[2023-06-29 00:18:49,088] [INFO] DFAST_QC pipeline started.
[2023-06-29 00:18:49,090] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 00:18:49,090] [INFO] DQC Reference Directory: /var/lib/cwl/stg24b2f5d2-b7f4-4c32-8add-68bcffa7a2d9/dqc_reference
[2023-06-29 00:18:50,309] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 00:18:50,310] [INFO] Task started: Prodigal
[2023-06-29 00:18:50,310] [INFO] Running command: gunzip -c /var/lib/cwl/stgd5f8bf45-fbba-49d8-9ebb-21339963c882/GCA_017646015.1_ASM1764601v1_genomic.fna.gz | prodigal -d GCA_017646015.1_ASM1764601v1_genomic.fna/cds.fna -a GCA_017646015.1_ASM1764601v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 00:18:56,661] [INFO] Task succeeded: Prodigal
[2023-06-29 00:18:56,661] [INFO] Task started: HMMsearch
[2023-06-29 00:18:56,662] [INFO] Running command: hmmsearch --tblout GCA_017646015.1_ASM1764601v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24b2f5d2-b7f4-4c32-8add-68bcffa7a2d9/dqc_reference/reference_markers.hmm GCA_017646015.1_ASM1764601v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 00:18:56,846] [INFO] Task succeeded: HMMsearch
[2023-06-29 00:18:56,847] [INFO] Found 6/6 markers.
[2023-06-29 00:18:56,869] [INFO] Query marker FASTA was written to GCA_017646015.1_ASM1764601v1_genomic.fna/markers.fasta
[2023-06-29 00:18:56,870] [INFO] Task started: Blastn
[2023-06-29 00:18:56,870] [INFO] Running command: blastn -query GCA_017646015.1_ASM1764601v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24b2f5d2-b7f4-4c32-8add-68bcffa7a2d9/dqc_reference/reference_markers.fasta -out GCA_017646015.1_ASM1764601v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:18:57,482] [INFO] Task succeeded: Blastn
[2023-06-29 00:18:57,485] [INFO] Selected 19 target genomes.
[2023-06-29 00:18:57,485] [INFO] Target genome list was writen to GCA_017646015.1_ASM1764601v1_genomic.fna/target_genomes.txt
[2023-06-29 00:18:57,489] [INFO] Task started: fastANI
[2023-06-29 00:18:57,490] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5f8bf45-fbba-49d8-9ebb-21339963c882/GCA_017646015.1_ASM1764601v1_genomic.fna.gz --refList GCA_017646015.1_ASM1764601v1_genomic.fna/target_genomes.txt --output GCA_017646015.1_ASM1764601v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 00:19:10,105] [INFO] Task succeeded: fastANI
[2023-06-29 00:19:10,106] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24b2f5d2-b7f4-4c32-8add-68bcffa7a2d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 00:19:10,106] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24b2f5d2-b7f4-4c32-8add-68bcffa7a2d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 00:19:10,108] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 00:19:10,108] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 00:19:10,108] [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
--------------------------------------------------------------------------------
[2023-06-29 00:19:10,110] [INFO] DFAST Taxonomy check result was written to GCA_017646015.1_ASM1764601v1_genomic.fna/tc_result.tsv
[2023-06-29 00:19:10,110] [INFO] ===== Taxonomy check completed =====
[2023-06-29 00:19:10,110] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 00:19:10,111] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24b2f5d2-b7f4-4c32-8add-68bcffa7a2d9/dqc_reference/checkm_data
[2023-06-29 00:19:10,113] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 00:19:10,143] [INFO] Task started: CheckM
[2023-06-29 00:19:10,144] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017646015.1_ASM1764601v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017646015.1_ASM1764601v1_genomic.fna/checkm_input GCA_017646015.1_ASM1764601v1_genomic.fna/checkm_result
[2023-06-29 00:19:35,029] [INFO] Task succeeded: CheckM
[2023-06-29 00:19:35,038] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.54%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 00:19:35,060] [INFO] ===== Completeness check finished =====
[2023-06-29 00:19:35,060] [INFO] ===== Start GTDB Search =====
[2023-06-29 00:19:35,060] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017646015.1_ASM1764601v1_genomic.fna/markers.fasta)
[2023-06-29 00:19:35,060] [INFO] Task started: Blastn
[2023-06-29 00:19:35,060] [INFO] Running command: blastn -query GCA_017646015.1_ASM1764601v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24b2f5d2-b7f4-4c32-8add-68bcffa7a2d9/dqc_reference/reference_markers_gtdb.fasta -out GCA_017646015.1_ASM1764601v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:19:36,084] [INFO] Task succeeded: Blastn
[2023-06-29 00:19:36,087] [INFO] Selected 19 target genomes.
[2023-06-29 00:19:36,087] [INFO] Target genome list was writen to GCA_017646015.1_ASM1764601v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 00:19:36,096] [INFO] Task started: fastANI
[2023-06-29 00:19:36,096] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5f8bf45-fbba-49d8-9ebb-21339963c882/GCA_017646015.1_ASM1764601v1_genomic.fna.gz --refList GCA_017646015.1_ASM1764601v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017646015.1_ASM1764601v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 00:19:46,515] [INFO] Task succeeded: fastANI
[2023-06-29 00:19:46,524] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 00:19:46,524] [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_017646015.1	s__UBA11452 sp017646015	100.0	750	761	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__Victivallales;f__UBA1829;g__UBA11452	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017503375.1	s__SIG79 sp017503375	77.0898	92	761	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__Victivallales;f__UBA1829;g__SIG79	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017456495.1	s__SIG79 sp017456495	77.0552	70	761	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__Victivallales;f__UBA1829;g__SIG79	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015061565.1	s__UBA11452 sp015061565	77.0428	86	761	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__Victivallales;f__UBA1829;g__UBA11452	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003526375.1	s__UBA11452 sp003526375	76.8689	66	761	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__Victivallales;f__UBA1829;g__UBA11452	95.0	98.98	98.49	0.91	0.85	5	-
GCA_017503545.1	s__RGIG8244 sp017503545	76.7766	89	761	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__Victivallales;f__UBA1829;g__RGIG8244	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017629515.1	s__RGIG5327 sp017629515	76.3845	70	761	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__Victivallales;f__UBA1829;g__RGIG5327	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002069785.1	s__UBA11452 sp002069785	76.0638	67	761	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__Victivallales;f__UBA1829;g__UBA11452	95.0	97.71	97.71	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-06-29 00:19:46,526] [INFO] GTDB search result was written to GCA_017646015.1_ASM1764601v1_genomic.fna/result_gtdb.tsv
[2023-06-29 00:19:46,526] [INFO] ===== GTDB Search completed =====
[2023-06-29 00:19:46,530] [INFO] DFAST_QC result json was written to GCA_017646015.1_ASM1764601v1_genomic.fna/dqc_result.json
[2023-06-29 00:19:46,530] [INFO] DFAST_QC completed!
[2023-06-29 00:19:46,530] [INFO] Total running time: 0h0m57s