[2024-01-24 12:14:35,731] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:35,733] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:35,733] [INFO] DQC Reference Directory: /var/lib/cwl/stgf9f45151-b07b-4673-9fa7-45ad5454bbbc/dqc_reference
[2024-01-24 12:14:37,000] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:37,001] [INFO] Task started: Prodigal
[2024-01-24 12:14:37,002] [INFO] Running command: gunzip -c /var/lib/cwl/stg75c363d0-d75f-4408-935e-8315c170a5b6/GCF_002849715.1_ASM284971v1_genomic.fna.gz | prodigal -d GCF_002849715.1_ASM284971v1_genomic.fna/cds.fna -a GCF_002849715.1_ASM284971v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:52,097] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:52,097] [INFO] Task started: HMMsearch
[2024-01-24 12:14:52,098] [INFO] Running command: hmmsearch --tblout GCF_002849715.1_ASM284971v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf9f45151-b07b-4673-9fa7-45ad5454bbbc/dqc_reference/reference_markers.hmm GCF_002849715.1_ASM284971v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:52,362] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:52,364] [INFO] Found 6/6 markers.
[2024-01-24 12:14:52,403] [INFO] Query marker FASTA was written to GCF_002849715.1_ASM284971v1_genomic.fna/markers.fasta
[2024-01-24 12:14:52,404] [INFO] Task started: Blastn
[2024-01-24 12:14:52,404] [INFO] Running command: blastn -query GCF_002849715.1_ASM284971v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9f45151-b07b-4673-9fa7-45ad5454bbbc/dqc_reference/reference_markers.fasta -out GCF_002849715.1_ASM284971v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:53,344] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:53,348] [INFO] Selected 21 target genomes.
[2024-01-24 12:14:53,349] [INFO] Target genome list was writen to GCF_002849715.1_ASM284971v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:53,357] [INFO] Task started: fastANI
[2024-01-24 12:14:53,357] [INFO] Running command: fastANI --query /var/lib/cwl/stg75c363d0-d75f-4408-935e-8315c170a5b6/GCF_002849715.1_ASM284971v1_genomic.fna.gz --refList GCF_002849715.1_ASM284971v1_genomic.fna/target_genomes.txt --output GCF_002849715.1_ASM284971v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:10,945] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:10,945] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf9f45151-b07b-4673-9fa7-45ad5454bbbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:10,946] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf9f45151-b07b-4673-9fa7-45ad5454bbbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:10,962] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:15:10,962] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:10,962] [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_002849715.1	37928	37928	type	True	100.0	1669	1676	95	conclusive
Arthrobacter crystallopoietes	strain=DSM 20117	GCA_900100805.1	37928	37928	type	True	99.9956	1655	1676	95	conclusive
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	79.9473	675	1676	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	79.1928	367	1676	95	below_threshold
Pseudarthrobacter chlorophenolicus	strain=A6	GCA_000022025.1	85085	85085	type	True	78.9813	399	1676	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	78.9481	403	1676	95	below_threshold
Pseudarthrobacter chlorophenolicus	strain=A6	GCA_900104315.1	85085	85085	type	True	78.8591	403	1676	95	below_threshold
Arthrobacter koreensis	strain=DSM 16760	GCA_009193255.1	199136	199136	type	True	78.8563	356	1676	95	below_threshold
Arthrobacter yangruifuii	strain=785	GCA_009192775.1	2606616	2606616	type	True	78.846	345	1676	95	below_threshold
Arthrobacter citreus	strain=DSM 20133	GCA_009192745.1	1670	1670	type	True	78.8263	348	1676	95	below_threshold
Pseudarthrobacter phenanthrenivorans	strain=Sphe3	GCA_000189535.1	361575	361575	type	True	78.7911	384	1676	95	below_threshold
Arthrobacter dokdonellae		GCA_003268655.1	2211210	2211210	type	True	78.7581	374	1676	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_017353495.1	2816859	2816859	type	True	78.7541	349	1676	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	78.7462	393	1676	95	below_threshold
Arthrobacter celericrescens	strain=NEAU-SA2	GCA_003614925.1	2320851	2320851	type	True	78.743	407	1676	95	below_threshold
Arthrobacter gallicola	strain=Sa2CUA1	GCA_014836775.1	2762225	2762225	type	True	78.6158	360	1676	95	below_threshold
Arthrobacter globiformis	strain=NBRC 12137	GCA_000238915.2	1665	1665	type	True	78.5599	415	1676	95	below_threshold
