[2023-07-01 07:47:39,047] [INFO] DFAST_QC pipeline started.
[2023-07-01 07:47:39,049] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 07:47:39,049] [INFO] DQC Reference Directory: /var/lib/cwl/stg34e9bb25-cf9f-41e2-b8e4-675d20bf3d59/dqc_reference
[2023-07-01 07:47:40,505] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 07:47:40,506] [INFO] Task started: Prodigal
[2023-07-01 07:47:40,507] [INFO] Running command: gunzip -c /var/lib/cwl/stg23689708-03b7-41ef-8452-155cacdf44c8/GCA_019058075.1_ASM1905807v1_genomic.fna.gz | prodigal -d GCA_019058075.1_ASM1905807v1_genomic.fna/cds.fna -a GCA_019058075.1_ASM1905807v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 07:47:44,982] [INFO] Task succeeded: Prodigal
[2023-07-01 07:47:44,982] [INFO] Task started: HMMsearch
[2023-07-01 07:47:44,982] [INFO] Running command: hmmsearch --tblout GCA_019058075.1_ASM1905807v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34e9bb25-cf9f-41e2-b8e4-675d20bf3d59/dqc_reference/reference_markers.hmm GCA_019058075.1_ASM1905807v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 07:47:45,235] [INFO] Task succeeded: HMMsearch
[2023-07-01 07:47:45,237] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg23689708-03b7-41ef-8452-155cacdf44c8/GCA_019058075.1_ASM1905807v1_genomic.fna.gz]
[2023-07-01 07:47:45,265] [INFO] Query marker FASTA was written to GCA_019058075.1_ASM1905807v1_genomic.fna/markers.fasta
[2023-07-01 07:47:45,265] [INFO] Task started: Blastn
[2023-07-01 07:47:45,265] [INFO] Running command: blastn -query GCA_019058075.1_ASM1905807v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34e9bb25-cf9f-41e2-b8e4-675d20bf3d59/dqc_reference/reference_markers.fasta -out GCA_019058075.1_ASM1905807v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 07:47:45,751] [INFO] Task succeeded: Blastn
[2023-07-01 07:47:45,755] [INFO] Selected 3 target genomes.
[2023-07-01 07:47:45,755] [INFO] Target genome list was writen to GCA_019058075.1_ASM1905807v1_genomic.fna/target_genomes.txt
[2023-07-01 07:47:45,757] [INFO] Task started: fastANI
[2023-07-01 07:47:45,757] [INFO] Running command: fastANI --query /var/lib/cwl/stg23689708-03b7-41ef-8452-155cacdf44c8/GCA_019058075.1_ASM1905807v1_genomic.fna.gz --refList GCA_019058075.1_ASM1905807v1_genomic.fna/target_genomes.txt --output GCA_019058075.1_ASM1905807v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 07:47:46,741] [INFO] Task succeeded: fastANI
[2023-07-01 07:47:46,742] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34e9bb25-cf9f-41e2-b8e4-675d20bf3d59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 07:47:46,742] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34e9bb25-cf9f-41e2-b8e4-675d20bf3d59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 07:47:46,755] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 07:47:46,755] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-07-01 07:47:46,755] [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
--------------------------------------------------------------------------------
[2023-07-01 07:47:46,769] [INFO] DFAST Taxonomy check result was written to GCA_019058075.1_ASM1905807v1_genomic.fna/tc_result.tsv
[2023-07-01 07:47:46,769] [INFO] ===== Taxonomy check completed =====
[2023-07-01 07:47:46,770] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 07:47:46,770] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34e9bb25-cf9f-41e2-b8e4-675d20bf3d59/dqc_reference/checkm_data
[2023-07-01 07:47:46,774] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 07:47:46,806] [INFO] Task started: CheckM
[2023-07-01 07:47:46,807] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019058075.1_ASM1905807v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019058075.1_ASM1905807v1_genomic.fna/checkm_input GCA_019058075.1_ASM1905807v1_genomic.fna/checkm_result
[2023-07-01 07:48:09,976] [INFO] Task succeeded: CheckM
[2023-07-01 07:48:09,977] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.79%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-07-01 07:48:10,002] [INFO] ===== Completeness check finished =====
[2023-07-01 07:48:10,003] [INFO] ===== Start GTDB Search =====
[2023-07-01 07:48:10,003] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019058075.1_ASM1905807v1_genomic.fna/markers.fasta)
[2023-07-01 07:48:10,003] [INFO] Task started: Blastn
[2023-07-01 07:48:10,004] [INFO] Running command: blastn -query GCA_019058075.1_ASM1905807v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34e9bb25-cf9f-41e2-b8e4-675d20bf3d59/dqc_reference/reference_markers_gtdb.fasta -out GCA_019058075.1_ASM1905807v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 07:48:10,481] [INFO] Task succeeded: Blastn
[2023-07-01 07:48:10,486] [INFO] Selected 8 target genomes.
