[2024-01-24 14:05:32,344] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:32,347] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:32,347] [INFO] DQC Reference Directory: /var/lib/cwl/stge36b8579-9ed4-4f86-a26f-fcaf8aae6149/dqc_reference
[2024-01-24 14:05:33,696] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:33,697] [INFO] Task started: Prodigal
[2024-01-24 14:05:33,697] [INFO] Running command: gunzip -c /var/lib/cwl/stg13dedaa1-14f6-4c40-987e-b4ebec976e4f/GCF_018866305.1_ASM1886630v1_genomic.fna.gz | prodigal -d GCF_018866305.1_ASM1886630v1_genomic.fna/cds.fna -a GCF_018866305.1_ASM1886630v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:46,671] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:46,671] [INFO] Task started: HMMsearch
[2024-01-24 14:05:46,671] [INFO] Running command: hmmsearch --tblout GCF_018866305.1_ASM1886630v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge36b8579-9ed4-4f86-a26f-fcaf8aae6149/dqc_reference/reference_markers.hmm GCF_018866305.1_ASM1886630v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:46,930] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:46,932] [INFO] Found 6/6 markers.
[2024-01-24 14:05:46,967] [INFO] Query marker FASTA was written to GCF_018866305.1_ASM1886630v1_genomic.fna/markers.fasta
[2024-01-24 14:05:46,968] [INFO] Task started: Blastn
[2024-01-24 14:05:46,968] [INFO] Running command: blastn -query GCF_018866305.1_ASM1886630v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge36b8579-9ed4-4f86-a26f-fcaf8aae6149/dqc_reference/reference_markers.fasta -out GCF_018866305.1_ASM1886630v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:48,017] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:48,020] [INFO] Selected 7 target genomes.
[2024-01-24 14:05:48,020] [INFO] Target genome list was writen to GCF_018866305.1_ASM1886630v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:48,023] [INFO] Task started: fastANI
[2024-01-24 14:05:48,023] [INFO] Running command: fastANI --query /var/lib/cwl/stg13dedaa1-14f6-4c40-987e-b4ebec976e4f/GCF_018866305.1_ASM1886630v1_genomic.fna.gz --refList GCF_018866305.1_ASM1886630v1_genomic.fna/target_genomes.txt --output GCF_018866305.1_ASM1886630v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:54,122] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:54,123] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge36b8579-9ed4-4f86-a26f-fcaf8aae6149/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:54,123] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge36b8579-9ed4-4f86-a26f-fcaf8aae6149/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:54,131] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:05:54,131] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:05:54,131] [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 sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	100.0	1304	1304	95	conclusive
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_017353495.1	2816859	2816859	type	True	99.9893	1290	1304	95	conclusive
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	83.3913	787	1304	95	below_threshold
Arthrobacter gandavensis	strain=JCM 13316	GCA_009192735.1	169960	169960	type	True	83.1772	803	1304	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	83.1399	783	1304	95	below_threshold
Arthrobacter citreus	strain=DSM 20133	GCA_009192745.1	1670	1670	type	True	80.476	570	1304	95	below_threshold
Arthrobacter gallicola	strain=Sa2CUA1	GCA_014836775.1	2762225	2762225	type	True	80.3208	545	1304	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:54,132] [INFO] DFAST Taxonomy check result was written to GCF_018866305.1_ASM1886630v1_genomic.fna/tc_result.tsv
[2024-01-24 14:05:54,133] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:54,133] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:54,133] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge36b8579-9ed4-4f86-a26f-fcaf8aae6149/dqc_reference/checkm_data
[2024-01-24 14:05:54,134] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:54,175] [INFO] Task started: CheckM
[2024-01-24 14:05:54,175] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018866305.1_ASM1886630v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018866305.1_ASM1886630v1_genomic.fna/checkm_input GCF_018866305.1_ASM1886630v1_genomic.fna/checkm_result
[2024-01-24 14:06:31,811] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:31,812] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:31,829] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:31,830] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:31,830] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018866305.1_ASM1886630v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:31,831] [INFO] Task started: Blastn
[2024-01-24 14:06:31,831] [INFO] Running command: blastn -query GCF_018866305.1_ASM1886630v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge36b8579-9ed4-4f86-a26f-fcaf8aae6149/dqc_reference/reference_markers_gtdb.fasta -out GCF_018866305.1_ASM1886630v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:33,308] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:33,312] [INFO] Selected 9 target genomes.
[2024-01-24 14:06:33,312] [INFO] Target genome list was writen to GCF_018866305.1_ASM1886630v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:33,320] [INFO] Task started: fastANI
[2024-01-24 14:06:33,321] [INFO] Running command: fastANI --query /var/lib/cwl/stg13dedaa1-14f6-4c40-987e-b4ebec976e4f/GCF_018866305.1_ASM1886630v1_genomic.fna.gz --refList GCF_018866305.1_ASM1886630v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018866305.1_ASM1886630v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:40,656] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:40,664] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:40,664] [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_018866305.1	s__Arthrobacter_B sp002929435	100.0	1304	1304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	98.36	96.67	0.94	0.92	8	conclusive
GCF_018622995.1	s__Arthrobacter_B sp018622995	83.3881	787	1304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	99.13	98.27	0.96	0.92	3	-
GCF_009192735.1	s__Arthrobacter_B gandavensis	83.2207	799	1304	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_009192775.1	s__Arthrobacter_B yangruifuii	81.2029	625	1304	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_009192745.1	s__Arthrobacter_B citreus	80.4758	570	1304	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_014836875.1	s__Arthrobacter_B sp014836875	80.3953	554	1304	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_014836775.1	s__Arthrobacter_B sp014836775	80.3378	543	1304	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	80.2678	547	1304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	98.39	98.39	0.92	0.92	2	-
GCA_900016675.1	s__Arthrobacter_B saudimassiliensis	80.0746	602	1304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:40,668] [INFO] GTDB search result was written to GCF_018866305.1_ASM1886630v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:40,669] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:40,671] [INFO] DFAST_QC result json was written to GCF_018866305.1_ASM1886630v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:40,672] [INFO] DFAST_QC completed!
[2024-01-24 14:06:40,672] [INFO] Total running time: 0h1m8s