Pseudarthrobacter polychromogenes	strain=CGMCC 1.1927	GCA_014644495.1	1676	1676	type	True	78.5333	377	1676	95	below_threshold
Paeniglutamicibacter cryotolerans	strain=DSM 22826	GCA_014190875.1	670079	670079	type	True	78.533	310	1676	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	78.4709	315	1676	95	below_threshold
Arthrobacter wenxiniae	strain=AETb3-4	GCA_013376105.1	2713570	2713570	type	True	78.2117	367	1676	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:10,965] [INFO] DFAST Taxonomy check result was written to GCF_002849715.1_ASM284971v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:10,966] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:10,966] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:10,967] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf9f45151-b07b-4673-9fa7-45ad5454bbbc/dqc_reference/checkm_data
[2024-01-24 12:15:10,968] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:11,017] [INFO] Task started: CheckM
[2024-01-24 12:15:11,018] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002849715.1_ASM284971v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002849715.1_ASM284971v1_genomic.fna/checkm_input GCF_002849715.1_ASM284971v1_genomic.fna/checkm_result
[2024-01-24 12:15:54,580] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:54,581] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:54,604] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:54,604] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:54,604] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002849715.1_ASM284971v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:54,605] [INFO] Task started: Blastn
[2024-01-24 12:15:54,605] [INFO] Running command: blastn -query GCF_002849715.1_ASM284971v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9f45151-b07b-4673-9fa7-45ad5454bbbc/dqc_reference/reference_markers_gtdb.fasta -out GCF_002849715.1_ASM284971v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:55,975] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:55,979] [INFO] Selected 12 target genomes.
[2024-01-24 12:15:55,979] [INFO] Target genome list was writen to GCF_002849715.1_ASM284971v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:55,997] [INFO] Task started: fastANI
[2024-01-24 12:15:55,997] [INFO] Running command: fastANI --query /var/lib/cwl/stg75c363d0-d75f-4408-935e-8315c170a5b6/GCF_002849715.1_ASM284971v1_genomic.fna.gz --refList GCF_002849715.1_ASM284971v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002849715.1_ASM284971v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:07,223] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:07,233] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:07,233] [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_002849715.1	s__Arthrobacter_F crystallopoietes	100.0	1673	1676	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_F	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_017603825.1	s__Arthrobacter_F crystallopoietes_B	92.1384	1278	1676	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_012952295.1	s__Arthrobacter_F sp012952295	91.7433	1299	1676	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_000328305.2	s__Arthrobacter_F crystallopoietes_A	80.8511	757	1676	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_012395835.1	s__Arthrobacter_F mobilis	79.9254	677	1676	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	79.9058	632	1676	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	79.8995	644	1676	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_001428365.1	s__Arthrobacter_I sp001428365	78.995	423	1676	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900016675.1	s__Arthrobacter_B saudimassiliensis	78.8608	445	1676	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_900168295.1	s__Pseudarthrobacter sp900168295	78.7362	380	1676	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	98.77	97.56	0.93	0.89	3	-
GCF_003614925.1	s__Arthrobacter_G celericrescens	78.7322	408	1676	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613755.1	s__Arthrobacter_I sp018613755	78.5557	396	1676	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:07,235] [INFO] GTDB search result was written to GCF_002849715.1_ASM284971v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:07,235] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:07,239] [INFO] DFAST_QC result json was written to GCF_002849715.1_ASM284971v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:07,239] [INFO] DFAST_QC completed!
[2024-01-24 12:16:07,240] [INFO] Total running time: 0h1m32s