[2024-01-24 11:05:03,929] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:03,930] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:03,931] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc8e97ad-b672-4ad8-8239-cdc078f1552f/dqc_reference
[2024-01-24 11:05:05,762] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:05,763] [INFO] Task started: Prodigal
[2024-01-24 11:05:05,763] [INFO] Running command: gunzip -c /var/lib/cwl/stg602a6dea-ca59-4b84-bf0b-1cf683f3b4fc/GCF_016820535.1_ASM1682053v1_genomic.fna.gz | prodigal -d GCF_016820535.1_ASM1682053v1_genomic.fna/cds.fna -a GCF_016820535.1_ASM1682053v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:19,052] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:19,053] [INFO] Task started: HMMsearch
[2024-01-24 11:05:19,053] [INFO] Running command: hmmsearch --tblout GCF_016820535.1_ASM1682053v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc8e97ad-b672-4ad8-8239-cdc078f1552f/dqc_reference/reference_markers.hmm GCF_016820535.1_ASM1682053v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:19,315] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:19,317] [INFO] Found 6/6 markers.
[2024-01-24 11:05:19,350] [INFO] Query marker FASTA was written to GCF_016820535.1_ASM1682053v1_genomic.fna/markers.fasta
[2024-01-24 11:05:19,351] [INFO] Task started: Blastn
[2024-01-24 11:05:19,351] [INFO] Running command: blastn -query GCF_016820535.1_ASM1682053v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc8e97ad-b672-4ad8-8239-cdc078f1552f/dqc_reference/reference_markers.fasta -out GCF_016820535.1_ASM1682053v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:20,267] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:20,270] [INFO] Selected 14 target genomes.
[2024-01-24 11:05:20,270] [INFO] Target genome list was writen to GCF_016820535.1_ASM1682053v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:20,275] [INFO] Task started: fastANI
[2024-01-24 11:05:20,275] [INFO] Running command: fastANI --query /var/lib/cwl/stg602a6dea-ca59-4b84-bf0b-1cf683f3b4fc/GCF_016820535.1_ASM1682053v1_genomic.fna.gz --refList GCF_016820535.1_ASM1682053v1_genomic.fna/target_genomes.txt --output GCF_016820535.1_ASM1682053v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:32,826] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:32,827] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc8e97ad-b672-4ad8-8239-cdc078f1552f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:32,827] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc8e97ad-b672-4ad8-8239-cdc078f1552f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:32,837] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:05:32,837] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:05:32,837] [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 stackebrandtii	strain=DSM 16005	GCA_017876675.1	272161	272161	type	True	88.773	1140	1387	95	below_threshold
Arthrobacter wenxiniae	strain=AETb3-4	GCA_013376105.1	2713570	2713570	type	True	81.5946	719	1387	95	below_threshold
Arthrobacter dokdonellae		GCA_003268655.1	2211210	2211210	type	True	81.3331	709	1387	95	below_threshold
Arthrobacter silviterrae	strain=DSM 27180	GCA_011045165.1	2026658	2026658	type	True	81.3217	747	1387	95	below_threshold
Arthrobacter glacialis	strain=HLT2-12-2	GCA_002909445.1	1664	1664	type	True	81.1204	705	1387	95	below_threshold
Arthrobacter alpinus	strain=DSM 22274	GCA_900105965.1	656366	656366	suspected-type	True	81.1093	695	1387	95	below_threshold
Arthrobacter livingstonensis	strain=LI2	GCA_003219815.1	670078	670078	type	True	81.0427	757	1387	95	below_threshold
Arthrobacter psychrochitiniphilus	strain=DSM 23143	GCA_013408645.1	291045	291045	type	True	80.6958	645	1387	95	below_threshold
Arthrobacter psychrochitiniphilus	strain=GP3	GCA_003185915.1	291045	291045	type	True	80.5932	637	1387	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	79.4036	331	1387	95	below_threshold
Arthrobacter cupressi	strain=DSM 24664	GCA_013409905.1	1045773	1045773	type	True	79.1109	408	1387	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	78.863	317	1387	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	78.8082	318	1387	95	below_threshold
Paenarthrobacter nicotinovorans	strain=ATCC 49919	GCA_021919345.1	29320	29320	suspected-type	True	78.4418	343	1387	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:32,839] [INFO] DFAST Taxonomy check result was written to GCF_016820535.1_ASM1682053v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:32,839] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:32,839] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:32,840] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc8e97ad-b672-4ad8-8239-cdc078f1552f/dqc_reference/checkm_data
[2024-01-24 11:05:32,840] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:32,883] [INFO] Task started: CheckM
[2024-01-24 11:05:32,883] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016820535.1_ASM1682053v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016820535.1_ASM1682053v1_genomic.fna/checkm_input GCF_016820535.1_ASM1682053v1_genomic.fna/checkm_result
[2024-01-24 11:06:14,914] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:14,915] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:14,929] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:14,929] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:14,930] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016820535.1_ASM1682053v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:14,930] [INFO] Task started: Blastn
[2024-01-24 11:06:14,930] [INFO] Running command: blastn -query GCF_016820535.1_ASM1682053v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc8e97ad-b672-4ad8-8239-cdc078f1552f/dqc_reference/reference_markers_gtdb.fasta -out GCF_016820535.1_ASM1682053v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:16,391] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:16,394] [INFO] Selected 11 target genomes.
[2024-01-24 11:06:16,394] [INFO] Target genome list was writen to GCF_016820535.1_ASM1682053v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:16,416] [INFO] Task started: fastANI
[2024-01-24 11:06:16,416] [INFO] Running command: fastANI --query /var/lib/cwl/stg602a6dea-ca59-4b84-bf0b-1cf683f3b4fc/GCF_016820535.1_ASM1682053v1_genomic.fna.gz --refList GCF_016820535.1_ASM1682053v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016820535.1_ASM1682053v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:27,090] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:27,097] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:27,098] [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_016820535.1	s__Specibacter sp016820535	100.0	1383	1387	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017876675.1	s__Specibacter stackebrandtii	88.773	1140	1387	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	83.5558	953	1387	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	81.9338	753	1387	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	81.6455	717	1387	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	81.5941	719	1387	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	81.3124	748	1387	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	81.2958	713	1387	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	81.1141	706	1387	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	80.9129	602	1387	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	80.5992	636	1387	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:27,100] [INFO] GTDB search result was written to GCF_016820535.1_ASM1682053v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:27,100] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:27,103] [INFO] DFAST_QC result json was written to GCF_016820535.1_ASM1682053v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:27,103] [INFO] DFAST_QC completed!
[2024-01-24 11:06:27,103] [INFO] Total running time: 0h1m23s