[2023-06-08 13:33:43,345] [INFO] DFAST_QC pipeline started.
[2023-06-08 13:33:43,348] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 13:33:43,349] [INFO] DQC Reference Directory: /var/lib/cwl/stgac87dbfb-121b-4295-90db-de16d91e55cf/dqc_reference
[2023-06-08 13:33:44,752] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 13:33:44,753] [INFO] Task started: Prodigal
[2023-06-08 13:33:44,754] [INFO] Running command: gunzip -c /var/lib/cwl/stg98c699c1-2c43-4f3e-90fe-f6c0edf3199b/GCA_947581765.1_Lapin-001_bin42_genomic.fna.gz | prodigal -d GCA_947581765.1_Lapin-001_bin42_genomic.fna/cds.fna -a GCA_947581765.1_Lapin-001_bin42_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 13:33:46,566] [INFO] Task succeeded: Prodigal
[2023-06-08 13:33:46,566] [INFO] Task started: HMMsearch
[2023-06-08 13:33:46,567] [INFO] Running command: hmmsearch --tblout GCA_947581765.1_Lapin-001_bin42_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac87dbfb-121b-4295-90db-de16d91e55cf/dqc_reference/reference_markers.hmm GCA_947581765.1_Lapin-001_bin42_genomic.fna/protein.faa > /dev/null
[2023-06-08 13:33:46,777] [INFO] Task succeeded: HMMsearch
[2023-06-08 13:33:46,780] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg98c699c1-2c43-4f3e-90fe-f6c0edf3199b/GCA_947581765.1_Lapin-001_bin42_genomic.fna.gz]
[2023-06-08 13:33:46,797] [INFO] Query marker FASTA was written to GCA_947581765.1_Lapin-001_bin42_genomic.fna/markers.fasta
[2023-06-08 13:33:46,798] [INFO] Task started: Blastn
[2023-06-08 13:33:46,798] [INFO] Running command: blastn -query GCA_947581765.1_Lapin-001_bin42_genomic.fna/markers.fasta -db /var/lib/cwl/stgac87dbfb-121b-4295-90db-de16d91e55cf/dqc_reference/reference_markers.fasta -out GCA_947581765.1_Lapin-001_bin42_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:33:47,417] [INFO] Task succeeded: Blastn
[2023-06-08 13:33:47,422] [INFO] Selected 15 target genomes.
[2023-06-08 13:33:47,422] [INFO] Target genome list was writen to GCA_947581765.1_Lapin-001_bin42_genomic.fna/target_genomes.txt
[2023-06-08 13:33:47,424] [INFO] Task started: fastANI
[2023-06-08 13:33:47,424] [INFO] Running command: fastANI --query /var/lib/cwl/stg98c699c1-2c43-4f3e-90fe-f6c0edf3199b/GCA_947581765.1_Lapin-001_bin42_genomic.fna.gz --refList GCA_947581765.1_Lapin-001_bin42_genomic.fna/target_genomes.txt --output GCA_947581765.1_Lapin-001_bin42_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 13:33:54,337] [INFO] Task succeeded: fastANI
[2023-06-08 13:33:54,337] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac87dbfb-121b-4295-90db-de16d91e55cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 13:33:54,337] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac87dbfb-121b-4295-90db-de16d91e55cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 13:33:54,339] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 13:33:54,339] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 13:33:54,339] [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
--------------------------------------------------------------------------------
[2023-06-08 13:33:54,341] [INFO] DFAST Taxonomy check result was written to GCA_947581765.1_Lapin-001_bin42_genomic.fna/tc_result.tsv
[2023-06-08 13:33:54,342] [INFO] ===== Taxonomy check completed =====
[2023-06-08 13:33:54,342] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 13:33:54,342] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac87dbfb-121b-4295-90db-de16d91e55cf/dqc_reference/checkm_data
[2023-06-08 13:33:54,345] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 13:33:54,365] [INFO] Task started: CheckM
[2023-06-08 13:33:54,365] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947581765.1_Lapin-001_bin42_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947581765.1_Lapin-001_bin42_genomic.fna/checkm_input GCA_947581765.1_Lapin-001_bin42_genomic.fna/checkm_result
[2023-06-08 13:34:08,335] [INFO] Task succeeded: CheckM
[2023-06-08 13:34:08,337] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 13:34:08,352] [INFO] ===== Completeness check finished =====
[2023-06-08 13:34:08,352] [INFO] ===== Start GTDB Search =====
[2023-06-08 13:34:08,353] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947581765.1_Lapin-001_bin42_genomic.fna/markers.fasta)
[2023-06-08 13:34:08,353] [INFO] Task started: Blastn
[2023-06-08 13:34:08,353] [INFO] Running command: blastn -query GCA_947581765.1_Lapin-001_bin42_genomic.fna/markers.fasta -db /var/lib/cwl/stgac87dbfb-121b-4295-90db-de16d91e55cf/dqc_reference/reference_markers_gtdb.fasta -out GCA_947581765.1_Lapin-001_bin42_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:34:09,063] [INFO] Task succeeded: Blastn
[2023-06-08 13:34:09,066] [INFO] Selected 14 target genomes.
[2023-06-08 13:34:09,066] [INFO] Target genome list was writen to GCA_947581765.1_Lapin-001_bin42_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 13:34:09,068] [INFO] Task started: fastANI
[2023-06-08 13:34:09,068] [INFO] Running command: fastANI --query /var/lib/cwl/stg98c699c1-2c43-4f3e-90fe-f6c0edf3199b/GCA_947581765.1_Lapin-001_bin42_genomic.fna.gz --refList GCA_947581765.1_Lapin-001_bin42_genomic.fna/target_genomes_gtdb.txt --output GCA_947581765.1_Lapin-001_bin42_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 13:34:12,193] [INFO] Task succeeded: fastANI
[2023-06-08 13:34:12,210] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 13:34:12,211] [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_902795975.1	s__UBA5578 sp902795975	79.3783	150	390	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5578	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002425325.1	s__UBA5578 sp002425325	78.8212	150	390	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5578	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017527675.1	s__RGIG6635 sp017527675	77.5106	73	390	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RGIG6635	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017536505.1	s__UMGS1613 sp017536505	77.1746	83	390	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS1613	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553395.1	s__UMGS1613 sp900553395	77.1501	58	390	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS1613	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550255.1	s__UBA5026 sp900550255	77.072	55	390	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5026	95.0	98.55	98.27	0.87	0.84	3	-
GCA_017462455.1	s__UMGS1613 sp017462455	76.8318	83	390	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS1613	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015059155.1	s__UMGS1613 sp015059155	76.5759	74	390	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS1613	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546275.1	s__UMGS872 sp900546275	76.5414	80	390	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS872	95.0	97.38	97.34	0.83	0.82	3	-
GCA_017484205.1	s__RGIG9169 sp017484205	76.4365	63	390	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RGIG9169	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015059545.1	s__UBA5026 sp015059545	76.3857	88	390	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5026	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 13:34:12,212] [INFO] GTDB search result was written to GCA_947581765.1_Lapin-001_bin42_genomic.fna/result_gtdb.tsv
[2023-06-08 13:34:12,213] [INFO] ===== GTDB Search completed =====
[2023-06-08 13:34:12,216] [INFO] DFAST_QC result json was written to GCA_947581765.1_Lapin-001_bin42_genomic.fna/dqc_result.json
[2023-06-08 13:34:12,216] [INFO] DFAST_QC completed!
[2023-06-08 13:34:12,216] [INFO] Total running time: 0h0m29s