[2023-06-30 15:48:26,969] [INFO] DFAST_QC pipeline started.
[2023-06-30 15:48:26,973] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 15:48:26,973] [INFO] DQC Reference Directory: /var/lib/cwl/stg47532519-5de7-40ed-baa1-4a34de6d5e42/dqc_reference
[2023-06-30 15:48:28,588] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 15:48:28,589] [INFO] Task started: Prodigal
[2023-06-30 15:48:28,589] [INFO] Running command: gunzip -c /var/lib/cwl/stg9184fa65-f740-4c9c-b219-ab3da75ec537/GCA_024280995.1_ASM2428099v1_genomic.fna.gz | prodigal -d GCA_024280995.1_ASM2428099v1_genomic.fna/cds.fna -a GCA_024280995.1_ASM2428099v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 15:48:46,171] [INFO] Task succeeded: Prodigal
[2023-06-30 15:48:46,171] [INFO] Task started: HMMsearch
[2023-06-30 15:48:46,171] [INFO] Running command: hmmsearch --tblout GCA_024280995.1_ASM2428099v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47532519-5de7-40ed-baa1-4a34de6d5e42/dqc_reference/reference_markers.hmm GCA_024280995.1_ASM2428099v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 15:48:46,449] [INFO] Task succeeded: HMMsearch
[2023-06-30 15:48:46,450] [INFO] Found 6/6 markers.
[2023-06-30 15:48:46,492] [INFO] Query marker FASTA was written to GCA_024280995.1_ASM2428099v1_genomic.fna/markers.fasta
[2023-06-30 15:48:46,493] [INFO] Task started: Blastn
[2023-06-30 15:48:46,493] [INFO] Running command: blastn -query GCA_024280995.1_ASM2428099v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47532519-5de7-40ed-baa1-4a34de6d5e42/dqc_reference/reference_markers.fasta -out GCA_024280995.1_ASM2428099v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:48:47,213] [INFO] Task succeeded: Blastn
[2023-06-30 15:48:47,217] [INFO] Selected 20 target genomes.
[2023-06-30 15:48:47,217] [INFO] Target genome list was writen to GCA_024280995.1_ASM2428099v1_genomic.fna/target_genomes.txt
[2023-06-30 15:48:47,219] [INFO] Task started: fastANI
[2023-06-30 15:48:47,219] [INFO] Running command: fastANI --query /var/lib/cwl/stg9184fa65-f740-4c9c-b219-ab3da75ec537/GCA_024280995.1_ASM2428099v1_genomic.fna.gz --refList GCA_024280995.1_ASM2428099v1_genomic.fna/target_genomes.txt --output GCA_024280995.1_ASM2428099v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 15:48:57,868] [INFO] Task succeeded: fastANI
[2023-06-30 15:48:57,869] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47532519-5de7-40ed-baa1-4a34de6d5e42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 15:48:57,869] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47532519-5de7-40ed-baa1-4a34de6d5e42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 15:48:57,878] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 15:48:57,878] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 15:48:57,878] [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
Nocardioides euryhalodurans	strain=MMS17-SY117	GCA_004564375.1	2518370	2518370	type	True	75.2463	77	984	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	75.199	50	984	95	below_threshold
Agromyces atrinae	strain=DSM 23870	GCA_013407835.1	592376	592376	type	True	75.1139	52	984	95	below_threshold
Janibacter indicus	strain=CGMCC 1.12511	GCA_900176385.1	857417	857417	type	True	75.0968	76	984	95	below_threshold
Janibacter anophelis	strain=NBRC 107843	GCA_001570945.1	319054	319054	type	True	75.0494	66	984	95	below_threshold
Nocardioides stalactiti	strain=1.0914	GCA_014180715.1	2755356	2755356	type	True	75.0295	81	984	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	74.8836	89	984	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	74.8784	84	984	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	74.8381	53	984	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 15:48:57,880] [INFO] DFAST Taxonomy check result was written to GCA_024280995.1_ASM2428099v1_genomic.fna/tc_result.tsv
[2023-06-30 15:48:57,881] [INFO] ===== Taxonomy check completed =====
[2023-06-30 15:48:57,881] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 15:48:57,881] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47532519-5de7-40ed-baa1-4a34de6d5e42/dqc_reference/checkm_data
[2023-06-30 15:48:57,883] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 15:48:57,921] [INFO] Task started: CheckM
[2023-06-30 15:48:57,922] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024280995.1_ASM2428099v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024280995.1_ASM2428099v1_genomic.fna/checkm_input GCA_024280995.1_ASM2428099v1_genomic.fna/checkm_result
[2023-06-30 15:49:45,687] [INFO] Task succeeded: CheckM
[2023-06-30 15:49:45,689] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 15:49:45,711] [INFO] ===== Completeness check finished =====
[2023-06-30 15:49:45,711] [INFO] ===== Start GTDB Search =====
[2023-06-30 15:49:45,711] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024280995.1_ASM2428099v1_genomic.fna/markers.fasta)
[2023-06-30 15:49:45,712] [INFO] Task started: Blastn
[2023-06-30 15:49:45,712] [INFO] Running command: blastn -query GCA_024280995.1_ASM2428099v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47532519-5de7-40ed-baa1-4a34de6d5e42/dqc_reference/reference_markers_gtdb.fasta -out GCA_024280995.1_ASM2428099v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:49:46,719] [INFO] Task succeeded: Blastn
[2023-06-30 15:49:46,724] [INFO] Selected 14 target genomes.
