[2024-01-24 11:43:40,707] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:40,710] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:40,711] [INFO] DQC Reference Directory: /var/lib/cwl/stg09771bce-a1b8-4215-b0d0-1d4c8a0c6c7c/dqc_reference
[2024-01-24 11:43:42,076] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:42,076] [INFO] Task started: Prodigal
[2024-01-24 11:43:42,077] [INFO] Running command: gunzip -c /var/lib/cwl/stg66e01349-db64-4ee1-b228-c88b323ac7de/GCF_022869865.1_ASM2286986v1_genomic.fna.gz | prodigal -d GCF_022869865.1_ASM2286986v1_genomic.fna/cds.fna -a GCF_022869865.1_ASM2286986v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:53,100] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:53,100] [INFO] Task started: HMMsearch
[2024-01-24 11:43:53,100] [INFO] Running command: hmmsearch --tblout GCF_022869865.1_ASM2286986v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09771bce-a1b8-4215-b0d0-1d4c8a0c6c7c/dqc_reference/reference_markers.hmm GCF_022869865.1_ASM2286986v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:53,415] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:53,416] [INFO] Found 6/6 markers.
[2024-01-24 11:43:53,466] [INFO] Query marker FASTA was written to GCF_022869865.1_ASM2286986v1_genomic.fna/markers.fasta
[2024-01-24 11:43:53,466] [INFO] Task started: Blastn
[2024-01-24 11:43:53,466] [INFO] Running command: blastn -query GCF_022869865.1_ASM2286986v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09771bce-a1b8-4215-b0d0-1d4c8a0c6c7c/dqc_reference/reference_markers.fasta -out GCF_022869865.1_ASM2286986v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:54,662] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:54,665] [INFO] Selected 15 target genomes.
[2024-01-24 11:43:54,665] [INFO] Target genome list was writen to GCF_022869865.1_ASM2286986v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:54,671] [INFO] Task started: fastANI
[2024-01-24 11:43:54,672] [INFO] Running command: fastANI --query /var/lib/cwl/stg66e01349-db64-4ee1-b228-c88b323ac7de/GCF_022869865.1_ASM2286986v1_genomic.fna.gz --refList GCF_022869865.1_ASM2286986v1_genomic.fna/target_genomes.txt --output GCF_022869865.1_ASM2286986v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:06,068] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:06,069] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09771bce-a1b8-4215-b0d0-1d4c8a0c6c7c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:06,069] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09771bce-a1b8-4215-b0d0-1d4c8a0c6c7c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:06,088] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:44:06,089] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:44:06,089] [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 yangruifuii	strain=785	GCA_009192775.1	2606616	2606616	type	True	83.7016	835	1154	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	81.3027	603	1154	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	81.2647	682	1154	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_017353495.1	2816859	2816859	type	True	81.2106	594	1154	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	81.1417	654	1154	95	below_threshold
Arthrobacter gandavensis	strain=JCM 13316	GCA_009192735.1	169960	169960	type	True	80.8974	599	1154	95	below_threshold
Arthrobacter citreus	strain=DSM 20133	GCA_009192745.1	1670	1670	type	True	80.7562	560	1154	95	below_threshold
Arthrobacter koreensis	strain=DSM 16760	GCA_009193255.1	199136	199136	type	True	80.6902	547	1154	95	below_threshold
Arthrobacter luteolus	strain=DSM 13067	GCA_008973725.1	98672	98672	type	True	80.5999	566	1154	95	below_threshold
Arthrobacter pullicola	strain=Sa2BUA2	GCA_014836875.1	2762224	2762224	type	True	80.4622	553	1154	95	below_threshold
Arthrobacter gallicola	strain=Sa2CUA1	GCA_014836775.1	2762225	2762225	type	True	80.2625	563	1154	95	below_threshold
Arthrobacter dokdonellae		GCA_003268655.1	2211210	2211210	type	True	78.6438	325	1154	95	below_threshold
Paeniglutamicibacter psychrophenolicus	strain=DSM 15454	GCA_017876575.1	257454	257454	type	True	78.4551	300	1154	95	below_threshold
Glutamicibacter mishrai	strain=S5-52	GCA_012221945.1	1775880	1775880	type	True	78.3026	182	1154	95	below_threshold
