[2023-06-13 22:41:37,681] [INFO] DFAST_QC pipeline started.
[2023-06-13 22:41:37,684] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 22:41:37,684] [INFO] DQC Reference Directory: /var/lib/cwl/stg789ad089-ada3-4b6c-9db3-455d296dad2a/dqc_reference
[2023-06-13 22:41:39,039] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 22:41:39,040] [INFO] Task started: Prodigal
[2023-06-13 22:41:39,041] [INFO] Running command: gunzip -c /var/lib/cwl/stg738af6dd-6a59-4975-bd2a-d51b86059daf/GCA_022708885.1_ASM2270888v1_genomic.fna.gz | prodigal -d GCA_022708885.1_ASM2270888v1_genomic.fna/cds.fna -a GCA_022708885.1_ASM2270888v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 22:41:43,891] [INFO] Task succeeded: Prodigal
[2023-06-13 22:41:43,892] [INFO] Task started: HMMsearch
[2023-06-13 22:41:43,892] [INFO] Running command: hmmsearch --tblout GCA_022708885.1_ASM2270888v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg789ad089-ada3-4b6c-9db3-455d296dad2a/dqc_reference/reference_markers.hmm GCA_022708885.1_ASM2270888v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 22:41:44,070] [INFO] Task succeeded: HMMsearch
[2023-06-13 22:41:44,072] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg738af6dd-6a59-4975-bd2a-d51b86059daf/GCA_022708885.1_ASM2270888v1_genomic.fna.gz]
[2023-06-13 22:41:44,097] [INFO] Query marker FASTA was written to GCA_022708885.1_ASM2270888v1_genomic.fna/markers.fasta
[2023-06-13 22:41:44,097] [INFO] Task started: Blastn
[2023-06-13 22:41:44,098] [INFO] Running command: blastn -query GCA_022708885.1_ASM2270888v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg789ad089-ada3-4b6c-9db3-455d296dad2a/dqc_reference/reference_markers.fasta -out GCA_022708885.1_ASM2270888v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 22:41:44,829] [INFO] Task succeeded: Blastn
[2023-06-13 22:41:44,834] [INFO] Selected 13 target genomes.
[2023-06-13 22:41:44,835] [INFO] Target genome list was writen to GCA_022708885.1_ASM2270888v1_genomic.fna/target_genomes.txt
[2023-06-13 22:41:44,838] [INFO] Task started: fastANI
[2023-06-13 22:41:44,838] [INFO] Running command: fastANI --query /var/lib/cwl/stg738af6dd-6a59-4975-bd2a-d51b86059daf/GCA_022708885.1_ASM2270888v1_genomic.fna.gz --refList GCA_022708885.1_ASM2270888v1_genomic.fna/target_genomes.txt --output GCA_022708885.1_ASM2270888v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 22:41:51,274] [INFO] Task succeeded: fastANI
[2023-06-13 22:41:51,275] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg789ad089-ada3-4b6c-9db3-455d296dad2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 22:41:51,275] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg789ad089-ada3-4b6c-9db3-455d296dad2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 22:41:51,286] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 22:41:51,287] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 22:41:51,287] [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
Conyzicola nivalis	strain=CGMCC 1.12813	GCA_014639655.1	1477021	1477021	type	True	79.8475	187	429	95	below_threshold
Conyzicola lurida	strain=DSM 105784	GCA_014204935.1	1172621	1172621	type	True	79.6422	212	429	95	below_threshold
Galbitalea soli	strain=DSM 105515	GCA_013410525.1	1268042	1268042	type	True	79.5138	172	429	95	below_threshold
Galbitalea soli	strain=NBRC 108727	GCA_010686725.1	1268042	1268042	type	True	79.5078	173	429	95	below_threshold
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	78.8881	155	429	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_003576155.1	1401995	1401995	type	True	78.6833	130	429	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_021952865.1	1401995	1401995	type	True	78.6513	145	429	95	below_threshold
Glaciihabitans tibetensis	strain=CGMCC 1.12484	GCA_003003265.1	1266600	1266600	type	True	78.2275	137	429	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	76.9524	92	429	95	below_threshold
Knoellia flava	strain=TL1	GCA_000768675.1	913969	913969	type	True	76.8812	82	429	95	below_threshold
Knoellia flava	strain=CGMCC 1.10749	GCA_014636255.1	913969	913969	type	True	76.8518	83	429	95	below_threshold
Flexivirga aerilata	strain=ID2601S	GCA_013002715.1	1656889	1656889	type	True	76.6556	64	429	95	below_threshold
Phycicoccus endophyticus	strain=CGMCC 4.7300	GCA_014646175.1	1690220	1690220	type	True	76.4192	60	429	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 22:41:51,289] [INFO] DFAST Taxonomy check result was written to GCA_022708885.1_ASM2270888v1_genomic.fna/tc_result.tsv
[2023-06-13 22:41:51,290] [INFO] ===== Taxonomy check completed =====
