[2024-01-24 13:37:06,663] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:06,669] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:06,670] [INFO] DQC Reference Directory: /var/lib/cwl/stg74f67156-47c7-4aad-833a-affa670a222a/dqc_reference
[2024-01-24 13:37:07,901] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:07,901] [INFO] Task started: Prodigal
[2024-01-24 13:37:07,902] [INFO] Running command: gunzip -c /var/lib/cwl/stg159c55cf-fa81-4e1e-a78c-329fd474642e/GCF_014694315.1_ASM1469431v1_genomic.fna.gz | prodigal -d GCF_014694315.1_ASM1469431v1_genomic.fna/cds.fna -a GCF_014694315.1_ASM1469431v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:22,567] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:22,567] [INFO] Task started: HMMsearch
[2024-01-24 13:37:22,568] [INFO] Running command: hmmsearch --tblout GCF_014694315.1_ASM1469431v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74f67156-47c7-4aad-833a-affa670a222a/dqc_reference/reference_markers.hmm GCF_014694315.1_ASM1469431v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:22,920] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:22,922] [INFO] Found 6/6 markers.
[2024-01-24 13:37:22,959] [INFO] Query marker FASTA was written to GCF_014694315.1_ASM1469431v1_genomic.fna/markers.fasta
[2024-01-24 13:37:22,960] [INFO] Task started: Blastn
[2024-01-24 13:37:22,960] [INFO] Running command: blastn -query GCF_014694315.1_ASM1469431v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74f67156-47c7-4aad-833a-affa670a222a/dqc_reference/reference_markers.fasta -out GCF_014694315.1_ASM1469431v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:24,133] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:24,136] [INFO] Selected 17 target genomes.
[2024-01-24 13:37:24,136] [INFO] Target genome list was writen to GCF_014694315.1_ASM1469431v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:24,144] [INFO] Task started: fastANI
[2024-01-24 13:37:24,144] [INFO] Running command: fastANI --query /var/lib/cwl/stg159c55cf-fa81-4e1e-a78c-329fd474642e/GCF_014694315.1_ASM1469431v1_genomic.fna.gz --refList GCF_014694315.1_ASM1469431v1_genomic.fna/target_genomes.txt --output GCF_014694315.1_ASM1469431v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:40,317] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:40,317] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74f67156-47c7-4aad-833a-affa670a222a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:40,318] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74f67156-47c7-4aad-833a-affa670a222a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:40,331] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:40,332] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:40,332] [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 ipis	strain=IA7	GCA_014694315.1	2716202	2716202	type	True	100.0	1496	1496	95	conclusive
Arthrobacter globiformis	strain=NBRC 12137	GCA_000238915.2	1665	1665	type	True	89.8934	1205	1496	95	below_threshold
Arthrobacter pascens	strain=DSM 20545	GCA_017052465.1	1677	1677	type	True	83.3271	992	1496	95	below_threshold
Pseudarthrobacter enclensis	strain=NIO-1008	GCA_001457025.1	993070	993070	type	True	81.6227	759	1496	95	below_threshold
Pseudarthrobacter enclensis	strain=NIO-1008	GCA_900094675.1	993070	993070	type	True	81.5921	763	1496	95	below_threshold
Pseudarthrobacter equi	strain=IMMIB L-1606	GCA_900105535.1	728066	728066	type	True	81.5165	758	1496	95	below_threshold
Pseudarthrobacter chlorophenolicus	strain=A6	GCA_900104315.1	85085	85085	type	True	81.5105	769	1496	95	below_threshold
Pseudarthrobacter polychromogenes	strain=CGMCC 1.1927	GCA_014644495.1	1676	1676	type	True	81.4779	736	1496	95	below_threshold
Pseudarthrobacter siccitolerans	strain=4J27	GCA_001046895.1	861266	861266	type	True	81.3774	778	1496	95	below_threshold
Arthrobacter cupressi	strain=CGMCC 1.10783	GCA_900099975.1	1045773	1045773	type	True	81.3006	675	1496	95	below_threshold
Arthrobacter cupressi	strain=DSM 24664	GCA_013409905.1	1045773	1045773	type	True	81.266	690	1496	95	below_threshold
Arthrobacter celericrescens	strain=NEAU-SA2	GCA_003614925.1	2320851	2320851	type	True	81.1824	683	1496	95	below_threshold
Arthrobacter ulcerisalmonis		GCA_900609065.1	2483813	2483813	type	True	80.3337	551	1496	95	below_threshold
Paenarthrobacter nicotinovorans	strain=ATCC 49919	GCA_021919345.1	29320	29320	suspected-type	True	80.2412	607	1496	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	79.0701	444	1496	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	78.8637	356	1496	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	78.7875	354	1496	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:40,333] [INFO] DFAST Taxonomy check result was written to GCF_014694315.1_ASM1469431v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:40,334] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:40,334] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:40,334] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74f67156-47c7-4aad-833a-affa670a222a/dqc_reference/checkm_data
[2024-01-24 13:37:40,335] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:40,377] [INFO] Task started: CheckM
[2024-01-24 13:37:40,377] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014694315.1_ASM1469431v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014694315.1_ASM1469431v1_genomic.fna/checkm_input GCF_014694315.1_ASM1469431v1_genomic.fna/checkm_result
[2024-01-24 13:38:22,776] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:22,778] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:22,797] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:22,797] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:22,798] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014694315.1_ASM1469431v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:22,798] [INFO] Task started: Blastn
[2024-01-24 13:38:22,798] [INFO] Running command: blastn -query GCF_014694315.1_ASM1469431v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74f67156-47c7-4aad-833a-affa670a222a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014694315.1_ASM1469431v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:24,524] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:24,527] [INFO] Selected 6 target genomes.
[2024-01-24 13:38:24,527] [INFO] Target genome list was writen to GCF_014694315.1_ASM1469431v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:24,533] [INFO] Task started: fastANI
[2024-01-24 13:38:24,533] [INFO] Running command: fastANI --query /var/lib/cwl/stg159c55cf-fa81-4e1e-a78c-329fd474642e/GCF_014694315.1_ASM1469431v1_genomic.fna.gz --refList GCF_014694315.1_ASM1469431v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014694315.1_ASM1469431v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:32,180] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:32,192] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:32,193] [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_014694315.1	s__Arthrobacter ipsi	100.0	1496	1496	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003261175.1	s__Arthrobacter globiformis_A	93.4573	1261	1496	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002892795.1	s__Arthrobacter sp002892795	92.7691	1264	1496	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613795.1	s__Arthrobacter sp018613795	92.6518	1254	1496	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000238915.1	s__Arthrobacter globiformis	89.8942	1204	1496	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001969265.1	s__Arthrobacter sp001969265	88.2595	1169	1496	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter	95.0	98.26	98.26	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:32,194] [INFO] GTDB search result was written to GCF_014694315.1_ASM1469431v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:32,195] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:32,206] [INFO] DFAST_QC result json was written to GCF_014694315.1_ASM1469431v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:32,207] [INFO] DFAST_QC completed!
[2024-01-24 13:38:32,207] [INFO] Total running time: 0h1m26s