[2023-06-14 01:26:53,062] [INFO] DFAST_QC pipeline started.
[2023-06-14 01:26:53,064] [INFO] DFAST_QC version: 0.5.7
[2023-06-14 01:26:53,064] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d9d2bca-8c96-4a96-8dd4-d25b96a75aea/dqc_reference
[2023-06-14 01:26:55,205] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-14 01:26:55,205] [INFO] Task started: Prodigal
[2023-06-14 01:26:55,206] [INFO] Running command: gunzip -c /var/lib/cwl/stgd8347362-3f13-4c99-aad3-51a798fc4743/GCA_022708925.1_ASM2270892v1_genomic.fna.gz | prodigal -d GCA_022708925.1_ASM2270892v1_genomic.fna/cds.fna -a GCA_022708925.1_ASM2270892v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-14 01:27:03,409] [INFO] Task succeeded: Prodigal
[2023-06-14 01:27:03,409] [INFO] Task started: HMMsearch
[2023-06-14 01:27:03,409] [INFO] Running command: hmmsearch --tblout GCA_022708925.1_ASM2270892v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d9d2bca-8c96-4a96-8dd4-d25b96a75aea/dqc_reference/reference_markers.hmm GCA_022708925.1_ASM2270892v1_genomic.fna/protein.faa > /dev/null
[2023-06-14 01:27:03,661] [INFO] Task succeeded: HMMsearch
[2023-06-14 01:27:03,663] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd8347362-3f13-4c99-aad3-51a798fc4743/GCA_022708925.1_ASM2270892v1_genomic.fna.gz]
[2023-06-14 01:27:03,695] [INFO] Query marker FASTA was written to GCA_022708925.1_ASM2270892v1_genomic.fna/markers.fasta
[2023-06-14 01:27:03,695] [INFO] Task started: Blastn
[2023-06-14 01:27:03,696] [INFO] Running command: blastn -query GCA_022708925.1_ASM2270892v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d9d2bca-8c96-4a96-8dd4-d25b96a75aea/dqc_reference/reference_markers.fasta -out GCA_022708925.1_ASM2270892v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:27:04,537] [INFO] Task succeeded: Blastn
[2023-06-14 01:27:04,542] [INFO] Selected 23 target genomes.
[2023-06-14 01:27:04,543] [INFO] Target genome list was writen to GCA_022708925.1_ASM2270892v1_genomic.fna/target_genomes.txt
[2023-06-14 01:27:04,568] [INFO] Task started: fastANI
[2023-06-14 01:27:04,569] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8347362-3f13-4c99-aad3-51a798fc4743/GCA_022708925.1_ASM2270892v1_genomic.fna.gz --refList GCA_022708925.1_ASM2270892v1_genomic.fna/target_genomes.txt --output GCA_022708925.1_ASM2270892v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-14 01:27:17,557] [INFO] Task succeeded: fastANI
[2023-06-14 01:27:17,558] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d9d2bca-8c96-4a96-8dd4-d25b96a75aea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-14 01:27:17,559] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d9d2bca-8c96-4a96-8dd4-d25b96a75aea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-14 01:27:17,581] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-14 01:27:17,581] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-14 01:27:17,581] [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
Phycicoccus flavus	strain=CMS6Z-2	GCA_004025965.2	2502783	2502783	type	True	78.1128	280	855	95	below_threshold
Janibacter anophelis	strain=NBRC 107843	GCA_001570945.1	319054	319054	type	True	78.1039	219	855	95	below_threshold
Intrasporangium chromatireducens	strain=Q5-1	GCA_000576575.1	1386088	1386088	type	True	78.0977	260	855	95	below_threshold
Pedococcus cremeus	strain=CGMCC 1.6963	GCA_900111375.1	587636	587636	type	True	78.0893	330	855	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	78.0637	267	855	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	78.0591	263	855	95	below_threshold
Phycicoccus endophyticus	strain=CGMCC 4.7300	GCA_014646175.1	1690220	1690220	type	True	78.018	277	855	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	77.9937	262	855	95	below_threshold
Knoellia subterranea	strain=KCTC 19937	GCA_000768685.1	184882	184882	type	True	77.9561	263	855	95	below_threshold
Phycicoccus endophyticus	strain=IP6SC6	GCA_011326735.1	1690220	1690220	type	True	77.9461	283	855	95	below_threshold
Janibacter hoylei	strain=PVAS-1	GCA_000297495.1	364298	364298	type	True	77.9025	219	855	95	below_threshold
Janibacter massiliensis	strain=Marseille-P4121	GCA_900289115.1	2058291	2058291	type	True	77.8356	204	855	95	below_threshold
Janibacter hoylei	strain=PVAS-1	GCA_004025845.1	364298	364298	type	True	77.8272	230	855	95	below_threshold
Knoellia sinensis	strain=KCTC 19936	GCA_000768705.1	136100	136100	type	True	77.7916	246	855	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	77.7648	242	855	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	77.5808	206	855	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	77.5593	222	855	95	below_threshold
Janibacter limosus	strain=NBRC 16128	GCA_001570985.1	53458	53458	type	True	77.5222	218	855	95	below_threshold
Janibacter cremeus	strain=DSM 26154	GCA_013409205.1	1285192	1285192	type	True	77.4884	205	855	95	below_threshold
Janibacter corallicola	strain=NBRC 107790	GCA_001570965.1	415212	415212	type	True	77.4071	201	855	95	below_threshold
