[2024-01-24 12:30:18,478] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:18,480] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:18,480] [INFO] DQC Reference Directory: /var/lib/cwl/stg6005fd05-668d-4757-89fd-feadb17d4e0a/dqc_reference
[2024-01-24 12:30:19,763] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:19,764] [INFO] Task started: Prodigal
[2024-01-24 12:30:19,764] [INFO] Running command: gunzip -c /var/lib/cwl/stg60c511ea-aac8-4e74-982c-b61f8bcc1623/GCF_003999975.1_ASM399997v1_genomic.fna.gz | prodigal -d GCF_003999975.1_ASM399997v1_genomic.fna/cds.fna -a GCF_003999975.1_ASM399997v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:50,636] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:50,637] [INFO] Task started: HMMsearch
[2024-01-24 12:30:50,637] [INFO] Running command: hmmsearch --tblout GCF_003999975.1_ASM399997v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6005fd05-668d-4757-89fd-feadb17d4e0a/dqc_reference/reference_markers.hmm GCF_003999975.1_ASM399997v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:51,173] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:51,174] [INFO] Found 6/6 markers.
[2024-01-24 12:30:51,260] [INFO] Query marker FASTA was written to GCF_003999975.1_ASM399997v1_genomic.fna/markers.fasta
[2024-01-24 12:30:51,260] [INFO] Task started: Blastn
[2024-01-24 12:30:51,260] [INFO] Running command: blastn -query GCF_003999975.1_ASM399997v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6005fd05-668d-4757-89fd-feadb17d4e0a/dqc_reference/reference_markers.fasta -out GCF_003999975.1_ASM399997v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:52,509] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:52,513] [INFO] Selected 13 target genomes.
[2024-01-24 12:30:52,514] [INFO] Target genome list was writen to GCF_003999975.1_ASM399997v1_genomic.fna/target_genomes.txt
[2024-01-24 12:30:52,529] [INFO] Task started: fastANI
[2024-01-24 12:30:52,530] [INFO] Running command: fastANI --query /var/lib/cwl/stg60c511ea-aac8-4e74-982c-b61f8bcc1623/GCF_003999975.1_ASM399997v1_genomic.fna.gz --refList GCF_003999975.1_ASM399997v1_genomic.fna/target_genomes.txt --output GCF_003999975.1_ASM399997v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:21,144] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:21,145] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6005fd05-668d-4757-89fd-feadb17d4e0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:21,145] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6005fd05-668d-4757-89fd-feadb17d4e0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:21,156] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:31:21,157] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:31:21,157] [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 lichenicola	strain=LDG1-01	GCA_016785085.1	2802976	2802976	type	True	84.5968	2085	3323	95	below_threshold
Actinoplanes ovalisporus	strain=LDG1-06	GCA_016834655.1	2810368	2810368	type	True	84.5183	2116	3323	95	below_threshold
Actinoplanes abujensis	strain=DSM 45518	GCA_014204895.1	882441	882441	type	True	84.269	2031	3323	95	below_threshold
Actinoplanes brasiliensis	strain=NBRC 13938	GCA_016862015.1	52695	52695	type	True	84.2566	1953	3323	95	below_threshold
Actinoplanes bogorensis	strain=NBRC 110975	GCA_018829635.1	1610840	1610840	type	True	84.2323	2030	3323	95	below_threshold
Actinoplanes brasiliensis	strain=DSM 43805	GCA_004362215.1	52695	52695	type	True	84.206	1991	3323	95	below_threshold
Actinoplanes deccanensis	strain=NBRC 13994	GCA_016862115.1	113561	113561	type	True	83.1193	2006	3323	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	80.4011	1480	3323	95	below_threshold
Actinoplanes cyaneus	strain=NBRC 14990	GCA_016862095.1	52696	52696	type	True	80.3989	1539	3323	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	78.712	915	3323	95	below_threshold
Prauserella aidingensis	strain=DSM 45266	GCA_024171865.1	387890	387890	type	True	76.1406	458	3323	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	76.0656	656	3323	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	76.0558	665	3323	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:21,159] [INFO] DFAST Taxonomy check result was written to GCF_003999975.1_ASM399997v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:21,160] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:21,160] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:21,161] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6005fd05-668d-4757-89fd-feadb17d4e0a/dqc_reference/checkm_data
[2024-01-24 12:31:21,163] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:21,256] [INFO] Task started: CheckM
[2024-01-24 12:31:21,256] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003999975.1_ASM399997v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003999975.1_ASM399997v1_genomic.fna/checkm_input GCF_003999975.1_ASM399997v1_genomic.fna/checkm_result
[2024-01-24 12:32:46,041] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:46,042] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:46,074] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:46,075] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:46,075] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003999975.1_ASM399997v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:46,076] [INFO] Task started: Blastn
[2024-01-24 12:32:46,076] [INFO] Running command: blastn -query GCF_003999975.1_ASM399997v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6005fd05-668d-4757-89fd-feadb17d4e0a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003999975.1_ASM399997v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:47,916] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:47,920] [INFO] Selected 10 target genomes.
[2024-01-24 12:32:47,920] [INFO] Target genome list was writen to GCF_003999975.1_ASM399997v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:47,929] [INFO] Task started: fastANI
[2024-01-24 12:32:47,930] [INFO] Running command: fastANI --query /var/lib/cwl/stg60c511ea-aac8-4e74-982c-b61f8bcc1623/GCF_003999975.1_ASM399997v1_genomic.fna.gz --refList GCF_003999975.1_ASM399997v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003999975.1_ASM399997v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:13,685] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:13,696] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:13,696] [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_003999975.1	s__Actinoplanes sp003999975	100.0	3316	3323	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016785085.1	s__Actinoplanes sp016785085	84.6105	2082	3323	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016834655.1	s__Actinoplanes sp016834655	84.5135	2117	3323	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204895.1	s__Actinoplanes abujensis	84.2876	2027	3323	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018829635.1	s__Actinoplanes bogorensis	84.2787	2020	3323	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362215.1	s__Actinoplanes brasiliensis	84.211	1990	3323	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016862115.1	s__Actinoplanes deccanensis	83.0965	2011	3323	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862175.1	s__Actinoplanes durhamensis	81.7707	1725	3323	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862095.1	s__Actinoplanes cyaneus	80.4044	1539	3323	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003001815.1	s__Actinoplanes italicus	80.2423	1613	3323	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:13,698] [INFO] GTDB search result was written to GCF_003999975.1_ASM399997v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:13,699] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:13,702] [INFO] DFAST_QC result json was written to GCF_003999975.1_ASM399997v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:13,702] [INFO] DFAST_QC completed!
[2024-01-24 12:33:13,702] [INFO] Total running time: 0h2m55s