[2023-06-28 04:20:28,897] [INFO] DFAST_QC pipeline started.
[2023-06-28 04:20:28,899] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 04:20:28,899] [INFO] DQC Reference Directory: /var/lib/cwl/stg4203fea1-4993-47cb-a6ce-04f4e640a93c/dqc_reference
[2023-06-28 04:20:30,207] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 04:20:30,208] [INFO] Task started: Prodigal
[2023-06-28 04:20:30,208] [INFO] Running command: gunzip -c /var/lib/cwl/stg13c05844-1e2f-495d-a14a-b6a45b6e7a3f/GCA_017444765.1_ASM1744476v1_genomic.fna.gz | prodigal -d GCA_017444765.1_ASM1744476v1_genomic.fna/cds.fna -a GCA_017444765.1_ASM1744476v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 04:20:39,227] [INFO] Task succeeded: Prodigal
[2023-06-28 04:20:39,228] [INFO] Task started: HMMsearch
[2023-06-28 04:20:39,228] [INFO] Running command: hmmsearch --tblout GCA_017444765.1_ASM1744476v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4203fea1-4993-47cb-a6ce-04f4e640a93c/dqc_reference/reference_markers.hmm GCA_017444765.1_ASM1744476v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 04:20:39,473] [INFO] Task succeeded: HMMsearch
[2023-06-28 04:20:39,474] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg13c05844-1e2f-495d-a14a-b6a45b6e7a3f/GCA_017444765.1_ASM1744476v1_genomic.fna.gz]
[2023-06-28 04:20:39,498] [INFO] Query marker FASTA was written to GCA_017444765.1_ASM1744476v1_genomic.fna/markers.fasta
[2023-06-28 04:20:39,498] [INFO] Task started: Blastn
[2023-06-28 04:20:39,499] [INFO] Running command: blastn -query GCA_017444765.1_ASM1744476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4203fea1-4993-47cb-a6ce-04f4e640a93c/dqc_reference/reference_markers.fasta -out GCA_017444765.1_ASM1744476v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:20:40,117] [INFO] Task succeeded: Blastn
[2023-06-28 04:20:40,120] [INFO] Selected 26 target genomes.
[2023-06-28 04:20:40,121] [INFO] Target genome list was writen to GCA_017444765.1_ASM1744476v1_genomic.fna/target_genomes.txt
[2023-06-28 04:20:40,123] [INFO] Task started: fastANI
[2023-06-28 04:20:40,123] [INFO] Running command: fastANI --query /var/lib/cwl/stg13c05844-1e2f-495d-a14a-b6a45b6e7a3f/GCA_017444765.1_ASM1744476v1_genomic.fna.gz --refList GCA_017444765.1_ASM1744476v1_genomic.fna/target_genomes.txt --output GCA_017444765.1_ASM1744476v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 04:20:54,249] [INFO] Task succeeded: fastANI
[2023-06-28 04:20:54,250] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4203fea1-4993-47cb-a6ce-04f4e640a93c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 04:20:54,250] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4203fea1-4993-47cb-a6ce-04f4e640a93c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 04:20:54,253] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 04:20:54,253] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 04:20:54,253] [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
--------------------------------------------------------------------------------
[2023-06-28 04:20:54,256] [INFO] DFAST Taxonomy check result was written to GCA_017444765.1_ASM1744476v1_genomic.fna/tc_result.tsv
[2023-06-28 04:20:54,256] [INFO] ===== Taxonomy check completed =====
[2023-06-28 04:20:54,256] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 04:20:54,257] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4203fea1-4993-47cb-a6ce-04f4e640a93c/dqc_reference/checkm_data
[2023-06-28 04:20:54,259] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 04:20:54,296] [INFO] Task started: CheckM
[2023-06-28 04:20:54,296] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017444765.1_ASM1744476v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017444765.1_ASM1744476v1_genomic.fna/checkm_input GCA_017444765.1_ASM1744476v1_genomic.fna/checkm_result
[2023-06-28 04:21:25,619] [INFO] Task succeeded: CheckM
[2023-06-28 04:21:25,620] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 3.98%
Strain heterogeneity: 16.67%
--------------------------------------------------------------------------------
[2023-06-28 04:21:25,643] [INFO] ===== Completeness check finished =====
[2023-06-28 04:21:25,643] [INFO] ===== Start GTDB Search =====
[2023-06-28 04:21:25,644] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017444765.1_ASM1744476v1_genomic.fna/markers.fasta)
[2023-06-28 04:21:25,644] [INFO] Task started: Blastn
[2023-06-28 04:21:25,644] [INFO] Running command: blastn -query GCA_017444765.1_ASM1744476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4203fea1-4993-47cb-a6ce-04f4e640a93c/dqc_reference/reference_markers_gtdb.fasta -out GCA_017444765.1_ASM1744476v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:21:26,644] [INFO] Task succeeded: Blastn
[2023-06-28 04:21:26,649] [INFO] Selected 9 target genomes.
[2023-06-28 04:21:26,649] [INFO] Target genome list was writen to GCA_017444765.1_ASM1744476v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 04:21:26,651] [INFO] Task started: fastANI
[2023-06-28 04:21:26,651] [INFO] Running command: fastANI --query /var/lib/cwl/stg13c05844-1e2f-495d-a14a-b6a45b6e7a3f/GCA_017444765.1_ASM1744476v1_genomic.fna.gz --refList GCA_017444765.1_ASM1744476v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017444765.1_ASM1744476v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 04:21:29,910] [INFO] Task succeeded: fastANI
[2023-06-28 04:21:29,922] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 04:21:29,922] [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_900316675.1	s__Cryptobacteroides sp900316675	98.2066	535	600	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.65	98.02	0.91	0.85	9	conclusive
GCA_900314395.1	s__Cryptobacteroides sp900314395	81.1752	284	600	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	99.48	98.95	0.92	0.85	3	-
GCA_017459075.1	s__Cryptobacteroides sp017459075	80.142	296	600	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902774045.1	s__Cryptobacteroides sp902774045	78.7839	186	600	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017443025.1	s__Cryptobacteroides sp017443025	78.4707	115	600	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.45	98.45	0.86	0.86	2	-
GCA_900167925.1	s__Cryptobacteroides sp900167925	77.5053	89	600	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.91	97.12	0.93	0.91	9	-
GCA_017618815.1	s__Cryptobacteroides sp017618815	77.08	73	600	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902779495.1	s__Cryptobacteroides sp902779495	76.7567	62	600	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	96.47	96.39	0.76	0.72	3	-
GCA_902803715.1	s__Cryptobacteroides sp902803715	76.3633	68	600	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.42	97.90	0.88	0.86	3	-
--------------------------------------------------------------------------------
[2023-06-28 04:21:29,924] [INFO] GTDB search result was written to GCA_017444765.1_ASM1744476v1_genomic.fna/result_gtdb.tsv
[2023-06-28 04:21:29,925] [INFO] ===== GTDB Search completed =====
[2023-06-28 04:21:29,927] [INFO] DFAST_QC result json was written to GCA_017444765.1_ASM1744476v1_genomic.fna/dqc_result.json
[2023-06-28 04:21:29,928] [INFO] DFAST_QC completed!
[2023-06-28 04:21:29,928] [INFO] Total running time: 0h1m1s