[2024-01-24 14:02:48,115] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:02:48,117] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:02:48,117] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b31724d-13b8-4a98-a245-5979553b74ed/dqc_reference
[2024-01-24 14:02:49,347] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:02:49,348] [INFO] Task started: Prodigal
[2024-01-24 14:02:49,348] [INFO] Running command: gunzip -c /var/lib/cwl/stga5466dfc-9553-4932-a97f-9157f38b1bef/GCF_020905375.1_ASM2090537v1_genomic.fna.gz | prodigal -d GCF_020905375.1_ASM2090537v1_genomic.fna/cds.fna -a GCF_020905375.1_ASM2090537v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:00,826] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:00,827] [INFO] Task started: HMMsearch
[2024-01-24 14:03:00,827] [INFO] Running command: hmmsearch --tblout GCF_020905375.1_ASM2090537v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b31724d-13b8-4a98-a245-5979553b74ed/dqc_reference/reference_markers.hmm GCF_020905375.1_ASM2090537v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:01,115] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:01,116] [INFO] Found 6/6 markers.
[2024-01-24 14:03:01,151] [INFO] Query marker FASTA was written to GCF_020905375.1_ASM2090537v1_genomic.fna/markers.fasta
[2024-01-24 14:03:01,152] [INFO] Task started: Blastn
[2024-01-24 14:03:01,152] [INFO] Running command: blastn -query GCF_020905375.1_ASM2090537v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b31724d-13b8-4a98-a245-5979553b74ed/dqc_reference/reference_markers.fasta -out GCF_020905375.1_ASM2090537v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:02,070] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:02,073] [INFO] Selected 16 target genomes.
[2024-01-24 14:03:02,074] [INFO] Target genome list was writen to GCF_020905375.1_ASM2090537v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:02,085] [INFO] Task started: fastANI
[2024-01-24 14:03:02,085] [INFO] Running command: fastANI --query /var/lib/cwl/stga5466dfc-9553-4932-a97f-9157f38b1bef/GCF_020905375.1_ASM2090537v1_genomic.fna.gz --refList GCF_020905375.1_ASM2090537v1_genomic.fna/target_genomes.txt --output GCF_020905375.1_ASM2090537v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:14,652] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:14,653] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b31724d-13b8-4a98-a245-5979553b74ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:14,653] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b31724d-13b8-4a98-a245-5979553b74ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:14,669] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:03:14,669] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:03:14,670] [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 cryoconiti	strain=Cr6-08	GCA_020905375.1	748907	748907	type	True	100.0	1172	1173	95	conclusive
Arthrobacter psychrochitiniphilus	strain=DSM 23143	GCA_013408645.1	291045	291045	type	True	79.0606	290	1173	95	below_threshold
Arthrobacter psychrochitiniphilus	strain=GP3	GCA_003185915.1	291045	291045	type	True	79.003	293	1173	95	below_threshold
Arthrobacter livingstonensis	strain=LI2	GCA_003219815.1	670078	670078	type	True	78.9976	437	1173	95	below_threshold
Arthrobacter silviterrae	strain=DSM 27180	GCA_011045165.1	2026658	2026658	type	True	78.9413	410	1173	95	below_threshold
Arthrobacter wenxiniae	strain=AETb3-4	GCA_013376105.1	2713570	2713570	type	True	78.7673	386	1173	95	below_threshold
Arthrobacter dokdonellae		GCA_003268655.1	2211210	2211210	type	True	78.7547	411	1173	95	below_threshold
Arthrobacter alpinus	strain=DSM 22274	GCA_900105965.1	656366	656366	suspected-type	True	78.7274	331	1173	95	below_threshold
Arthrobacter glacialis	strain=HLT2-12-2	GCA_002909445.1	1664	1664	type	True	78.7059	354	1173	95	below_threshold
Arthrobacter psychrolactophilus	strain=B7	GCA_003219795.1	92442	92442	type	True	78.6839	295	1173	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	77.5961	116	1173	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	76.5277	109	1173	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:14,672] [INFO] DFAST Taxonomy check result was written to GCF_020905375.1_ASM2090537v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:14,672] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:14,672] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:14,672] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b31724d-13b8-4a98-a245-5979553b74ed/dqc_reference/checkm_data
[2024-01-24 14:03:14,674] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:14,749] [INFO] Task started: CheckM
[2024-01-24 14:03:14,750] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020905375.1_ASM2090537v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020905375.1_ASM2090537v1_genomic.fna/checkm_input GCF_020905375.1_ASM2090537v1_genomic.fna/checkm_result
[2024-01-24 14:03:51,807] [INFO] Task succeeded: CheckM
[2024-01-24 14:03:51,808] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:03:51,829] [INFO] ===== Completeness check finished =====
[2024-01-24 14:03:51,830] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:03:51,830] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020905375.1_ASM2090537v1_genomic.fna/markers.fasta)
[2024-01-24 14:03:51,831] [INFO] Task started: Blastn
[2024-01-24 14:03:51,831] [INFO] Running command: blastn -query GCF_020905375.1_ASM2090537v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b31724d-13b8-4a98-a245-5979553b74ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_020905375.1_ASM2090537v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:52,980] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:52,984] [INFO] Selected 18 target genomes.
[2024-01-24 14:03:52,985] [INFO] Target genome list was writen to GCF_020905375.1_ASM2090537v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:03:53,004] [INFO] Task started: fastANI
[2024-01-24 14:03:53,004] [INFO] Running command: fastANI --query /var/lib/cwl/stga5466dfc-9553-4932-a97f-9157f38b1bef/GCF_020905375.1_ASM2090537v1_genomic.fna.gz --refList GCF_020905375.1_ASM2090537v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020905375.1_ASM2090537v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:04:06,543] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:06,558] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:04:06,558] [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_001294625.1	s__Specibacter alpinus_A	79.2786	405	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	99.52	99.48	0.93	0.92	3	-
GCF_001281315.1	s__Specibacter sp001281315	79.2287	386	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017353415.1	s__Specibacter sp017353415	79.111	316	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003185915.1	s__Specibacter psychrochitiniphilus	79.033	291	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002929305.1	s__Specibacter sp002929305	78.9982	386	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003219815.1	s__Specibacter livingstonensis	78.9873	438	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013376095.1	s__Specibacter sp013376095	78.9641	362	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011045165.1	s__Specibacter silviterrae	78.9364	411	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013376105.1	s__Specibacter sp013376105	78.7639	385	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000785535.1	s__Specibacter sp000785535	78.7583	343	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003268655.1	s__Specibacter dokdonellae	78.7441	412	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002909445.1	s__Specibacter glacialis	78.7337	353	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	99.29	99.29	0.92	0.92	2	-
GCF_900105965.1	s__Specibacter alpinus	78.7274	331	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	96.92	96.92	0.91	0.91	2	-
GCF_003219795.1	s__Specibacter psychrolactophilus	78.6839	295	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001445575.1	s__Specibacter alpinus_C	78.6719	340	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876675.1	s__Specibacter stackebrandtii	78.6659	340	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002929705.1	s__Specibacter sp002929705	78.6299	339	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482545.1	s__Specibacter sp000482545	78.1008	262	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:04:06,560] [INFO] GTDB search result was written to GCF_020905375.1_ASM2090537v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:04:06,561] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:04:06,565] [INFO] DFAST_QC result json was written to GCF_020905375.1_ASM2090537v1_genomic.fna/dqc_result.json
[2024-01-24 14:04:06,565] [INFO] DFAST_QC completed!
[2024-01-24 14:04:06,565] [INFO] Total running time: 0h1m18s