[2023-06-13 22:41:51,290] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 22:41:51,291] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg789ad089-ada3-4b6c-9db3-455d296dad2a/dqc_reference/checkm_data
[2023-06-13 22:41:51,292] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 22:41:51,315] [INFO] Task started: CheckM
[2023-06-13 22:41:51,315] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022708885.1_ASM2270888v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022708885.1_ASM2270888v1_genomic.fna/checkm_input GCA_022708885.1_ASM2270888v1_genomic.fna/checkm_result
[2023-06-13 22:42:11,757] [INFO] Task succeeded: CheckM
[2023-06-13 22:42:11,758] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.45%
Contamintation: 12.96%
Strain heterogeneity: 23.53%
--------------------------------------------------------------------------------
[2023-06-13 22:42:11,787] [INFO] ===== Completeness check finished =====
[2023-06-13 22:42:11,788] [INFO] ===== Start GTDB Search =====
[2023-06-13 22:42:11,788] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022708885.1_ASM2270888v1_genomic.fna/markers.fasta)
[2023-06-13 22:42:11,788] [INFO] Task started: Blastn
[2023-06-13 22:42:11,788] [INFO] Running command: blastn -query GCA_022708885.1_ASM2270888v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg789ad089-ada3-4b6c-9db3-455d296dad2a/dqc_reference/reference_markers_gtdb.fasta -out GCA_022708885.1_ASM2270888v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 22:42:12,718] [INFO] Task succeeded: Blastn
[2023-06-13 22:42:12,729] [INFO] Selected 15 target genomes.
[2023-06-13 22:42:12,730] [INFO] Target genome list was writen to GCA_022708885.1_ASM2270888v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 22:42:12,757] [INFO] Task started: fastANI
[2023-06-13 22:42:12,757] [INFO] Running command: fastANI --query /var/lib/cwl/stg738af6dd-6a59-4975-bd2a-d51b86059daf/GCA_022708885.1_ASM2270888v1_genomic.fna.gz --refList GCA_022708885.1_ASM2270888v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022708885.1_ASM2270888v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 22:42:20,471] [INFO] Task succeeded: fastANI
[2023-06-13 22:42:20,484] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 22:42:20,484] [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_001725325.1	s__Rhodoglobus sp001725325	81.339	241	429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	100.00	100.00	1.00	1.00	3	-
GCA_903920435.1	s__Rhodoglobus sp903920435	81.0469	230	429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	98.49	97.73	0.85	0.78	4	-
GCF_014639655.1	s__Conyzicola nivalis	79.8319	188	429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Conyzicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013297645.1	s__JAAFHU01 sp013297645	79.7576	166	429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__JAAFHU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204935.1	s__Conyzicola lurida	79.6206	213	429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Conyzicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010686725.1	s__Galbitalea soli	79.5078	173	429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Galbitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002797715.1	s__Diaminobutyricimonas aerilata	79.1721	187	429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Diaminobutyricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015752305.1	s__Rhodoglobus sp015752305	79.1497	183	429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797855.1	s__Compostimonas suwonensis	78.9405	180	429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Compostimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003265.1	s__Glaciihabitans tibetensis	78.2559	136	429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Glaciihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768675.1	s__Knoellia flava	76.9095	81	429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016707175.1	s__GCA-2748155 sp016707175	76.6735	56	429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__GCA-2748155	95.0	98.89	98.81	0.91	0.85	4	-
GCA_016704565.1	s__GCA-2748155 sp016704565	76.0191	52	429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__GCA-2748155	95.0	97.96	97.36	0.89	0.86	3	-
--------------------------------------------------------------------------------
[2023-06-13 22:42:20,487] [INFO] GTDB search result was written to GCA_022708885.1_ASM2270888v1_genomic.fna/result_gtdb.tsv
[2023-06-13 22:42:20,487] [INFO] ===== GTDB Search completed =====
[2023-06-13 22:42:20,492] [INFO] DFAST_QC result json was written to GCA_022708885.1_ASM2270888v1_genomic.fna/dqc_result.json
[2023-06-13 22:42:20,493] [INFO] DFAST_QC completed!
[2023-06-13 22:42:20,493] [INFO] Total running time: 0h0m43s