[2023-06-28 21:19:25,740] [INFO] DFAST_QC pipeline started.
[2023-06-28 21:19:25,748] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 21:19:25,748] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c30be20-6506-4042-a1a6-4b752d158d2e/dqc_reference
[2023-06-28 21:19:26,973] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 21:19:26,974] [INFO] Task started: Prodigal
[2023-06-28 21:19:26,975] [INFO] Running command: gunzip -c /var/lib/cwl/stg080582fa-35a5-491f-970b-6744538023bc/GCA_027310325.1_ASM2731032v1_genomic.fna.gz | prodigal -d GCA_027310325.1_ASM2731032v1_genomic.fna/cds.fna -a GCA_027310325.1_ASM2731032v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 21:19:31,511] [INFO] Task succeeded: Prodigal
[2023-06-28 21:19:31,512] [INFO] Task started: HMMsearch
[2023-06-28 21:19:31,512] [INFO] Running command: hmmsearch --tblout GCA_027310325.1_ASM2731032v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c30be20-6506-4042-a1a6-4b752d158d2e/dqc_reference/reference_markers.hmm GCA_027310325.1_ASM2731032v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 21:19:31,763] [INFO] Task succeeded: HMMsearch
[2023-06-28 21:19:31,764] [INFO] Found 6/6 markers.
[2023-06-28 21:19:31,797] [INFO] Query marker FASTA was written to GCA_027310325.1_ASM2731032v1_genomic.fna/markers.fasta
[2023-06-28 21:19:31,797] [INFO] Task started: Blastn
[2023-06-28 21:19:31,798] [INFO] Running command: blastn -query GCA_027310325.1_ASM2731032v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c30be20-6506-4042-a1a6-4b752d158d2e/dqc_reference/reference_markers.fasta -out GCA_027310325.1_ASM2731032v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:19:32,421] [INFO] Task succeeded: Blastn
[2023-06-28 21:19:32,426] [INFO] Selected 20 target genomes.
[2023-06-28 21:19:32,427] [INFO] Target genome list was writen to GCA_027310325.1_ASM2731032v1_genomic.fna/target_genomes.txt
[2023-06-28 21:19:32,428] [INFO] Task started: fastANI
[2023-06-28 21:19:32,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg080582fa-35a5-491f-970b-6744538023bc/GCA_027310325.1_ASM2731032v1_genomic.fna.gz --refList GCA_027310325.1_ASM2731032v1_genomic.fna/target_genomes.txt --output GCA_027310325.1_ASM2731032v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 21:19:46,312] [INFO] Task succeeded: fastANI
[2023-06-28 21:19:46,312] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c30be20-6506-4042-a1a6-4b752d158d2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 21:19:46,313] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c30be20-6506-4042-a1a6-4b752d158d2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 21:19:46,314] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 21:19:46,314] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 21:19:46,315] [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 21:19:46,316] [INFO] DFAST Taxonomy check result was written to GCA_027310325.1_ASM2731032v1_genomic.fna/tc_result.tsv
[2023-06-28 21:19:46,317] [INFO] ===== Taxonomy check completed =====
[2023-06-28 21:19:46,317] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 21:19:46,317] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c30be20-6506-4042-a1a6-4b752d158d2e/dqc_reference/checkm_data
[2023-06-28 21:19:46,320] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 21:19:46,346] [INFO] Task started: CheckM
[2023-06-28 21:19:46,347] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027310325.1_ASM2731032v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027310325.1_ASM2731032v1_genomic.fna/checkm_input GCA_027310325.1_ASM2731032v1_genomic.fna/checkm_result
[2023-06-28 21:20:07,567] [INFO] Task succeeded: CheckM
[2023-06-28 21:20:07,568] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 2.03%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-28 21:20:07,591] [INFO] ===== Completeness check finished =====
[2023-06-28 21:20:07,591] [INFO] ===== Start GTDB Search =====
[2023-06-28 21:20:07,592] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027310325.1_ASM2731032v1_genomic.fna/markers.fasta)
[2023-06-28 21:20:07,592] [INFO] Task started: Blastn
[2023-06-28 21:20:07,592] [INFO] Running command: blastn -query GCA_027310325.1_ASM2731032v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c30be20-6506-4042-a1a6-4b752d158d2e/dqc_reference/reference_markers_gtdb.fasta -out GCA_027310325.1_ASM2731032v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:20:08,520] [INFO] Task succeeded: Blastn
[2023-06-28 21:20:08,525] [INFO] Selected 16 target genomes.
