[2023-06-28 05:09:16,552] [INFO] DFAST_QC pipeline started.
[2023-06-28 05:09:16,554] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 05:09:16,554] [INFO] DQC Reference Directory: /var/lib/cwl/stg11efd709-afe0-45d0-8074-d53955d76e45/dqc_reference
[2023-06-28 05:09:17,852] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 05:09:17,853] [INFO] Task started: Prodigal
[2023-06-28 05:09:17,853] [INFO] Running command: gunzip -c /var/lib/cwl/stga60f1f27-4a01-469e-b9da-4cbe8fa46f27/GCA_019246845.1_ASM1924684v1_genomic.fna.gz | prodigal -d GCA_019246845.1_ASM1924684v1_genomic.fna/cds.fna -a GCA_019246845.1_ASM1924684v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 05:09:24,068] [INFO] Task succeeded: Prodigal
[2023-06-28 05:09:24,069] [INFO] Task started: HMMsearch
[2023-06-28 05:09:24,069] [INFO] Running command: hmmsearch --tblout GCA_019246845.1_ASM1924684v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11efd709-afe0-45d0-8074-d53955d76e45/dqc_reference/reference_markers.hmm GCA_019246845.1_ASM1924684v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 05:09:24,298] [INFO] Task succeeded: HMMsearch
[2023-06-28 05:09:24,299] [WARNING] Found 4/6 markers. [/var/lib/cwl/stga60f1f27-4a01-469e-b9da-4cbe8fa46f27/GCA_019246845.1_ASM1924684v1_genomic.fna.gz]
[2023-06-28 05:09:24,331] [INFO] Query marker FASTA was written to GCA_019246845.1_ASM1924684v1_genomic.fna/markers.fasta
[2023-06-28 05:09:24,331] [INFO] Task started: Blastn
[2023-06-28 05:09:24,331] [INFO] Running command: blastn -query GCA_019246845.1_ASM1924684v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11efd709-afe0-45d0-8074-d53955d76e45/dqc_reference/reference_markers.fasta -out GCA_019246845.1_ASM1924684v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 05:09:24,859] [INFO] Task succeeded: Blastn
[2023-06-28 05:09:24,864] [INFO] Selected 15 target genomes.
[2023-06-28 05:09:24,864] [INFO] Target genome list was writen to GCA_019246845.1_ASM1924684v1_genomic.fna/target_genomes.txt
[2023-06-28 05:09:24,866] [INFO] Task started: fastANI
[2023-06-28 05:09:24,866] [INFO] Running command: fastANI --query /var/lib/cwl/stga60f1f27-4a01-469e-b9da-4cbe8fa46f27/GCA_019246845.1_ASM1924684v1_genomic.fna.gz --refList GCA_019246845.1_ASM1924684v1_genomic.fna/target_genomes.txt --output GCA_019246845.1_ASM1924684v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 05:09:33,836] [INFO] Task succeeded: fastANI
[2023-06-28 05:09:33,837] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11efd709-afe0-45d0-8074-d53955d76e45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 05:09:33,837] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11efd709-afe0-45d0-8074-d53955d76e45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 05:09:33,839] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 05:09:33,839] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 05:09:33,839] [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 05:09:33,842] [INFO] DFAST Taxonomy check result was written to GCA_019246845.1_ASM1924684v1_genomic.fna/tc_result.tsv
[2023-06-28 05:09:33,842] [INFO] ===== Taxonomy check completed =====
[2023-06-28 05:09:33,843] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 05:09:33,843] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11efd709-afe0-45d0-8074-d53955d76e45/dqc_reference/checkm_data
[2023-06-28 05:09:33,847] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 05:09:33,883] [INFO] Task started: CheckM
[2023-06-28 05:09:33,883] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019246845.1_ASM1924684v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019246845.1_ASM1924684v1_genomic.fna/checkm_input GCA_019246845.1_ASM1924684v1_genomic.fna/checkm_result
[2023-06-28 05:09:59,101] [INFO] Task succeeded: CheckM
[2023-06-28 05:09:59,103] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.67%
Contamintation: 0.93%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-28 05:09:59,126] [INFO] ===== Completeness check finished =====
[2023-06-28 05:09:59,126] [INFO] ===== Start GTDB Search =====
[2023-06-28 05:09:59,127] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019246845.1_ASM1924684v1_genomic.fna/markers.fasta)
[2023-06-28 05:09:59,127] [INFO] Task started: Blastn
[2023-06-28 05:09:59,127] [INFO] Running command: blastn -query GCA_019246845.1_ASM1924684v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11efd709-afe0-45d0-8074-d53955d76e45/dqc_reference/reference_markers_gtdb.fasta -out GCA_019246845.1_ASM1924684v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 05:09:59,650] [INFO] Task succeeded: Blastn
[2023-06-28 05:09:59,654] [INFO] Selected 9 target genomes.
[2023-06-28 05:09:59,654] [INFO] Target genome list was writen to GCA_019246845.1_ASM1924684v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 05:09:59,660] [INFO] Task started: fastANI
[2023-06-28 05:09:59,661] [INFO] Running command: fastANI --query /var/lib/cwl/stga60f1f27-4a01-469e-b9da-4cbe8fa46f27/GCA_019246845.1_ASM1924684v1_genomic.fna.gz --refList GCA_019246845.1_ASM1924684v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019246845.1_ASM1924684v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 05:10:06,733] [INFO] Task succeeded: fastANI
[2023-06-28 05:10:06,750] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 05:10:06,750] [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_019247865.1	s__JACMLC01 sp019247865	81.1518	302	556	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__JACMLC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014379795.1	s__JACMLC01 sp014379795	79.4351	221	556	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__JACMLC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003223935.1	s__QHXQ01 sp003223935	77.3645	121	556	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__QHXQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014534425.1	s__JACVRN01 sp014534425	77.021	154	556	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__JACVRN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013698055.1	s__QHXM01 sp013698055	76.7948	86	556	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__QHXM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003222945.1	s__QHXM01 sp003222945	76.7505	112	556	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__QHXM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003222975.1	s__QHXN01 sp003222975	76.4294	141	556	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__QHXN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019242475.1	s__QHXN01 sp019242475	76.3471	142	556	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__QHXN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013813825.1	s__JACCRA01 sp013813825	76.2761	58	556	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__JACCRA01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 05:10:06,752] [INFO] GTDB search result was written to GCA_019246845.1_ASM1924684v1_genomic.fna/result_gtdb.tsv
[2023-06-28 05:10:06,753] [INFO] ===== GTDB Search completed =====
[2023-06-28 05:10:06,756] [INFO] DFAST_QC result json was written to GCA_019246845.1_ASM1924684v1_genomic.fna/dqc_result.json
[2023-06-28 05:10:06,756] [INFO] DFAST_QC completed!
[2023-06-28 05:10:06,756] [INFO] Total running time: 0h0m50s