[2023-06-27 03:24:52,580] [INFO] DFAST_QC pipeline started.
[2023-06-27 03:24:52,591] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 03:24:52,592] [INFO] DQC Reference Directory: /var/lib/cwl/stg002d437f-d9c0-4422-bf68-40836f21196d/dqc_reference
[2023-06-27 03:24:53,829] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 03:24:53,829] [INFO] Task started: Prodigal
[2023-06-27 03:24:53,830] [INFO] Running command: gunzip -c /var/lib/cwl/stg4dce2b4d-5ccc-48d3-be92-30e1888f5983/GCA_002712365.2_ASM271236v2_genomic.fna.gz | prodigal -d GCA_002712365.2_ASM271236v2_genomic.fna/cds.fna -a GCA_002712365.2_ASM271236v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 03:24:55,234] [INFO] Task succeeded: Prodigal
[2023-06-27 03:24:55,235] [INFO] Task started: HMMsearch
[2023-06-27 03:24:55,235] [INFO] Running command: hmmsearch --tblout GCA_002712365.2_ASM271236v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg002d437f-d9c0-4422-bf68-40836f21196d/dqc_reference/reference_markers.hmm GCA_002712365.2_ASM271236v2_genomic.fna/protein.faa > /dev/null
[2023-06-27 03:24:55,421] [INFO] Task succeeded: HMMsearch
[2023-06-27 03:24:55,422] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg4dce2b4d-5ccc-48d3-be92-30e1888f5983/GCA_002712365.2_ASM271236v2_genomic.fna.gz]
[2023-06-27 03:24:55,440] [INFO] Query marker FASTA was written to GCA_002712365.2_ASM271236v2_genomic.fna/markers.fasta
[2023-06-27 03:24:55,441] [INFO] Task started: Blastn
[2023-06-27 03:24:55,441] [INFO] Running command: blastn -query GCA_002712365.2_ASM271236v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg002d437f-d9c0-4422-bf68-40836f21196d/dqc_reference/reference_markers.fasta -out GCA_002712365.2_ASM271236v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 03:24:55,943] [INFO] Task succeeded: Blastn
[2023-06-27 03:24:55,948] [INFO] Selected 13 target genomes.
[2023-06-27 03:24:55,949] [INFO] Target genome list was writen to GCA_002712365.2_ASM271236v2_genomic.fna/target_genomes.txt
[2023-06-27 03:24:55,956] [INFO] Task started: fastANI
[2023-06-27 03:24:55,956] [INFO] Running command: fastANI --query /var/lib/cwl/stg4dce2b4d-5ccc-48d3-be92-30e1888f5983/GCA_002712365.2_ASM271236v2_genomic.fna.gz --refList GCA_002712365.2_ASM271236v2_genomic.fna/target_genomes.txt --output GCA_002712365.2_ASM271236v2_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 03:25:00,501] [INFO] Task succeeded: fastANI
[2023-06-27 03:25:00,501] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg002d437f-d9c0-4422-bf68-40836f21196d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 03:25:00,502] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg002d437f-d9c0-4422-bf68-40836f21196d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 03:25:00,516] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 03:25:00,516] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 03:25:00,517] [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
--------------------------------------------------------------------------------
[2023-06-27 03:25:00,519] [INFO] DFAST Taxonomy check result was written to GCA_002712365.2_ASM271236v2_genomic.fna/tc_result.tsv
[2023-06-27 03:25:00,520] [INFO] ===== Taxonomy check completed =====
[2023-06-27 03:25:00,520] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 03:25:00,521] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg002d437f-d9c0-4422-bf68-40836f21196d/dqc_reference/checkm_data
[2023-06-27 03:25:00,524] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 03:25:00,538] [INFO] Task started: CheckM
[2023-06-27 03:25:00,538] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002712365.2_ASM271236v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002712365.2_ASM271236v2_genomic.fna/checkm_input GCA_002712365.2_ASM271236v2_genomic.fna/checkm_result
[2023-06-27 03:25:13,512] [INFO] Task succeeded: CheckM
[2023-06-27 03:25:13,514] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 03:25:13,539] [INFO] ===== Completeness check finished =====
[2023-06-27 03:25:13,539] [INFO] ===== Start GTDB Search =====
[2023-06-27 03:25:13,540] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002712365.2_ASM271236v2_genomic.fna/markers.fasta)
[2023-06-27 03:25:13,540] [INFO] Task started: Blastn
[2023-06-27 03:25:13,540] [INFO] Running command: blastn -query GCA_002712365.2_ASM271236v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg002d437f-d9c0-4422-bf68-40836f21196d/dqc_reference/reference_markers_gtdb.fasta -out GCA_002712365.2_ASM271236v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 03:25:14,033] [INFO] Task succeeded: Blastn
[2023-06-27 03:25:14,037] [INFO] Selected 12 target genomes.
[2023-06-27 03:25:14,037] [INFO] Target genome list was writen to GCA_002712365.2_ASM271236v2_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 03:25:14,066] [INFO] Task started: fastANI
[2023-06-27 03:25:14,067] [INFO] Running command: fastANI --query /var/lib/cwl/stg4dce2b4d-5ccc-48d3-be92-30e1888f5983/GCA_002712365.2_ASM271236v2_genomic.fna.gz --refList GCA_002712365.2_ASM271236v2_genomic.fna/target_genomes_gtdb.txt --output GCA_002712365.2_ASM271236v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 03:25:17,392] [INFO] Task succeeded: fastANI
[2023-06-27 03:25:17,401] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 03:25:17,401] [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_002167555.2	s__TMED58 sp002167555	97.0717	262	286	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__UBA1144;f__UBA1144;g__TMED58	95.0	97.87	96.79	0.94	0.92	5	conclusive
GCA_002701865.2	s__TMED58 sp002701865	78.931	137	286	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__UBA1144;f__UBA1144;g__TMED58	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018654605.1	s__TMED58 sp018654605	78.3663	132	286	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__UBA1144;f__UBA1144;g__TMED58	95.0	99.90	99.90	0.96	0.96	2	-
GCA_905181755.1	s__TMED58 sp905181755	78.1913	78	286	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__UBA1144;f__UBA1144;g__TMED58	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701925.2	s__GCA-2701925 sp002701925	77.3995	74	286	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__UBA1144;f__UBA1144;g__GCA-2701925	95.0	97.33	97.15	0.95	0.94	4	-
--------------------------------------------------------------------------------
[2023-06-27 03:25:17,414] [INFO] GTDB search result was written to GCA_002712365.2_ASM271236v2_genomic.fna/result_gtdb.tsv
[2023-06-27 03:25:17,415] [INFO] ===== GTDB Search completed =====
[2023-06-27 03:25:17,418] [INFO] DFAST_QC result json was written to GCA_002712365.2_ASM271236v2_genomic.fna/dqc_result.json
[2023-06-27 03:25:17,419] [INFO] DFAST_QC completed!
[2023-06-27 03:25:17,419] [INFO] Total running time: 0h0m25s