[2023-06-28 21:20:08,525] [INFO] Target genome list was writen to GCA_027310325.1_ASM2731032v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 21:20:08,533] [INFO] Task started: fastANI
[2023-06-28 21:20:08,533] [INFO] Running command: fastANI --query /var/lib/cwl/stg080582fa-35a5-491f-970b-6744538023bc/GCA_027310325.1_ASM2731032v1_genomic.fna.gz --refList GCA_027310325.1_ASM2731032v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027310325.1_ASM2731032v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 21:20:14,469] [INFO] Task succeeded: fastANI
[2023-06-28 21:20:14,489] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 21:20:14,489] [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_016219015.1	s__JACRCL01 sp016219015	77.522	134	502	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_016235365.1	s__JACRLF01 sp016235365	77.3271	90	502	d__Bacteria;p__Desulfobacterota;c__GWC2-55-46;o__GWC2-55-46;f__GWC2-55-46;g__JACRLF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016234955.1	s__JACRLF01 sp016234955	77.2427	68	502	d__Bacteria;p__Desulfobacterota;c__GWC2-55-46;o__GWC2-55-46;f__GWC2-55-46;g__JACRLF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001797465.1	s__GWB2-55-19 sp001797465	77.2369	105	502	d__Bacteria;p__Desulfobacterota;c__GWC2-55-46;o__GWC2-55-46;f__GWC2-55-46;g__GWB2-55-19	95.0	99.81	99.78	0.97	0.95	3	-
GCA_016219075.1	s__JACRCH01 sp016219075	77.1285	93	502	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_016219115.1	s__JACRCH01 sp016219115	77.1235	101	502	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_016218095.1	s__GWB2-55-19 sp016218095	76.9594	93	502	d__Bacteria;p__Desulfobacterota;c__GWC2-55-46;o__GWC2-55-46;f__GWC2-55-46;g__GWB2-55-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001595385.3	s__UBA5799 sp001595385	76.8474	103	502	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_905339405.1	s__GWA2-54-12 sp905339405	76.7106	97	502	d__Bacteria;p__Desulfobacterota;c__GWC2-55-46;o__GWC2-55-46;f__GWC2-55-46;g__GWA2-54-12	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016212705.1	s__GWB2-55-19 sp016212705	76.6366	88	502	d__Bacteria;p__Desulfobacterota;c__GWC2-55-46;o__GWC2-55-46;f__GWC2-55-46;g__GWB2-55-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016218105.1	s__GWB2-55-19 sp016218105	76.5242	89	502	d__Bacteria;p__Desulfobacterota;c__GWC2-55-46;o__GWC2-55-46;f__GWC2-55-46;g__GWB2-55-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001797415.1	s__UBA5799 sp001797415	76.3286	79	502	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_001795535.1	s__GWA2-54-12 sp001795535	76.1566	54	502	d__Bacteria;p__Desulfobacterota;c__GWC2-55-46;o__GWC2-55-46;f__GWC2-55-46;g__GWA2-54-12	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 21:20:14,491] [INFO] GTDB search result was written to GCA_027310325.1_ASM2731032v1_genomic.fna/result_gtdb.tsv
[2023-06-28 21:20:14,491] [INFO] ===== GTDB Search completed =====
[2023-06-28 21:20:14,495] [INFO] DFAST_QC result json was written to GCA_027310325.1_ASM2731032v1_genomic.fna/dqc_result.json
[2023-06-28 21:20:14,495] [INFO] DFAST_QC completed!
[2023-06-28 21:20:14,495] [INFO] Total running time: 0h0m49s