[2024-01-24 10:47:06,542] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,544] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,544] [INFO] DQC Reference Directory: /var/lib/cwl/stgc4c96c6f-3016-46bf-a321-e9f1d30b5729/dqc_reference
[2024-01-24 10:47:12,100] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,104] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,105] [INFO] Running command: gunzip -c /var/lib/cwl/stg04444618-c413-40d9-91d5-3ba07e62ec55/GCF_026011795.1_ASM2601179v1_genomic.fna.gz | prodigal -d GCF_026011795.1_ASM2601179v1_genomic.fna/cds.fna -a GCF_026011795.1_ASM2601179v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:24,337] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:24,337] [INFO] Task started: HMMsearch
[2024-01-24 10:47:24,337] [INFO] Running command: hmmsearch --tblout GCF_026011795.1_ASM2601179v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc4c96c6f-3016-46bf-a321-e9f1d30b5729/dqc_reference/reference_markers.hmm GCF_026011795.1_ASM2601179v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:24,651] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:24,652] [INFO] Found 6/6 markers.
[2024-01-24 10:47:24,697] [INFO] Query marker FASTA was written to GCF_026011795.1_ASM2601179v1_genomic.fna/markers.fasta
[2024-01-24 10:47:24,697] [INFO] Task started: Blastn
[2024-01-24 10:47:24,698] [INFO] Running command: blastn -query GCF_026011795.1_ASM2601179v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4c96c6f-3016-46bf-a321-e9f1d30b5729/dqc_reference/reference_markers.fasta -out GCF_026011795.1_ASM2601179v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:25,854] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:25,858] [INFO] Selected 20 target genomes.
[2024-01-24 10:47:25,858] [INFO] Target genome list was writen to GCF_026011795.1_ASM2601179v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:25,867] [INFO] Task started: fastANI
[2024-01-24 10:47:25,867] [INFO] Running command: fastANI --query /var/lib/cwl/stg04444618-c413-40d9-91d5-3ba07e62ec55/GCF_026011795.1_ASM2601179v1_genomic.fna.gz --refList GCF_026011795.1_ASM2601179v1_genomic.fna/target_genomes.txt --output GCF_026011795.1_ASM2601179v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:41,906] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:41,906] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc4c96c6f-3016-46bf-a321-e9f1d30b5729/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:41,907] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc4c96c6f-3016-46bf-a321-e9f1d30b5729/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:41,922] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:47:41,922] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:47:41,923] [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 crystallopoietes	strain=DSM 20117	GCA_900100805.1	37928	37928	type	True	80.7317	803	1449	95	below_threshold
Arthrobacter crystallopoietes	strain=DSM 20117	GCA_002849715.1	37928	37928	type	True	80.661	803	1449	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	80.6303	725	1449	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	78.9528	398	1449	95	below_threshold
Arthrobacter celericrescens	strain=NEAU-SA2	GCA_003614925.1	2320851	2320851	type	True	78.9356	450	1449	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	78.921	405	1449	95	below_threshold
Arthrobacter citreus	strain=DSM 20133	GCA_009192745.1	1670	1670	type	True	78.9011	382	1449	95	below_threshold
Arthrobacter yangruifuii	strain=785	GCA_009192775.1	2606616	2606616	type	True	78.7785	375	1449	95	below_threshold
Pseudarthrobacter siccitolerans	strain=4J27	GCA_001046895.1	861266	861266	type	True	78.7142	386	1449	95	below_threshold
Arthrobacter globiformis	strain=NBRC 12137	GCA_000238915.2	1665	1665	type	True	78.7037	457	1449	95	below_threshold
Arthrobacter koreensis	strain=DSM 16760	GCA_009193255.1	199136	199136	type	True	78.6879	386	1449	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	78.6301	372	1449	95	below_threshold
Pseudarthrobacter polychromogenes	strain=CGMCC 1.1927	GCA_014644495.1	1676	1676	type	True	78.6156	408	1449	95	below_threshold
Zhihengliuella salsuginis	strain=KCTC 19466	GCA_014651715.1	578222	578222	type	True	78.5234	372	1449	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	78.3645	372	1449	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_017353495.1	2816859	2816859	type	True	78.3612	367	1449	95	below_threshold
Arthrobacter crusticola	strain=SLN-3	GCA_004357995.1	2547960	2547960	type	True	78.3347	382	1449	95	below_threshold
Tersicoccus solisilvae	strain=CGMCC 1.15480	GCA_014643255.1	1882339	1882339	type	True	78.3085	374	1449	95	below_threshold
Zhihengliuella halotolerans	strain=DSM 17364	GCA_004217565.1	370736	370736	type	True	78.1622	342	1449	95	below_threshold
Citricoccus muralis	strain=DSM 14442	GCA_003386075.1	169134	169134	type	True	78.1551	293	1449	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:41,925] [INFO] DFAST Taxonomy check result was written to GCF_026011795.1_ASM2601179v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:41,925] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:41,925] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:41,926] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc4c96c6f-3016-46bf-a321-e9f1d30b5729/dqc_reference/checkm_data
