[2023-06-27 11:30:34,114] [INFO] DFAST_QC pipeline started.
[2023-06-27 11:30:34,117] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 11:30:34,118] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc816deb-1ca8-406c-96ab-ebb1f59828e0/dqc_reference
[2023-06-27 11:30:35,480] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 11:30:35,481] [INFO] Task started: Prodigal
[2023-06-27 11:30:35,481] [INFO] Running command: gunzip -c /var/lib/cwl/stg44ef1006-dea5-4083-a3b1-23f95f9379cb/GCA_026193405.1_ASM2619340v1_genomic.fna.gz | prodigal -d GCA_026193405.1_ASM2619340v1_genomic.fna/cds.fna -a GCA_026193405.1_ASM2619340v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 11:30:39,439] [INFO] Task succeeded: Prodigal
[2023-06-27 11:30:39,440] [INFO] Task started: HMMsearch
[2023-06-27 11:30:39,440] [INFO] Running command: hmmsearch --tblout GCA_026193405.1_ASM2619340v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc816deb-1ca8-406c-96ab-ebb1f59828e0/dqc_reference/reference_markers.hmm GCA_026193405.1_ASM2619340v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 11:30:39,717] [INFO] Task succeeded: HMMsearch
[2023-06-27 11:30:39,719] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg44ef1006-dea5-4083-a3b1-23f95f9379cb/GCA_026193405.1_ASM2619340v1_genomic.fna.gz]
[2023-06-27 11:30:39,749] [INFO] Query marker FASTA was written to GCA_026193405.1_ASM2619340v1_genomic.fna/markers.fasta
[2023-06-27 11:30:39,749] [INFO] Task started: Blastn
[2023-06-27 11:30:39,749] [INFO] Running command: blastn -query GCA_026193405.1_ASM2619340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc816deb-1ca8-406c-96ab-ebb1f59828e0/dqc_reference/reference_markers.fasta -out GCA_026193405.1_ASM2619340v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:30:40,450] [INFO] Task succeeded: Blastn
[2023-06-27 11:30:40,453] [INFO] Selected 13 target genomes.
[2023-06-27 11:30:40,454] [INFO] Target genome list was writen to GCA_026193405.1_ASM2619340v1_genomic.fna/target_genomes.txt
[2023-06-27 11:30:40,456] [INFO] Task started: fastANI
[2023-06-27 11:30:40,456] [INFO] Running command: fastANI --query /var/lib/cwl/stg44ef1006-dea5-4083-a3b1-23f95f9379cb/GCA_026193405.1_ASM2619340v1_genomic.fna.gz --refList GCA_026193405.1_ASM2619340v1_genomic.fna/target_genomes.txt --output GCA_026193405.1_ASM2619340v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 11:30:48,260] [INFO] Task succeeded: fastANI
[2023-06-27 11:30:48,260] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc816deb-1ca8-406c-96ab-ebb1f59828e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 11:30:48,261] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc816deb-1ca8-406c-96ab-ebb1f59828e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 11:30:48,263] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 11:30:48,264] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 11:30:48,264] [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 11:30:48,266] [INFO] DFAST Taxonomy check result was written to GCA_026193405.1_ASM2619340v1_genomic.fna/tc_result.tsv
[2023-06-27 11:30:48,267] [INFO] ===== Taxonomy check completed =====
[2023-06-27 11:30:48,267] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 11:30:48,268] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc816deb-1ca8-406c-96ab-ebb1f59828e0/dqc_reference/checkm_data
[2023-06-27 11:30:48,272] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 11:30:48,322] [INFO] Task started: CheckM
[2023-06-27 11:30:48,323] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026193405.1_ASM2619340v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026193405.1_ASM2619340v1_genomic.fna/checkm_input GCA_026193405.1_ASM2619340v1_genomic.fna/checkm_result
[2023-06-27 11:31:08,393] [INFO] Task succeeded: CheckM
[2023-06-27 11:31:08,394] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 11:31:08,416] [INFO] ===== Completeness check finished =====
[2023-06-27 11:31:08,416] [INFO] ===== Start GTDB Search =====
[2023-06-27 11:31:08,418] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026193405.1_ASM2619340v1_genomic.fna/markers.fasta)
[2023-06-27 11:31:08,419] [INFO] Task started: Blastn
[2023-06-27 11:31:08,419] [INFO] Running command: blastn -query GCA_026193405.1_ASM2619340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc816deb-1ca8-406c-96ab-ebb1f59828e0/dqc_reference/reference_markers_gtdb.fasta -out GCA_026193405.1_ASM2619340v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:31:09,245] [INFO] Task succeeded: Blastn
[2023-06-27 11:31:09,249] [INFO] Selected 18 target genomes.
[2023-06-27 11:31:09,249] [INFO] Target genome list was writen to GCA_026193405.1_ASM2619340v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 11:31:09,262] [INFO] Task started: fastANI
[2023-06-27 11:31:09,263] [INFO] Running command: fastANI --query /var/lib/cwl/stg44ef1006-dea5-4083-a3b1-23f95f9379cb/GCA_026193405.1_ASM2619340v1_genomic.fna.gz --refList GCA_026193405.1_ASM2619340v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026193405.1_ASM2619340v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 11:31:20,009] [INFO] Task succeeded: fastANI
[2023-06-27 11:31:20,018] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 11:31:20,018] [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_014860115.1	s__IGN2 sp014860115	77.3305	178	527	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__IGN2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013388525.1	s__IGN2 sp013388525	77.234	111	527	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__IGN2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716565.1	s__IGN2 sp016716565	77.0921	147	527	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__IGN2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013285405.1	s__IGN2 sp013285405	76.9735	121	527	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__IGN2	95.0	99.60	98.20	0.96	0.86	8	-
GCA_013042995.1	s__IGN2 sp013042995	76.0037	94	527	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__IGN2	95.0	99.79	99.74	0.93	0.91	5	-
GCA_002050295.1	s__IGN3 sp002050295	75.8497	52	527	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__IGN3	95.0	99.89	99.89	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-06-27 11:31:20,020] [INFO] GTDB search result was written to GCA_026193405.1_ASM2619340v1_genomic.fna/result_gtdb.tsv
[2023-06-27 11:31:20,021] [INFO] ===== GTDB Search completed =====
[2023-06-27 11:31:20,026] [INFO] DFAST_QC result json was written to GCA_026193405.1_ASM2619340v1_genomic.fna/dqc_result.json
[2023-06-27 11:31:20,026] [INFO] DFAST_QC completed!
[2023-06-27 11:31:20,026] [INFO] Total running time: 0h0m46s