[2023-06-28 00:20:48,058] [INFO] DFAST_QC pipeline started.
[2023-06-28 00:20:48,061] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 00:20:48,061] [INFO] DQC Reference Directory: /var/lib/cwl/stg52151dde-fc51-481c-a5e3-3dc5d2571234/dqc_reference
[2023-06-28 00:20:49,277] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 00:20:49,278] [INFO] Task started: Prodigal
[2023-06-28 00:20:49,278] [INFO] Running command: gunzip -c /var/lib/cwl/stgdbc28065-54d8-44f4-a5aa-49512092aad4/GCA_017608625.1_ASM1760862v1_genomic.fna.gz | prodigal -d GCA_017608625.1_ASM1760862v1_genomic.fna/cds.fna -a GCA_017608625.1_ASM1760862v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 00:20:50,386] [INFO] Task succeeded: Prodigal
[2023-06-28 00:20:50,386] [INFO] Task started: HMMsearch
[2023-06-28 00:20:50,387] [INFO] Running command: hmmsearch --tblout GCA_017608625.1_ASM1760862v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52151dde-fc51-481c-a5e3-3dc5d2571234/dqc_reference/reference_markers.hmm GCA_017608625.1_ASM1760862v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 00:20:50,598] [INFO] Task succeeded: HMMsearch
[2023-06-28 00:20:50,600] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgdbc28065-54d8-44f4-a5aa-49512092aad4/GCA_017608625.1_ASM1760862v1_genomic.fna.gz]
[2023-06-28 00:20:50,611] [INFO] Query marker FASTA was written to GCA_017608625.1_ASM1760862v1_genomic.fna/markers.fasta
[2023-06-28 00:20:50,612] [INFO] Task started: Blastn
[2023-06-28 00:20:50,612] [INFO] Running command: blastn -query GCA_017608625.1_ASM1760862v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52151dde-fc51-481c-a5e3-3dc5d2571234/dqc_reference/reference_markers.fasta -out GCA_017608625.1_ASM1760862v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:20:51,183] [INFO] Task succeeded: Blastn
[2023-06-28 00:20:51,186] [INFO] Selected 9 target genomes.
[2023-06-28 00:20:51,187] [INFO] Target genome list was writen to GCA_017608625.1_ASM1760862v1_genomic.fna/target_genomes.txt
[2023-06-28 00:20:51,189] [INFO] Task started: fastANI
[2023-06-28 00:20:51,189] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbc28065-54d8-44f4-a5aa-49512092aad4/GCA_017608625.1_ASM1760862v1_genomic.fna.gz --refList GCA_017608625.1_ASM1760862v1_genomic.fna/target_genomes.txt --output GCA_017608625.1_ASM1760862v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 00:20:55,857] [INFO] Task succeeded: fastANI
[2023-06-28 00:20:55,858] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52151dde-fc51-481c-a5e3-3dc5d2571234/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 00:20:55,858] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52151dde-fc51-481c-a5e3-3dc5d2571234/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 00:20:55,860] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 00:20:55,860] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 00:20:55,860] [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 00:20:55,863] [INFO] DFAST Taxonomy check result was written to GCA_017608625.1_ASM1760862v1_genomic.fna/tc_result.tsv
[2023-06-28 00:20:55,864] [INFO] ===== Taxonomy check completed =====
[2023-06-28 00:20:55,864] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 00:20:55,864] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52151dde-fc51-481c-a5e3-3dc5d2571234/dqc_reference/checkm_data
[2023-06-28 00:20:55,867] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 00:20:55,882] [INFO] Task started: CheckM
[2023-06-28 00:20:55,883] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017608625.1_ASM1760862v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017608625.1_ASM1760862v1_genomic.fna/checkm_input GCA_017608625.1_ASM1760862v1_genomic.fna/checkm_result
[2023-06-28 00:21:08,601] [INFO] Task succeeded: CheckM
[2023-06-28 00:21:08,602] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 00:21:08,631] [INFO] ===== Completeness check finished =====
[2023-06-28 00:21:08,631] [INFO] ===== Start GTDB Search =====
[2023-06-28 00:21:08,631] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017608625.1_ASM1760862v1_genomic.fna/markers.fasta)
[2023-06-28 00:21:08,632] [INFO] Task started: Blastn
[2023-06-28 00:21:08,632] [INFO] Running command: blastn -query GCA_017608625.1_ASM1760862v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52151dde-fc51-481c-a5e3-3dc5d2571234/dqc_reference/reference_markers_gtdb.fasta -out GCA_017608625.1_ASM1760862v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:21:09,247] [INFO] Task succeeded: Blastn
[2023-06-28 00:21:09,251] [INFO] Selected 9 target genomes.
[2023-06-28 00:21:09,251] [INFO] Target genome list was writen to GCA_017608625.1_ASM1760862v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 00:21:09,257] [INFO] Task started: fastANI
[2023-06-28 00:21:09,257] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbc28065-54d8-44f4-a5aa-49512092aad4/GCA_017608625.1_ASM1760862v1_genomic.fna.gz --refList GCA_017608625.1_ASM1760862v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017608625.1_ASM1760862v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 00:21:11,202] [INFO] Task succeeded: fastANI
[2023-06-28 00:21:11,211] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 00:21:11,212] [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_017608625.1	s__JAFCFN01 sp017608625	100.0	209	209	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Woesearchaeales;f__JAFCFN01;g__JAFCFN01	95.0	99.94	99.92	0.93	0.85	4	conclusive
--------------------------------------------------------------------------------
[2023-06-28 00:21:11,220] [INFO] GTDB search result was written to GCA_017608625.1_ASM1760862v1_genomic.fna/result_gtdb.tsv
[2023-06-28 00:21:11,222] [INFO] ===== GTDB Search completed =====
[2023-06-28 00:21:11,226] [INFO] DFAST_QC result json was written to GCA_017608625.1_ASM1760862v1_genomic.fna/dqc_result.json
[2023-06-28 00:21:11,226] [INFO] DFAST_QC completed!
[2023-06-28 00:21:11,226] [INFO] Total running time: 0h0m23s