Georgenia ruanii	strain=JCM 15130	GCA_009193175.1	348442	348442	type	True	76.5873	166	855	95	below_threshold
Georgenia thermotolerans	strain=DSM 21501	GCA_009299305.1	527326	527326	type	True	76.4372	181	855	95	below_threshold
Georgenia thermotolerans	strain=NBRC 104148	GCA_009193185.1	527326	527326	type	True	76.4159	185	855	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-14 01:27:17,583] [INFO] DFAST Taxonomy check result was written to GCA_022708925.1_ASM2270892v1_genomic.fna/tc_result.tsv
[2023-06-14 01:27:17,584] [INFO] ===== Taxonomy check completed =====
[2023-06-14 01:27:17,584] [INFO] ===== Start completeness check using CheckM =====
[2023-06-14 01:27:17,584] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d9d2bca-8c96-4a96-8dd4-d25b96a75aea/dqc_reference/checkm_data
[2023-06-14 01:27:17,586] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-14 01:27:17,618] [INFO] Task started: CheckM
[2023-06-14 01:27:17,618] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022708925.1_ASM2270892v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022708925.1_ASM2270892v1_genomic.fna/checkm_input GCA_022708925.1_ASM2270892v1_genomic.fna/checkm_result
[2023-06-14 01:27:46,506] [INFO] Task succeeded: CheckM
[2023-06-14 01:27:46,508] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.35%
Contamintation: 2.70%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-14 01:27:46,531] [INFO] ===== Completeness check finished =====
[2023-06-14 01:27:46,531] [INFO] ===== Start GTDB Search =====
[2023-06-14 01:27:46,531] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022708925.1_ASM2270892v1_genomic.fna/markers.fasta)
[2023-06-14 01:27:46,532] [INFO] Task started: Blastn
[2023-06-14 01:27:46,532] [INFO] Running command: blastn -query GCA_022708925.1_ASM2270892v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d9d2bca-8c96-4a96-8dd4-d25b96a75aea/dqc_reference/reference_markers_gtdb.fasta -out GCA_022708925.1_ASM2270892v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:27:47,816] [INFO] Task succeeded: Blastn
[2023-06-14 01:27:47,821] [INFO] Selected 12 target genomes.
[2023-06-14 01:27:47,821] [INFO] Target genome list was writen to GCA_022708925.1_ASM2270892v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-14 01:27:47,930] [INFO] Task started: fastANI
[2023-06-14 01:27:47,931] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8347362-3f13-4c99-aad3-51a798fc4743/GCA_022708925.1_ASM2270892v1_genomic.fna.gz --refList GCA_022708925.1_ASM2270892v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022708925.1_ASM2270892v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-14 01:27:56,595] [INFO] Task succeeded: fastANI
[2023-06-14 01:27:56,617] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-14 01:27:56,617] [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
GCA_016707175.1	s__GCA-2748155 sp016707175	98.3086	804	855	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__GCA-2748155	95.0	98.89	98.81	0.91	0.85	4	conclusive
GCA_016704565.1	s__GCA-2748155 sp016704565	83.7652	627	855	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__GCA-2748155	95.0	97.96	97.36	0.89	0.86	3	-
GCA_016711095.1	s__GCA-2748155 sp016711095	79.9852	416	855	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__GCA-2748155	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016710645.1	s__GCA-2748155 sp016710645	79.9764	398	855	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__GCA-2748155	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016710385.1	s__GCA-2748155 sp016710385	79.4593	425	855	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__GCA-2748155	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716205.1	s__Oryzihumus leptocrescens	78.6322	308	855	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Oryzihumus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002748155.1	s__GCA-2748155 sp002748155	78.5211	179	855	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__GCA-2748155	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646815.1	s__Terrabacter tumescens	78.2855	329	855	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004025965.2	s__Phycicoccus flavus	78.0877	282	855	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111375.1	s__Pedococcus cremeus	78.0837	330	855	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	95.41	95.41	0.91	0.91	2	-
GCF_000768705.1	s__Knoellia sinensis	77.7885	247	855	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570965.1	s__Janibacter corallicola	77.3787	203	855	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-14 01:27:56,620] [INFO] GTDB search result was written to GCA_022708925.1_ASM2270892v1_genomic.fna/result_gtdb.tsv
[2023-06-14 01:27:56,620] [INFO] ===== GTDB Search completed =====
[2023-06-14 01:27:56,624] [INFO] DFAST_QC result json was written to GCA_022708925.1_ASM2270892v1_genomic.fna/dqc_result.json
[2023-06-14 01:27:56,625] [INFO] DFAST_QC completed!
[2023-06-14 01:27:56,625] [INFO] Total running time: 0h1m4s