strain=DSM 43393	GCA_024648825.1	438851	438851	type	True	77.8226	820	2727	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:41:54,021] [INFO] DFAST Taxonomy check result was written to GCF_021391495.1_ASM2139149v1_genomic.fna/tc_result.tsv
[2024-01-25 17:41:54,021] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:41:54,022] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:41:54,022] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbaa26b81-ac22-46c5-9018-c598943ccef7/dqc_reference/checkm_data
[2024-01-25 17:41:54,022] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:41:54,098] [INFO] Task started: CheckM
[2024-01-25 17:41:54,098] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021391495.1_ASM2139149v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021391495.1_ASM2139149v1_genomic.fna/checkm_input GCF_021391495.1_ASM2139149v1_genomic.fna/checkm_result
[2024-01-25 17:43:57,715] [INFO] Task succeeded: CheckM
[2024-01-25 17:43:57,716] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:43:57,740] [INFO] ===== Completeness check finished =====
[2024-01-25 17:43:57,740] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:43:57,741] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021391495.1_ASM2139149v1_genomic.fna/markers.fasta)
[2024-01-25 17:43:57,741] [INFO] Task started: Blastn
[2024-01-25 17:43:57,741] [INFO] Running command: blastn -query GCF_021391495.1_ASM2139149v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbaa26b81-ac22-46c5-9018-c598943ccef7/dqc_reference/reference_markers_gtdb.fasta -out GCF_021391495.1_ASM2139149v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:59,825] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:59,828] [INFO] Selected 12 target genomes.
[2024-01-25 17:43:59,828] [INFO] Target genome list was writen to GCF_021391495.1_ASM2139149v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:43:59,841] [INFO] Task started: fastANI
[2024-01-25 17:43:59,841] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c6e32c6-6e3d-4dd1-9282-44a04bf84944/GCF_021391495.1_ASM2139149v1_genomic.fna.gz --refList GCF_021391495.1_ASM2139149v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021391495.1_ASM2139149v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:44:23,633] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:23,641] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:44:23,641] [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_007713745.1	s__Amycolatopsis acidiphila	99.9428	2567	2727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_014191255.1	s__Amycolatopsis bartoniae	85.3765	1660	2727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.98	99.98	0.99	0.99	3	-
GCF_006152065.1	s__Amycolatopsis alkalitolerans	85.3309	1480	2727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114035.1	s__Amycolatopsis sacchari	85.1217	1594	2727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009707865.1	s__Amycolatopsis pithecellobii	83.8971	1269	2727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007713735.2	s__Amycolatopsis acidicola	82.9341	1467	2727	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	82.7934	1422	2727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385215.1	s__Amycolatopsis thermalba	82.2926	1355	2727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.72	99.30	0.96	0.93	4	-
GCF_007713715.1	s__Amycolatopsis rhizosphaerae	82.1488	1090	2727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410405.1	s__Amycolatopsis endophytica	81.9278	1313	2727	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	80.7827	1163	2727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119165.1	s__Amycolatopsis australiensis	80.2981	1333	2727	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 17:44:23,642] [INFO] GTDB search result was written to GCF_021391495.1_ASM2139149v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:44:23,643] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:44:23,645] [INFO] DFAST_QC result json was written to GCF_021391495.1_ASM2139149v1_genomic.fna/dqc_result.json
[2024-01-25 17:44:23,646] [INFO] DFAST_QC completed!
[2024-01-25 17:44:23,646] [INFO] Total running time: 0h3m18s