[2023-06-19 03:53:47,749] [INFO] DFAST_QC pipeline started.
[2023-06-19 03:53:47,752] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 03:53:47,752] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d4ad8b4-e19e-4daf-9d12-cf4aa275aa46/dqc_reference
[2023-06-19 03:53:49,486] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 03:53:49,487] [INFO] Task started: Prodigal
[2023-06-19 03:53:49,487] [INFO] Running command: gunzip -c /var/lib/cwl/stg40545c37-555b-41c6-8eb6-7de14c3bc4c5/GCA_018694785.1_ASM1869478v1_genomic.fna.gz | prodigal -d GCA_018694785.1_ASM1869478v1_genomic.fna/cds.fna -a GCA_018694785.1_ASM1869478v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 03:53:53,421] [INFO] Task succeeded: Prodigal
[2023-06-19 03:53:53,421] [INFO] Task started: HMMsearch
[2023-06-19 03:53:53,421] [INFO] Running command: hmmsearch --tblout GCA_018694785.1_ASM1869478v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d4ad8b4-e19e-4daf-9d12-cf4aa275aa46/dqc_reference/reference_markers.hmm GCA_018694785.1_ASM1869478v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 03:53:53,626] [INFO] Task succeeded: HMMsearch
[2023-06-19 03:53:53,628] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg40545c37-555b-41c6-8eb6-7de14c3bc4c5/GCA_018694785.1_ASM1869478v1_genomic.fna.gz]
[2023-06-19 03:53:53,649] [INFO] Query marker FASTA was written to GCA_018694785.1_ASM1869478v1_genomic.fna/markers.fasta
[2023-06-19 03:53:53,650] [INFO] Task started: Blastn
[2023-06-19 03:53:53,650] [INFO] Running command: blastn -query GCA_018694785.1_ASM1869478v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d4ad8b4-e19e-4daf-9d12-cf4aa275aa46/dqc_reference/reference_markers.fasta -out GCA_018694785.1_ASM1869478v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 03:53:54,258] [INFO] Task succeeded: Blastn
[2023-06-19 03:53:54,262] [INFO] Selected 25 target genomes.
[2023-06-19 03:53:54,263] [INFO] Target genome list was writen to GCA_018694785.1_ASM1869478v1_genomic.fna/target_genomes.txt
[2023-06-19 03:53:54,269] [INFO] Task started: fastANI
[2023-06-19 03:53:54,270] [INFO] Running command: fastANI --query /var/lib/cwl/stg40545c37-555b-41c6-8eb6-7de14c3bc4c5/GCA_018694785.1_ASM1869478v1_genomic.fna.gz --refList GCA_018694785.1_ASM1869478v1_genomic.fna/target_genomes.txt --output GCA_018694785.1_ASM1869478v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 03:54:07,604] [INFO] Task succeeded: fastANI
[2023-06-19 03:54:07,605] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d4ad8b4-e19e-4daf-9d12-cf4aa275aa46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 03:54:07,606] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d4ad8b4-e19e-4daf-9d12-cf4aa275aa46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 03:54:07,608] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 03:54:07,608] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 03:54:07,608] [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
--------------------------------------------------------------------------------
[2023-06-19 03:54:07,610] [INFO] DFAST Taxonomy check result was written to GCA_018694785.1_ASM1869478v1_genomic.fna/tc_result.tsv
[2023-06-19 03:54:07,611] [INFO] ===== Taxonomy check completed =====
[2023-06-19 03:54:07,611] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 03:54:07,612] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d4ad8b4-e19e-4daf-9d12-cf4aa275aa46/dqc_reference/checkm_data
[2023-06-19 03:54:07,616] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 03:54:07,635] [INFO] Task started: CheckM
[2023-06-19 03:54:07,635] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018694785.1_ASM1869478v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018694785.1_ASM1869478v1_genomic.fna/checkm_input GCA_018694785.1_ASM1869478v1_genomic.fna/checkm_result
[2023-06-19 03:54:26,795] [INFO] Task succeeded: CheckM
[2023-06-19 03:54:26,796] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 17.07%
Strain heterogeneity: 40.00%
--------------------------------------------------------------------------------
[2023-06-19 03:54:26,821] [INFO] ===== Completeness check finished =====
[2023-06-19 03:54:26,821] [INFO] ===== Start GTDB Search =====
[2023-06-19 03:54:26,822] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018694785.1_ASM1869478v1_genomic.fna/markers.fasta)
[2023-06-19 03:54:26,822] [INFO] Task started: Blastn
[2023-06-19 03:54:26,823] [INFO] Running command: blastn -query GCA_018694785.1_ASM1869478v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d4ad8b4-e19e-4daf-9d12-cf4aa275aa46/dqc_reference/reference_markers_gtdb.fasta -out GCA_018694785.1_ASM1869478v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 03:54:27,744] [INFO] Task succeeded: Blastn
[2023-06-19 03:54:27,755] [INFO] Selected 10 target genomes.
[2023-06-19 03:54:27,755] [INFO] Target genome list was writen to GCA_018694785.1_ASM1869478v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 03:54:27,761] [INFO] Task started: fastANI
[2023-06-19 03:54:27,761] [INFO] Running command: fastANI --query /var/lib/cwl/stg40545c37-555b-41c6-8eb6-7de14c3bc4c5/GCA_018694785.1_ASM1869478v1_genomic.fna.gz --refList GCA_018694785.1_ASM1869478v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018694785.1_ASM1869478v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 03:54:30,309] [INFO] Task succeeded: fastANI
[2023-06-19 03:54:30,320] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 03:54:30,321] [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_905478185.1	s__UWMA-0277 sp905478185	96.665	270	307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	96.67	96.67	0.88	0.88	2	conclusive
GCA_905478765.1	s__UWMA-0277 sp905478765	93.9261	268	307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479165.1	s__UWMA-0277 sp905479165	93.8018	238	307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018664745.1	s__UWMA-0277 sp018664745	81.4761	165	307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014384505.1	s__UWMA-0277 sp014384505	80.2443	171	307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181635.1	s__UWMA-0277 sp905181635	79.8468	111	307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018645865.1	s__UWMA-0277 sp018645865	79.6223	148	307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	99.24	99.14	0.74	0.70	3	-
GCA_002705205.1	s__GCA-2705205 sp002705205	77.7301	124	307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2705205	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002730985.1	s__BACL11 sp002730985	77.583	98	307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__BACL11	95.0	97.22	97.22	0.84	0.84	2	-
GCA_002693745.1	s__BACL11 sp002693745	76.7485	71	307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__BACL11	95.0	98.58	98.58	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-06-19 03:54:30,323] [INFO] GTDB search result was written to GCA_018694785.1_ASM1869478v1_genomic.fna/result_gtdb.tsv
[2023-06-19 03:54:30,323] [INFO] ===== GTDB Search completed =====
[2023-06-19 03:54:30,326] [INFO] DFAST_QC result json was written to GCA_018694785.1_ASM1869478v1_genomic.fna/dqc_result.json
[2023-06-19 03:54:30,326] [INFO] DFAST_QC completed!
[2023-06-19 03:54:30,326] [INFO] Total running time: 0h0m43s