[2023-06-28 21:01:58,195] [INFO] DFAST_QC pipeline started.
[2023-06-28 21:01:58,199] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 21:01:58,199] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a95c5f4-c901-42a2-b660-df644c5bf0a7/dqc_reference
[2023-06-28 21:01:59,542] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 21:01:59,543] [INFO] Task started: Prodigal
[2023-06-28 21:01:59,544] [INFO] Running command: gunzip -c /var/lib/cwl/stg9a7ce4ca-0678-4b48-b518-9c6dd26786f3/GCA_015492495.1_ASM1549249v1_genomic.fna.gz | prodigal -d GCA_015492495.1_ASM1549249v1_genomic.fna/cds.fna -a GCA_015492495.1_ASM1549249v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 21:02:05,587] [INFO] Task succeeded: Prodigal
[2023-06-28 21:02:05,587] [INFO] Task started: HMMsearch
[2023-06-28 21:02:05,587] [INFO] Running command: hmmsearch --tblout GCA_015492495.1_ASM1549249v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a95c5f4-c901-42a2-b660-df644c5bf0a7/dqc_reference/reference_markers.hmm GCA_015492495.1_ASM1549249v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 21:02:05,903] [INFO] Task succeeded: HMMsearch
[2023-06-28 21:02:05,904] [INFO] Found 6/6 markers.
[2023-06-28 21:02:05,930] [INFO] Query marker FASTA was written to GCA_015492495.1_ASM1549249v1_genomic.fna/markers.fasta
[2023-06-28 21:02:05,931] [INFO] Task started: Blastn
[2023-06-28 21:02:05,931] [INFO] Running command: blastn -query GCA_015492495.1_ASM1549249v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a95c5f4-c901-42a2-b660-df644c5bf0a7/dqc_reference/reference_markers.fasta -out GCA_015492495.1_ASM1549249v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:02:06,538] [INFO] Task succeeded: Blastn
[2023-06-28 21:02:06,542] [INFO] Selected 22 target genomes.
[2023-06-28 21:02:06,543] [INFO] Target genome list was writen to GCA_015492495.1_ASM1549249v1_genomic.fna/target_genomes.txt
[2023-06-28 21:02:06,545] [INFO] Task started: fastANI
[2023-06-28 21:02:06,545] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a7ce4ca-0678-4b48-b518-9c6dd26786f3/GCA_015492495.1_ASM1549249v1_genomic.fna.gz --refList GCA_015492495.1_ASM1549249v1_genomic.fna/target_genomes.txt --output GCA_015492495.1_ASM1549249v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 21:02:18,071] [INFO] Task succeeded: fastANI
[2023-06-28 21:02:18,071] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a95c5f4-c901-42a2-b660-df644c5bf0a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 21:02:18,072] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a95c5f4-c901-42a2-b660-df644c5bf0a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 21:02:18,073] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 21:02:18,073] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 21:02:18,073] [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 21:02:18,077] [INFO] DFAST Taxonomy check result was written to GCA_015492495.1_ASM1549249v1_genomic.fna/tc_result.tsv
[2023-06-28 21:02:18,078] [INFO] ===== Taxonomy check completed =====
[2023-06-28 21:02:18,078] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 21:02:18,078] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a95c5f4-c901-42a2-b660-df644c5bf0a7/dqc_reference/checkm_data
[2023-06-28 21:02:18,081] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 21:02:18,113] [INFO] Task started: CheckM
[2023-06-28 21:02:18,114] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015492495.1_ASM1549249v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015492495.1_ASM1549249v1_genomic.fna/checkm_input GCA_015492495.1_ASM1549249v1_genomic.fna/checkm_result
[2023-06-28 21:02:42,241] [INFO] Task succeeded: CheckM
[2023-06-28 21:02:42,242] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 21:02:42,268] [INFO] ===== Completeness check finished =====
[2023-06-28 21:02:42,269] [INFO] ===== Start GTDB Search =====
[2023-06-28 21:02:42,269] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015492495.1_ASM1549249v1_genomic.fna/markers.fasta)
[2023-06-28 21:02:42,270] [INFO] Task started: Blastn
[2023-06-28 21:02:42,270] [INFO] Running command: blastn -query GCA_015492495.1_ASM1549249v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a95c5f4-c901-42a2-b660-df644c5bf0a7/dqc_reference/reference_markers_gtdb.fasta -out GCA_015492495.1_ASM1549249v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:02:43,007] [INFO] Task succeeded: Blastn
[2023-06-28 21:02:43,013] [INFO] Selected 20 target genomes.
[2023-06-28 21:02:43,014] [INFO] Target genome list was writen to GCA_015492495.1_ASM1549249v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 21:02:43,059] [INFO] Task started: fastANI
[2023-06-28 21:02:43,059] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a7ce4ca-0678-4b48-b518-9c6dd26786f3/GCA_015492495.1_ASM1549249v1_genomic.fna.gz --refList GCA_015492495.1_ASM1549249v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015492495.1_ASM1549249v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 21:02:53,647] [INFO] Task succeeded: fastANI
[2023-06-28 21:02:53,662] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 21:02:53,662] [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_015492495.1	s__S146-62 sp015492495	100.0	691	694	d__Bacteria;p__Desulfobacterota;c__GWC2-55-46;o__GWC2-55-46;f__DRQE01;g__S146-62	95.0	98.98	98.98	0.92	0.92	2	conclusive
GCA_016219105.1	s__JACRCI01 sp016219105	76.8976	87	694	d__Bacteria;p__Desulfobacterota;c__GWC2-55-46;o__GWC2-55-46;f__DRQE01;g__JACRCI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011375175.1	s__DRME01 sp011375175	76.6359	101	694	d__Bacteria;p__Desulfobacterota;c__GWC2-55-46;o__GWC2-55-46;f__DRME01;g__DRME01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016219015.1	s__JACRCL01 sp016219015	76.5903	93	694	d__Bacteria;p__Desulfobacterota;c__GWC2-55-46;o__GWC2-55-46;f__GWC2-55-46;g__JACRCL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002418185.1	s__UBA5799 sp002418185	76.4593	80	694	d__Bacteria;p__Desulfobacterota;c__GWC2-55-46;o__GWC2-55-46;f__GWC2-55-46;g__UBA5799	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016219075.1	s__JACRCH01 sp016219075	76.3903	56	694	d__Bacteria;p__Desulfobacterota;c__GWC2-55-46;o__GWC2-55-46;f__GWC2-55-46;g__JACRCH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001595385.3	s__UBA5799 sp001595385	76.2375	87	694	d__Bacteria;p__Desulfobacterota;c__GWC2-55-46;o__GWC2-55-46;f__GWC2-55-46;g__UBA5799	95.0	99.99	99.97	1.00	1.00	5	-
GCA_015492245.1	s__DRQE01 sp015492245	75.9186	54	694	d__Bacteria;p__Desulfobacterota;c__GWC2-55-46;o__GWC2-55-46;f__DRQE01;g__DRQE01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 21:02:53,666] [INFO] GTDB search result was written to GCA_015492495.1_ASM1549249v1_genomic.fna/result_gtdb.tsv
[2023-06-28 21:02:53,667] [INFO] ===== GTDB Search completed =====
[2023-06-28 21:02:53,670] [INFO] DFAST_QC result json was written to GCA_015492495.1_ASM1549249v1_genomic.fna/dqc_result.json
[2023-06-28 21:02:53,670] [INFO] DFAST_QC completed!
[2023-06-28 21:02:53,671] [INFO] Total running time: 0h0m55s