[2023-06-13 13:20:17,666] [INFO] DFAST_QC pipeline started.
[2023-06-13 13:20:17,670] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 13:20:17,670] [INFO] DQC Reference Directory: /var/lib/cwl/stg92e97986-2755-4439-8211-bd5c93cbf3cd/dqc_reference
[2023-06-13 13:20:19,483] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 13:20:19,484] [INFO] Task started: Prodigal
[2023-06-13 13:20:19,484] [INFO] Running command: gunzip -c /var/lib/cwl/stg34fe94e3-c93b-4ddb-a08a-aa03d0bc3948/GCA_022449585.1_ASM2244958v1_genomic.fna.gz | prodigal -d GCA_022449585.1_ASM2244958v1_genomic.fna/cds.fna -a GCA_022449585.1_ASM2244958v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 13:20:26,535] [INFO] Task succeeded: Prodigal
[2023-06-13 13:20:26,535] [INFO] Task started: HMMsearch
[2023-06-13 13:20:26,535] [INFO] Running command: hmmsearch --tblout GCA_022449585.1_ASM2244958v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg92e97986-2755-4439-8211-bd5c93cbf3cd/dqc_reference/reference_markers.hmm GCA_022449585.1_ASM2244958v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 13:20:26,704] [INFO] Task succeeded: HMMsearch
[2023-06-13 13:20:26,705] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg34fe94e3-c93b-4ddb-a08a-aa03d0bc3948/GCA_022449585.1_ASM2244958v1_genomic.fna.gz]
[2023-06-13 13:20:26,728] [INFO] Query marker FASTA was written to GCA_022449585.1_ASM2244958v1_genomic.fna/markers.fasta
[2023-06-13 13:20:26,728] [INFO] Task started: Blastn
[2023-06-13 13:20:26,728] [INFO] Running command: blastn -query GCA_022449585.1_ASM2244958v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92e97986-2755-4439-8211-bd5c93cbf3cd/dqc_reference/reference_markers.fasta -out GCA_022449585.1_ASM2244958v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:20:27,423] [INFO] Task succeeded: Blastn
[2023-06-13 13:20:27,428] [INFO] Selected 21 target genomes.
[2023-06-13 13:20:27,428] [INFO] Target genome list was writen to GCA_022449585.1_ASM2244958v1_genomic.fna/target_genomes.txt
[2023-06-13 13:20:27,442] [INFO] Task started: fastANI
[2023-06-13 13:20:27,442] [INFO] Running command: fastANI --query /var/lib/cwl/stg34fe94e3-c93b-4ddb-a08a-aa03d0bc3948/GCA_022449585.1_ASM2244958v1_genomic.fna.gz --refList GCA_022449585.1_ASM2244958v1_genomic.fna/target_genomes.txt --output GCA_022449585.1_ASM2244958v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 13:20:42,205] [INFO] Task succeeded: fastANI
[2023-06-13 13:20:42,205] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg92e97986-2755-4439-8211-bd5c93cbf3cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 13:20:42,206] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg92e97986-2755-4439-8211-bd5c93cbf3cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 13:20:42,217] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 13:20:42,217] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 13:20:42,217] [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
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.9733	178	757	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.764	180	757	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.5385	144	757	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	76.4431	74	757	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.0791	120	757	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	75.521	58	757	95	below_threshold
Stackebrandtia albiflava	strain=DSM 45044	GCA_007994225.1	406432	406432	type	True	75.449	64	757	95	below_threshold
Nocardiopsis potens	strain=DSM 45234	GCA_000341105.1	1246458	1246458	type	True	75.3078	108	757	95	below_threshold
Nocardia transvalensis	strain=DSM 43582	GCA_014203315.1	37333	37333	type	True	75.2157	70	757	95	below_threshold
Micromonospora matsumotoense	strain=DSM 44100	GCA_900091525.1	121616	121616	type	True	75.2114	104	757	95	below_threshold
Actinoplanes teichomyceticus	strain=DSM 43866	GCA_007829915.1	1867	1867	type	True	75.2078	93	757	95	below_threshold
Actinoplanes teichomyceticus	strain=ATCC 31121	GCA_003711105.1	1867	1867	type	True	75.1988	94	757	95	below_threshold
Nocardia transvalensis	strain=NBRC 15921	GCA_000308875.1	37333	37333	type	True	75.1512	68	757	95	below_threshold