Paeniglutamicibacter terrestris	strain=ANT13_2	GCA_012271785.1	2723403	2723403	type	True	77.7194	186	1154	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:06,091] [INFO] DFAST Taxonomy check result was written to GCF_022869865.1_ASM2286986v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:06,091] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:06,092] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:06,092] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09771bce-a1b8-4215-b0d0-1d4c8a0c6c7c/dqc_reference/checkm_data
[2024-01-24 11:44:06,093] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:06,138] [INFO] Task started: CheckM
[2024-01-24 11:44:06,138] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022869865.1_ASM2286986v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022869865.1_ASM2286986v1_genomic.fna/checkm_input GCF_022869865.1_ASM2286986v1_genomic.fna/checkm_result
[2024-01-24 11:44:41,176] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:41,177] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:41,195] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:41,196] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:41,196] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022869865.1_ASM2286986v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:41,196] [INFO] Task started: Blastn
[2024-01-24 11:44:41,197] [INFO] Running command: blastn -query GCF_022869865.1_ASM2286986v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09771bce-a1b8-4215-b0d0-1d4c8a0c6c7c/dqc_reference/reference_markers_gtdb.fasta -out GCF_022869865.1_ASM2286986v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:42,843] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:42,847] [INFO] Selected 15 target genomes.
[2024-01-24 11:44:42,848] [INFO] Target genome list was writen to GCF_022869865.1_ASM2286986v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:42,875] [INFO] Task started: fastANI
[2024-01-24 11:44:42,875] [INFO] Running command: fastANI --query /var/lib/cwl/stg66e01349-db64-4ee1-b228-c88b323ac7de/GCF_022869865.1_ASM2286986v1_genomic.fna.gz --refList GCF_022869865.1_ASM2286986v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022869865.1_ASM2286986v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:54,098] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:54,118] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:44:54,118] [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_009192775.1	s__Arthrobacter_B yangruifuii	83.7132	833	1154	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_018622995.1	s__Arthrobacter_B sp018622995	81.289	684	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	99.13	98.27	0.96	0.92	3	-
GCF_018866305.1	s__Arthrobacter_B sp002929435	81.2836	603	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	98.36	96.67	0.94	0.92	8	-
GCF_009192735.1	s__Arthrobacter_B gandavensis	80.876	601	1154	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_009192745.1	s__Arthrobacter_B citreus	80.749	561	1154	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_009193255.1	s__Arthrobacter_B koreensis	80.6902	547	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	99.08	99.08	0.97	0.97	2	-
GCF_015355785.1	s__Arthrobacter_B gandavensis_A	80.5751	560	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900016675.1	s__Arthrobacter_B saudimassiliensis	80.5592	620	1154	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_001307035.1	s__Arthrobacter_B sp001307035	80.5444	544	1154	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_014836875.1	s__Arthrobacter_B sp014836875	80.4473	554	1154	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_014836775.1	s__Arthrobacter_B sp014836775	80.2513	563	1154	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_012395835.1	s__Arthrobacter_F mobilis	78.8792	375	1154	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_003268655.1	s__Specibacter dokdonellae	78.5702	325	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428075.1	s__Pseudarthrobacter sp001428075	78.4676	333	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374905.1	s__Pseudarthrobacter sp000374905	78.3474	341	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	98.45	96.91	0.92	0.90	5	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:54,120] [INFO] GTDB search result was written to GCF_022869865.1_ASM2286986v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:54,121] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:54,124] [INFO] DFAST_QC result json was written to GCF_022869865.1_ASM2286986v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:54,124] [INFO] DFAST_QC completed!
[2024-01-24 11:44:54,125] [INFO] Total running time: 0h1m13s