[2024-01-24 10:47:41,927] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:41,970] [INFO] Task started: CheckM
[2024-01-24 10:47:41,970] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026011795.1_ASM2601179v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026011795.1_ASM2601179v1_genomic.fna/checkm_input GCF_026011795.1_ASM2601179v1_genomic.fna/checkm_result
[2024-01-24 10:48:20,165] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:20,166] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:20,183] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:20,183] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:20,184] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026011795.1_ASM2601179v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:20,184] [INFO] Task started: Blastn
[2024-01-24 10:48:20,184] [INFO] Running command: blastn -query GCF_026011795.1_ASM2601179v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4c96c6f-3016-46bf-a321-e9f1d30b5729/dqc_reference/reference_markers_gtdb.fasta -out GCF_026011795.1_ASM2601179v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:21,924] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:21,927] [INFO] Selected 21 target genomes.
[2024-01-24 10:48:21,927] [INFO] Target genome list was writen to GCF_026011795.1_ASM2601179v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:21,942] [INFO] Task started: fastANI
[2024-01-24 10:48:21,942] [INFO] Running command: fastANI --query /var/lib/cwl/stg04444618-c413-40d9-91d5-3ba07e62ec55/GCF_026011795.1_ASM2601179v1_genomic.fna.gz --refList GCF_026011795.1_ASM2601179v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026011795.1_ASM2601179v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:39,064] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:39,080] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:48:39,081] [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_000328305.2	s__Arthrobacter_F crystallopoietes_A	83.9841	912	1449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017603825.1	s__Arthrobacter_F crystallopoietes_B	80.7182	746	1449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_F	95.0	98.89	98.89	0.92	0.92	2	-
GCF_002849715.1	s__Arthrobacter_F crystallopoietes	80.6686	802	1449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_F	95.0	100.00	100.00	0.99	0.99	2	-
GCF_012395835.1	s__Arthrobacter_F mobilis	80.5992	729	1449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012952295.1	s__Arthrobacter_F sp012952295	80.5783	750	1449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005047635.1	s__Arthrobacter_F sp005047635	80.2355	643	1449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004000035.1	s__Arthrobacter_F sulfonylureivorans	80.2276	631	1449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900016675.1	s__Arthrobacter_B saudimassiliensis	79.4758	479	1449	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_008580665.1	s__Zafaria cholistanensis	79.0349	430	1449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Zafaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007858535.1	s__Arthrobacter_I sp007858535	78.9962	475	1449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428365.1	s__Arthrobacter_I sp001428365	78.9679	479	1449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946885.1	s__Specibacter cremeus	78.9347	436	1449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009192775.1	s__Arthrobacter_B yangruifuii	78.7782	375	1449	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_001512305.1	s__Arthrobacter_I sp001512305	78.7013	486	1449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715165.1	s__Pseudarthrobacter sp006715165	78.6337	433	1449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003208335.1	s__Pseudarthrobacter sp003208335	78.5815	418	1449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002929375.1	s__Arthrobacter_D sp002929375	78.5269	376	1449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374905.1	s__Pseudarthrobacter sp000374905	78.4958	430	1449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	98.45	96.91	0.92	0.90	5	-
GCF_001307035.1	s__Arthrobacter_B sp001307035	78.4562	360	1449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	98.39	98.39	0.92	0.92	2	-
GCF_001968825.1	s__Tersicoccus sp001968825	78.4179	362	1449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Tersicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013376095.1	s__Specibacter sp013376095	78.2859	398	1449	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 10:48:39,082] [INFO] GTDB search result was written to GCF_026011795.1_ASM2601179v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:39,083] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:39,087] [INFO] DFAST_QC result json was written to GCF_026011795.1_ASM2601179v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:39,087] [INFO] DFAST_QC completed!
[2024-01-24 10:48:39,087] [INFO] Total running time: 0h1m33s