Actinoplanes teichomyceticus	strain=NBRC 13999	GCA_016862415.1	1867	1867	type	True	75.1362	91	757	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 13:20:42,219] [INFO] DFAST Taxonomy check result was written to GCA_022449585.1_ASM2244958v1_genomic.fna/tc_result.tsv
[2023-06-13 13:20:42,220] [INFO] ===== Taxonomy check completed =====
[2023-06-13 13:20:42,220] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 13:20:42,220] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg92e97986-2755-4439-8211-bd5c93cbf3cd/dqc_reference/checkm_data
[2023-06-13 13:20:42,221] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 13:20:42,245] [INFO] Task started: CheckM
[2023-06-13 13:20:42,245] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022449585.1_ASM2244958v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022449585.1_ASM2244958v1_genomic.fna/checkm_input GCA_022449585.1_ASM2244958v1_genomic.fna/checkm_result
[2023-06-13 13:21:06,926] [INFO] Task succeeded: CheckM
[2023-06-13 13:21:06,927] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 13:21:06,946] [INFO] ===== Completeness check finished =====
[2023-06-13 13:21:06,946] [INFO] ===== Start GTDB Search =====
[2023-06-13 13:21:06,947] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022449585.1_ASM2244958v1_genomic.fna/markers.fasta)
[2023-06-13 13:21:06,947] [INFO] Task started: Blastn
[2023-06-13 13:21:06,947] [INFO] Running command: blastn -query GCA_022449585.1_ASM2244958v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92e97986-2755-4439-8211-bd5c93cbf3cd/dqc_reference/reference_markers_gtdb.fasta -out GCA_022449585.1_ASM2244958v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:21:08,128] [INFO] Task succeeded: Blastn
[2023-06-13 13:21:08,132] [INFO] Selected 11 target genomes.
[2023-06-13 13:21:08,132] [INFO] Target genome list was writen to GCA_022449585.1_ASM2244958v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 13:21:08,136] [INFO] Task started: fastANI
[2023-06-13 13:21:08,136] [INFO] Running command: fastANI --query /var/lib/cwl/stg34fe94e3-c93b-4ddb-a08a-aa03d0bc3948/GCA_022449585.1_ASM2244958v1_genomic.fna.gz --refList GCA_022449585.1_ASM2244958v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022449585.1_ASM2244958v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 13:21:13,386] [INFO] Task succeeded: fastANI
[2023-06-13 13:21:13,395] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 13:21:13,395] [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_012961035.1	s__UBA9410 sp012961035	98.1295	616	757	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	99.67	99.67	0.93	0.93	2	conclusive
GCA_014240365.1	s__UBA9410 sp014240365	88.8231	583	757	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	98.11	98.07	0.86	0.84	5	-
GCA_016845305.1	s__UBA9410 sp016845305	81.1249	513	757	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239855.1	s__UBA9410 sp014239855	80.5608	478	757	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002727895.1	s__UBA9410 sp002727895	79.9405	360	757	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	97.12	97.12	0.93	0.93	2	-
GCA_014237715.1	s__UBA9410 sp014237715	79.7442	433	757	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	98.52	98.52	0.97	0.97	2	-
GCA_002346745.1	s__S20-B6 sp002346745	79.2053	380	757	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	97.72	96.97	0.85	0.81	8	-
GCA_002699725.1	s__S20-B6 sp002699725	79.1578	334	757	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	98.58	98.41	0.87	0.86	3	-
GCA_002717365.1	s__UBA9410 sp002717365	78.9557	312	757	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014381945.1	s__S20-B6 sp014381945	78.7568	331	757	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 13:21:13,398] [INFO] GTDB search result was written to GCA_022449585.1_ASM2244958v1_genomic.fna/result_gtdb.tsv
[2023-06-13 13:21:13,398] [INFO] ===== GTDB Search completed =====
[2023-06-13 13:21:13,402] [INFO] DFAST_QC result json was written to GCA_022449585.1_ASM2244958v1_genomic.fna/dqc_result.json
[2023-06-13 13:21:13,402] [INFO] DFAST_QC completed!
[2023-06-13 13:21:13,402] [INFO] Total running time: 0h0m56s