[2023-06-28 12:14:17,846] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:14:17,850] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:14:17,850] [INFO] DQC Reference Directory: /var/lib/cwl/stgffa5ff37-5362-4f54-9191-e510936812b2/dqc_reference
[2023-06-28 12:14:20,160] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:14:20,161] [INFO] Task started: Prodigal
[2023-06-28 12:14:20,161] [INFO] Running command: gunzip -c /var/lib/cwl/stg6fbee891-7186-4245-90ec-9fccfce22b0a/GCA_027032175.1_ASM2703217v1_genomic.fna.gz | prodigal -d GCA_027032175.1_ASM2703217v1_genomic.fna/cds.fna -a GCA_027032175.1_ASM2703217v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:14:25,372] [INFO] Task succeeded: Prodigal
[2023-06-28 12:14:25,372] [INFO] Task started: HMMsearch
[2023-06-28 12:14:25,372] [INFO] Running command: hmmsearch --tblout GCA_027032175.1_ASM2703217v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgffa5ff37-5362-4f54-9191-e510936812b2/dqc_reference/reference_markers.hmm GCA_027032175.1_ASM2703217v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:14:25,579] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:14:25,581] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg6fbee891-7186-4245-90ec-9fccfce22b0a/GCA_027032175.1_ASM2703217v1_genomic.fna.gz]
[2023-06-28 12:14:25,610] [INFO] Query marker FASTA was written to GCA_027032175.1_ASM2703217v1_genomic.fna/markers.fasta
[2023-06-28 12:14:25,610] [INFO] Task started: Blastn
[2023-06-28 12:14:25,610] [INFO] Running command: blastn -query GCA_027032175.1_ASM2703217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgffa5ff37-5362-4f54-9191-e510936812b2/dqc_reference/reference_markers.fasta -out GCA_027032175.1_ASM2703217v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:14:26,342] [INFO] Task succeeded: Blastn
[2023-06-28 12:14:26,349] [INFO] Selected 26 target genomes.
[2023-06-28 12:14:26,349] [INFO] Target genome list was writen to GCA_027032175.1_ASM2703217v1_genomic.fna/target_genomes.txt
[2023-06-28 12:14:26,351] [INFO] Task started: fastANI
[2023-06-28 12:14:26,351] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fbee891-7186-4245-90ec-9fccfce22b0a/GCA_027032175.1_ASM2703217v1_genomic.fna.gz --refList GCA_027032175.1_ASM2703217v1_genomic.fna/target_genomes.txt --output GCA_027032175.1_ASM2703217v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:14:41,167] [INFO] Task succeeded: fastANI
[2023-06-28 12:14:41,167] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgffa5ff37-5362-4f54-9191-e510936812b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:14:41,168] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgffa5ff37-5362-4f54-9191-e510936812b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:14:41,171] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:14:41,172] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 12:14:41,172] [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 12:14:41,174] [INFO] DFAST Taxonomy check result was written to GCA_027032175.1_ASM2703217v1_genomic.fna/tc_result.tsv
[2023-06-28 12:14:41,175] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:14:41,176] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:14:41,176] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgffa5ff37-5362-4f54-9191-e510936812b2/dqc_reference/checkm_data
[2023-06-28 12:14:41,180] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:14:41,211] [INFO] Task started: CheckM
[2023-06-28 12:14:41,211] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027032175.1_ASM2703217v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027032175.1_ASM2703217v1_genomic.fna/checkm_input GCA_027032175.1_ASM2703217v1_genomic.fna/checkm_result
[2023-06-28 12:15:03,574] [INFO] Task succeeded: CheckM
[2023-06-28 12:15:03,576] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 4.63%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 12:15:03,599] [INFO] ===== Completeness check finished =====
[2023-06-28 12:15:03,599] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:15:03,599] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027032175.1_ASM2703217v1_genomic.fna/markers.fasta)
[2023-06-28 12:15:03,600] [INFO] Task started: Blastn
[2023-06-28 12:15:03,600] [INFO] Running command: blastn -query GCA_027032175.1_ASM2703217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgffa5ff37-5362-4f54-9191-e510936812b2/dqc_reference/reference_markers_gtdb.fasta -out GCA_027032175.1_ASM2703217v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:15:04,784] [INFO] Task succeeded: Blastn
[2023-06-28 12:15:04,790] [INFO] Selected 21 target genomes.
[2023-06-28 12:15:04,790] [INFO] Target genome list was writen to GCA_027032175.1_ASM2703217v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:15:04,826] [INFO] Task started: fastANI
[2023-06-28 12:15:04,826] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fbee891-7186-4245-90ec-9fccfce22b0a/GCA_027032175.1_ASM2703217v1_genomic.fna.gz --refList GCA_027032175.1_ASM2703217v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027032175.1_ASM2703217v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:15:14,009] [INFO] Task succeeded: fastANI
[2023-06-28 12:15:14,018] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 12:15:14,018] [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_015491735.1	s__DRMK01 sp015491735	80.0568	157	324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DRMK01;f__DRMK01;g__DRMK01	95.0	99.89	99.89	0.95	0.95	2	-
GCA_015488495.1	s__DRMK01 sp015488495	78.1319	103	324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DRMK01;f__DRMK01;g__DRMK01	95.0	98.86	98.62	0.82	0.79	5	-
GCA_011322575.1	s__DRMK01 sp011322575	77.9343	61	324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DRMK01;f__DRMK01;g__DRMK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015490535.1	s__DRMK01 sp015490535	77.7457	86	324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DRMK01;f__DRMK01;g__DRMK01	95.0	99.14	99.14	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-06-28 12:15:14,021] [INFO] GTDB search result was written to GCA_027032175.1_ASM2703217v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:15:14,021] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:15:14,023] [INFO] DFAST_QC result json was written to GCA_027032175.1_ASM2703217v1_genomic.fna/dqc_result.json
[2023-06-28 12:15:14,024] [INFO] DFAST_QC completed!
[2023-06-28 12:15:14,024] [INFO] Total running time: 0h0m56s