[2023-06-13 17:55:49,887] [INFO] DFAST_QC pipeline started.
[2023-06-13 17:55:49,890] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 17:55:49,890] [INFO] DQC Reference Directory: /var/lib/cwl/stgfbc206ac-54d4-4915-957b-36c04e57a81c/dqc_reference
[2023-06-13 17:55:51,617] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 17:55:51,618] [INFO] Task started: Prodigal
[2023-06-13 17:55:51,618] [INFO] Running command: gunzip -c /var/lib/cwl/stgab54b4fd-ff4f-41e0-a09c-ffdec5ad0dbf/GCA_003451995.1_ASM345199v1_genomic.fna.gz | prodigal -d GCA_003451995.1_ASM345199v1_genomic.fna/cds.fna -a GCA_003451995.1_ASM345199v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 17:55:54,083] [INFO] Task succeeded: Prodigal
[2023-06-13 17:55:54,084] [INFO] Task started: HMMsearch
[2023-06-13 17:55:54,084] [INFO] Running command: hmmsearch --tblout GCA_003451995.1_ASM345199v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfbc206ac-54d4-4915-957b-36c04e57a81c/dqc_reference/reference_markers.hmm GCA_003451995.1_ASM345199v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 17:55:54,285] [INFO] Task succeeded: HMMsearch
[2023-06-13 17:55:54,287] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgab54b4fd-ff4f-41e0-a09c-ffdec5ad0dbf/GCA_003451995.1_ASM345199v1_genomic.fna.gz]
[2023-06-13 17:55:54,303] [INFO] Query marker FASTA was written to GCA_003451995.1_ASM345199v1_genomic.fna/markers.fasta
[2023-06-13 17:55:54,304] [INFO] Task started: Blastn
[2023-06-13 17:55:54,304] [INFO] Running command: blastn -query GCA_003451995.1_ASM345199v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbc206ac-54d4-4915-957b-36c04e57a81c/dqc_reference/reference_markers.fasta -out GCA_003451995.1_ASM345199v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:55:55,152] [INFO] Task succeeded: Blastn
[2023-06-13 17:55:55,158] [INFO] Selected 9 target genomes.
[2023-06-13 17:55:55,159] [INFO] Target genome list was writen to GCA_003451995.1_ASM345199v1_genomic.fna/target_genomes.txt
[2023-06-13 17:55:55,162] [INFO] Task started: fastANI
[2023-06-13 17:55:55,162] [INFO] Running command: fastANI --query /var/lib/cwl/stgab54b4fd-ff4f-41e0-a09c-ffdec5ad0dbf/GCA_003451995.1_ASM345199v1_genomic.fna.gz --refList GCA_003451995.1_ASM345199v1_genomic.fna/target_genomes.txt --output GCA_003451995.1_ASM345199v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 17:56:01,696] [INFO] Task succeeded: fastANI
[2023-06-13 17:56:01,697] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfbc206ac-54d4-4915-957b-36c04e57a81c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 17:56:01,697] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfbc206ac-54d4-4915-957b-36c04e57a81c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 17:56:01,699] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 17:56:01,699] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 17:56:01,699] [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
--------------------------------------------------------------------------------
[2023-06-13 17:56:01,701] [INFO] DFAST Taxonomy check result was written to GCA_003451995.1_ASM345199v1_genomic.fna/tc_result.tsv
[2023-06-13 17:56:01,702] [INFO] ===== Taxonomy check completed =====
[2023-06-13 17:56:01,702] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 17:56:01,702] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfbc206ac-54d4-4915-957b-36c04e57a81c/dqc_reference/checkm_data
[2023-06-13 17:56:01,706] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 17:56:01,725] [INFO] Task started: CheckM
[2023-06-13 17:56:01,726] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003451995.1_ASM345199v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003451995.1_ASM345199v1_genomic.fna/checkm_input GCA_003451995.1_ASM345199v1_genomic.fna/checkm_result
[2023-06-13 17:56:17,236] [INFO] Task succeeded: CheckM
[2023-06-13 17:56:17,237] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 49.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 17:56:17,261] [INFO] ===== Completeness check finished =====
[2023-06-13 17:56:17,262] [INFO] ===== Start GTDB Search =====
[2023-06-13 17:56:17,263] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003451995.1_ASM345199v1_genomic.fna/markers.fasta)
[2023-06-13 17:56:17,263] [INFO] Task started: Blastn
[2023-06-13 17:56:17,263] [INFO] Running command: blastn -query GCA_003451995.1_ASM345199v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbc206ac-54d4-4915-957b-36c04e57a81c/dqc_reference/reference_markers_gtdb.fasta -out GCA_003451995.1_ASM345199v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:56:17,728] [INFO] Task succeeded: Blastn
[2023-06-13 17:56:17,732] [INFO] Selected 9 target genomes.
[2023-06-13 17:56:17,733] [INFO] Target genome list was writen to GCA_003451995.1_ASM345199v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 17:56:17,742] [INFO] Task started: fastANI
[2023-06-13 17:56:17,742] [INFO] Running command: fastANI --query /var/lib/cwl/stgab54b4fd-ff4f-41e0-a09c-ffdec5ad0dbf/GCA_003451995.1_ASM345199v1_genomic.fna.gz --refList GCA_003451995.1_ASM345199v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003451995.1_ASM345199v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 17:56:23,553] [INFO] Task succeeded: fastANI
[2023-06-13 17:56:23,564] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 17:56:23,565] [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_001509095.1	s__58-81 sp001509095	97.3919	209	271	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Thermovirgaceae;g__58-81	95.0	98.51	97.39	0.78	0.69	4	conclusive
GCA_012729145.1	s__58-81 sp012729145	91.2067	242	271	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Thermovirgaceae;g__58-81	95.0	99.73	99.73	0.92	0.92	2	-
GCA_002070395.1	s__58-81 sp002070395	78.5876	130	271	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Thermovirgaceae;g__58-81	95.0	99.80	99.72	0.97	0.95	4	-
GCA_012523215.1	s__58-81 sp012523215	77.7308	74	271	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Thermovirgaceae;g__58-81	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 17:56:23,567] [INFO] GTDB search result was written to GCA_003451995.1_ASM345199v1_genomic.fna/result_gtdb.tsv
[2023-06-13 17:56:23,568] [INFO] ===== GTDB Search completed =====
[2023-06-13 17:56:23,571] [INFO] DFAST_QC result json was written to GCA_003451995.1_ASM345199v1_genomic.fna/dqc_result.json
[2023-06-13 17:56:23,571] [INFO] DFAST_QC completed!
[2023-06-13 17:56:23,571] [INFO] Total running time: 0h0m34s