[2024-01-24 15:18:50,745] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:50,748] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:50,748] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c21798f-5577-4a66-a775-c8e10ce8b38a/dqc_reference
[2024-01-24 15:18:52,173] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:52,174] [INFO] Task started: Prodigal
[2024-01-24 15:18:52,174] [INFO] Running command: gunzip -c /var/lib/cwl/stgc911f306-fff5-4f92-a0d5-0da779d3cc62/GCF_013408645.1_ASM1340864v1_genomic.fna.gz | prodigal -d GCF_013408645.1_ASM1340864v1_genomic.fna/cds.fna -a GCF_013408645.1_ASM1340864v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:06,952] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:06,953] [INFO] Task started: HMMsearch
[2024-01-24 15:19:06,953] [INFO] Running command: hmmsearch --tblout GCF_013408645.1_ASM1340864v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c21798f-5577-4a66-a775-c8e10ce8b38a/dqc_reference/reference_markers.hmm GCF_013408645.1_ASM1340864v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:07,241] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:07,242] [INFO] Found 6/6 markers.
[2024-01-24 15:19:07,288] [INFO] Query marker FASTA was written to GCF_013408645.1_ASM1340864v1_genomic.fna/markers.fasta
[2024-01-24 15:19:07,289] [INFO] Task started: Blastn
[2024-01-24 15:19:07,289] [INFO] Running command: blastn -query GCF_013408645.1_ASM1340864v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c21798f-5577-4a66-a775-c8e10ce8b38a/dqc_reference/reference_markers.fasta -out GCF_013408645.1_ASM1340864v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:08,165] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:08,169] [INFO] Selected 14 target genomes.
[2024-01-24 15:19:08,170] [INFO] Target genome list was writen to GCF_013408645.1_ASM1340864v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:08,176] [INFO] Task started: fastANI
[2024-01-24 15:19:08,177] [INFO] Running command: fastANI --query /var/lib/cwl/stgc911f306-fff5-4f92-a0d5-0da779d3cc62/GCF_013408645.1_ASM1340864v1_genomic.fna.gz --refList GCF_013408645.1_ASM1340864v1_genomic.fna/target_genomes.txt --output GCF_013408645.1_ASM1340864v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:19,911] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:19,912] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c21798f-5577-4a66-a775-c8e10ce8b38a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:19,912] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c21798f-5577-4a66-a775-c8e10ce8b38a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:19,924] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:19:19,924] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:19,925] [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 psychrochitiniphilus	strain=DSM 23143	GCA_013408645.1	291045	291045	type	True	100.0	1366	1367	95	conclusive
Arthrobacter psychrochitiniphilus	strain=GP3	GCA_003185915.1	291045	291045	type	True	99.9832	1330	1367	95	conclusive
Arthrobacter stackebrandtii	strain=DSM 16005	GCA_017876675.1	272161	272161	type	True	80.9191	691	1367	95	below_threshold
Arthrobacter alpinus	strain=DSM 22274	GCA_900105965.1	656366	656366	suspected-type	True	80.5707	602	1367	95	below_threshold
Arthrobacter glacialis	strain=HLT2-12-2	GCA_002909445.1	1664	1664	type	True	80.4582	611	1367	95	below_threshold
Arthrobacter psychrolactophilus	strain=B7	GCA_003219795.1	92442	92442	type	True	80.1351	513	1367	95	below_threshold
Arthrobacter livingstonensis	strain=LI2	GCA_003219815.1	670078	670078	type	True	79.5011	569	1367	95	below_threshold
Arthrobacter wenxiniae	strain=AETb3-4	GCA_013376105.1	2713570	2713570	type	True	79.3023	507	1367	95	below_threshold
Arthrobacter cryoconiti	strain=Cr6-08	GCA_020905375.1	748907	748907	type	True	78.7995	302	1367	95	below_threshold
Arthrobacter cupressi	strain=DSM 24664	GCA_013409905.1	1045773	1045773	type	True	78.723	220	1367	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	78.7151	182	1367	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	78.4048	202	1367	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_017353495.1	2816859	2816859	type	True	78.0282	200	1367	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	77.1877	165	1367	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:19,926] [INFO] DFAST Taxonomy check result was written to GCF_013408645.1_ASM1340864v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:19,927] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:19,927] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:19,927] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c21798f-5577-4a66-a775-c8e10ce8b38a/dqc_reference/checkm_data
[2024-01-24 15:19:19,928] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:19,972] [INFO] Task started: CheckM
[2024-01-24 15:19:19,972] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013408645.1_ASM1340864v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013408645.1_ASM1340864v1_genomic.fna/checkm_input GCF_013408645.1_ASM1340864v1_genomic.fna/checkm_result
[2024-01-24 15:20:02,113] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:02,114] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:02,135] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:02,135] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:02,135] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013408645.1_ASM1340864v1_genomic.fna/markers.fasta)
[2024-01-24 15:20:02,136] [INFO] Task started: Blastn
[2024-01-24 15:20:02,136] [INFO] Running command: blastn -query GCF_013408645.1_ASM1340864v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c21798f-5577-4a66-a775-c8e10ce8b38a/dqc_reference/reference_markers_gtdb.fasta -out GCF_013408645.1_ASM1340864v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:03,356] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:03,360] [INFO] Selected 12 target genomes.
[2024-01-24 15:20:03,360] [INFO] Target genome list was writen to GCF_013408645.1_ASM1340864v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:03,376] [INFO] Task started: fastANI
[2024-01-24 15:20:03,377] [INFO] Running command: fastANI --query /var/lib/cwl/stgc911f306-fff5-4f92-a0d5-0da779d3cc62/GCF_013408645.1_ASM1340864v1_genomic.fna.gz --refList GCF_013408645.1_ASM1340864v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013408645.1_ASM1340864v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:14,150] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:14,168] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:14,168] [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_003185915.1	s__Specibacter psychrochitiniphilus	99.9832	1330	1367	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001445575.1	s__Specibacter alpinus_C	81.2407	726	1367	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	80.9507	711	1367	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	80.9261	688	1367	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	80.9019	692	1367	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016820535.1	s__Specibacter sp016820535	80.7296	645	1367	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105965.1	s__Specibacter alpinus	80.5634	606	1367	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	96.92	96.92	0.91	0.91	2	-
GCF_002909445.1	s__Specibacter glacialis	80.4676	610	1367	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	99.29	99.29	0.92	0.92	2	-
GCF_017353415.1	s__Specibacter sp017353415	80.3403	578	1367	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001281315.1	s__Specibacter sp001281315	80.1568	551	1367	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	79.5012	568	1367	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	79.2977	508	1367	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 15:20:14,170] [INFO] GTDB search result was written to GCF_013408645.1_ASM1340864v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:14,171] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:14,174] [INFO] DFAST_QC result json was written to GCF_013408645.1_ASM1340864v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:14,174] [INFO] DFAST_QC completed!
[2024-01-24 15:20:14,174] [INFO] Total running time: 0h1m23s