[2024-01-25 20:07:35,873] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:07:35,874] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:07:35,874] [INFO] DQC Reference Directory: /var/lib/cwl/stgbad0807a-30a5-4f57-9a08-a33b4025c942/dqc_reference
[2024-01-25 20:07:37,030] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:07:37,031] [INFO] Task started: Prodigal
[2024-01-25 20:07:37,031] [INFO] Running command: gunzip -c /var/lib/cwl/stgbb518f52-4fc4-4e9b-aaf8-99dce7861239/GCF_017898065.1_ASM1789806v1_genomic.fna.gz | prodigal -d GCF_017898065.1_ASM1789806v1_genomic.fna/cds.fna -a GCF_017898065.1_ASM1789806v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:07:46,708] [INFO] Task succeeded: Prodigal
[2024-01-25 20:07:46,708] [INFO] Task started: HMMsearch
[2024-01-25 20:07:46,708] [INFO] Running command: hmmsearch --tblout GCF_017898065.1_ASM1789806v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbad0807a-30a5-4f57-9a08-a33b4025c942/dqc_reference/reference_markers.hmm GCF_017898065.1_ASM1789806v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:07:46,922] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:07:46,923] [INFO] Found 6/6 markers.
[2024-01-25 20:07:46,951] [INFO] Query marker FASTA was written to GCF_017898065.1_ASM1789806v1_genomic.fna/markers.fasta
[2024-01-25 20:07:46,952] [INFO] Task started: Blastn
[2024-01-25 20:07:46,952] [INFO] Running command: blastn -query GCF_017898065.1_ASM1789806v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbad0807a-30a5-4f57-9a08-a33b4025c942/dqc_reference/reference_markers.fasta -out GCF_017898065.1_ASM1789806v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:47,943] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:47,946] [INFO] Selected 6 target genomes.
[2024-01-25 20:07:47,946] [INFO] Target genome list was writen to GCF_017898065.1_ASM1789806v1_genomic.fna/target_genomes.txt
[2024-01-25 20:07:47,958] [INFO] Task started: fastANI
[2024-01-25 20:07:47,958] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb518f52-4fc4-4e9b-aaf8-99dce7861239/GCF_017898065.1_ASM1789806v1_genomic.fna.gz --refList GCF_017898065.1_ASM1789806v1_genomic.fna/target_genomes.txt --output GCF_017898065.1_ASM1789806v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:07:53,303] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:53,304] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbad0807a-30a5-4f57-9a08-a33b4025c942/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:07:53,304] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbad0807a-30a5-4f57-9a08-a33b4025c942/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:07:53,310] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:07:53,310] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:07:53,310] [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
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	100.0	1182	1182	95	conclusive
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	99.9988	1182	1182	95	conclusive
Arthrobacter gandavensis	strain=JCM 13316	GCA_009192735.1	169960	169960	type	True	83.7247	786	1182	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	83.2499	773	1182	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_017353495.1	2816859	2816859	type	True	83.1611	784	1182	95	below_threshold
Arthrobacter pullicola	strain=Sa2BUA2	GCA_014836875.1	2762224	2762224	type	True	80.7514	580	1182	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:07:53,311] [INFO] DFAST Taxonomy check result was written to GCF_017898065.1_ASM1789806v1_genomic.fna/tc_result.tsv
[2024-01-25 20:07:53,312] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:07:53,312] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:07:53,312] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbad0807a-30a5-4f57-9a08-a33b4025c942/dqc_reference/checkm_data
[2024-01-25 20:07:53,313] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:07:53,349] [INFO] Task started: CheckM
[2024-01-25 20:07:53,349] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017898065.1_ASM1789806v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017898065.1_ASM1789806v1_genomic.fna/checkm_input GCF_017898065.1_ASM1789806v1_genomic.fna/checkm_result
[2024-01-25 20:08:22,720] [INFO] Task succeeded: CheckM
[2024-01-25 20:08:22,722] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:08:22,738] [INFO] ===== Completeness check finished =====
[2024-01-25 20:08:22,738] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:08:22,740] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017898065.1_ASM1789806v1_genomic.fna/markers.fasta)
[2024-01-25 20:08:22,740] [INFO] Task started: Blastn
[2024-01-25 20:08:22,740] [INFO] Running command: blastn -query GCF_017898065.1_ASM1789806v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbad0807a-30a5-4f57-9a08-a33b4025c942/dqc_reference/reference_markers_gtdb.fasta -out GCF_017898065.1_ASM1789806v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:08:24,368] [INFO] Task succeeded: Blastn
[2024-01-25 20:08:24,371] [INFO] Selected 11 target genomes.
[2024-01-25 20:08:24,371] [INFO] Target genome list was writen to GCF_017898065.1_ASM1789806v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:08:24,378] [INFO] Task started: fastANI
[2024-01-25 20:08:24,379] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb518f52-4fc4-4e9b-aaf8-99dce7861239/GCF_017898065.1_ASM1789806v1_genomic.fna.gz --refList GCF_017898065.1_ASM1789806v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017898065.1_ASM1789806v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:08:33,082] [INFO] Task succeeded: fastANI
[2024-01-25 20:08:33,090] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:08:33,090] [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_018622995.1	s__Arthrobacter_B sp018622995	99.9988	1182	1182	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	99.13	98.27	0.96	0.92	3	conclusive
GCF_009192735.1	s__Arthrobacter_B gandavensis	83.7247	786	1182	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018866305.1	s__Arthrobacter_B sp002929435	83.2391	774	1182	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	98.36	96.67	0.94	0.92	8	-
GCF_009192775.1	s__Arthrobacter_B yangruifuii	81.4205	687	1182	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	97.52	97.52	0.93	0.93	2	-
GCF_014836875.1	s__Arthrobacter_B sp014836875	80.736	581	1182	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900016675.1	s__Arthrobacter_B saudimassiliensis	80.6942	664	1182	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001307035.1	s__Arthrobacter_B sp001307035	80.5853	561	1182	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	98.39	98.39	0.92	0.92	2	-
GCF_001552075.1	s__Arthrobacter_B luteolus	80.5703	601	1182	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014836775.1	s__Arthrobacter_B sp014836775	80.4362	598	1182	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482545.1	s__Specibacter sp000482545	79.4201	400	1182	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016892645.1	s__Arthrobacter_H sp016892645	78.4764	340	1182	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_H	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:08:33,091] [INFO] GTDB search result was written to GCF_017898065.1_ASM1789806v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:08:33,092] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:08:33,094] [INFO] DFAST_QC result json was written to GCF_017898065.1_ASM1789806v1_genomic.fna/dqc_result.json
[2024-01-25 20:08:33,094] [INFO] DFAST_QC completed!
[2024-01-25 20:08:33,094] [INFO] Total running time: 0h0m57s