[2023-07-01 07:48:10,486] [INFO] Target genome list was writen to GCA_019058075.1_ASM1905807v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 07:48:10,508] [INFO] Task started: fastANI
[2023-07-01 07:48:10,508] [INFO] Running command: fastANI --query /var/lib/cwl/stg23689708-03b7-41ef-8452-155cacdf44c8/GCA_019058075.1_ASM1905807v1_genomic.fna.gz --refList GCA_019058075.1_ASM1905807v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019058075.1_ASM1905807v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 07:48:17,974] [INFO] Task succeeded: fastANI
[2023-07-01 07:48:17,988] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 07:48:17,989] [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_019057865.1	s__Loki-b32 sp019057865	97.2949	703	772	d__Archaea;p__Asgardarchaeota;c__Lokiarchaeia;o__CR-4;f__SOKP01;g__Loki-b32	95.0	96.46	95.72	0.89	0.80	7	conclusive
GCA_016839585.1	s__Loki-b32 sp016839585	93.0778	560	772	d__Archaea;p__Asgardarchaeota;c__Lokiarchaeia;o__CR-4;f__SOKP01;g__Loki-b32	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005223125.1	s__Loki-b32 sp005223125	78.0624	228	772	d__Archaea;p__Asgardarchaeota;c__Lokiarchaeia;o__CR-4;f__SOKP01;g__Loki-b32	95.0	97.09	96.02	0.70	0.58	3	-
GCA_019058365.1	s__Loki-b32 sp019058365	77.2023	213	772	d__Archaea;p__Asgardarchaeota;c__Lokiarchaeia;o__CR-4;f__SOKP01;g__Loki-b32	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013375485.1	s__Loki-b32 sp013375485	77.1208	221	772	d__Archaea;p__Asgardarchaeota;c__Lokiarchaeia;o__CR-4;f__SOKP01;g__Loki-b32	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019057975.1	s__Loki-b32 sp019057975	76.9809	160	772	d__Archaea;p__Asgardarchaeota;c__Lokiarchaeia;o__CR-4;f__SOKP01;g__Loki-b32	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016839655.1	s__Loki-b32 sp016839655	76.5385	162	772	d__Archaea;p__Asgardarchaeota;c__Lokiarchaeia;o__CR-4;f__SOKP01;g__Loki-b32	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019057775.1	s__Loki-b32 sp019057775	76.46	169	772	d__Archaea;p__Asgardarchaeota;c__Lokiarchaeia;o__CR-4;f__SOKP01;g__Loki-b32	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 07:48:17,999] [INFO] GTDB search result was written to GCA_019058075.1_ASM1905807v1_genomic.fna/result_gtdb.tsv
[2023-07-01 07:48:18,000] [INFO] ===== GTDB Search completed =====
[2023-07-01 07:48:18,003] [INFO] DFAST_QC result json was written to GCA_019058075.1_ASM1905807v1_genomic.fna/dqc_result.json
[2023-07-01 07:48:18,004] [INFO] DFAST_QC completed!
[2023-07-01 07:48:18,004] [INFO] Total running time: 0h0m39s