[2023-06-30 15:49:46,724] [INFO] Target genome list was writen to GCA_024280995.1_ASM2428099v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 15:49:46,732] [INFO] Task started: fastANI
[2023-06-30 15:49:46,732] [INFO] Running command: fastANI --query /var/lib/cwl/stg9184fa65-f740-4c9c-b219-ab3da75ec537/GCA_024280995.1_ASM2428099v1_genomic.fna.gz --refList GCA_024280995.1_ASM2428099v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024280995.1_ASM2428099v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 15:49:54,988] [INFO] Task succeeded: fastANI
[2023-06-30 15:49:55,007] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 15:49:55,008] [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_005889135.1	s__40CM-4-65-16 sp005889135	81.3451	549	984	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__Dormibacterales;f__Dormibacteraceae;g__40CM-4-65-16	95.0	99.06	98.96	0.92	0.90	3	-
GCA_005889495.1	s__40CM-4-65-16 sp005889495	81.224	535	984	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__Dormibacterales;f__Dormibacteraceae;g__40CM-4-65-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005879675.1	s__40CM-4-65-16 sp005879675	80.9595	445	984	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__Dormibacterales;f__Dormibacteraceae;g__40CM-4-65-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005883575.1	s__40CM-4-65-16 sp005883575	80.2778	548	984	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__Dormibacterales;f__Dormibacteraceae;g__40CM-4-65-16	95.0	99.47	99.47	0.89	0.89	2	-
GCA_005880345.1	s__40CM-4-65-16 sp005880345	80.0407	295	984	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__Dormibacterales;f__Dormibacteraceae;g__40CM-4-65-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005880795.1	s__40CM-4-65-16 sp005880795	79.8134	490	984	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__Dormibacterales;f__Dormibacteraceae;g__40CM-4-65-16	95.0	99.34	99.06	0.87	0.86	4	-
GCA_005887685.1	s__40CM-4-65-16 sp005887685	79.8011	470	984	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__Dormibacterales;f__Dormibacteraceae;g__40CM-4-65-16	95.0	99.31	99.31	0.86	0.86	2	-
GCA_005882135.1	s__40CM-4-65-16 sp005882135	79.7142	430	984	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__Dormibacterales;f__Dormibacteraceae;g__40CM-4-65-16	95.0	99.34	99.09	0.85	0.80	5	-
GCA_005882115.1	s__40CM-4-65-16 sp001917775	79.7108	493	984	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__Dormibacterales;f__Dormibacteraceae;g__40CM-4-65-16	95.0	99.11	98.19	0.91	0.88	7	-
GCA_005881335.1	s__40CM-4-65-16 sp005881335	79.7066	402	984	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__Dormibacterales;f__Dormibacteraceae;g__40CM-4-65-16	95.0	98.02	97.44	0.80	0.76	5	-
GCA_005889085.1	s__40CM-4-65-16 sp005889085	79.5796	439	984	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__Dormibacterales;f__Dormibacteraceae;g__40CM-4-65-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005881275.1	s__40CM-4-65-16 sp005881275	79.4851	464	984	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__Dormibacterales;f__Dormibacteraceae;g__40CM-4-65-16	95.0	99.08	98.61	0.90	0.85	4	-
GCA_005880525.1	s__CF-118 sp005880525	78.7801	272	984	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__Dormibacterales;f__Dormibacteraceae;g__CF-118	95.0	97.95	97.81	0.79	0.75	3	-
GCA_005879985.1	s__CF-118 sp005879985	78.6725	357	984	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__Dormibacterales;f__Dormibacteraceae;g__CF-118	95.0	99.16	99.16	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2023-06-30 15:49:55,010] [INFO] GTDB search result was written to GCA_024280995.1_ASM2428099v1_genomic.fna/result_gtdb.tsv
[2023-06-30 15:49:55,010] [INFO] ===== GTDB Search completed =====
[2023-06-30 15:49:55,014] [INFO] DFAST_QC result json was written to GCA_024280995.1_ASM2428099v1_genomic.fna/dqc_result.json
[2023-06-30 15:49:55,015] [INFO] DFAST_QC completed!
[2023-06-30 15:49:55,015] [INFO] Total running time: 0h1m28s