[2023-06-27 13:28:58,000] [INFO] DFAST_QC pipeline started.
[2023-06-27 13:28:58,002] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 13:28:58,002] [INFO] DQC Reference Directory: /var/lib/cwl/stgf6685a43-bb3b-4820-8a13-804463585269/dqc_reference
[2023-06-27 13:29:00,344] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 13:29:00,346] [INFO] Task started: Prodigal
[2023-06-27 13:29:00,346] [INFO] Running command: gunzip -c /var/lib/cwl/stgb405c7c3-027e-44d0-b527-2b3e2bfa9a24/GCA_026399635.1_ASM2639963v1_genomic.fna.gz | prodigal -d GCA_026399635.1_ASM2639963v1_genomic.fna/cds.fna -a GCA_026399635.1_ASM2639963v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 13:29:02,340] [INFO] Task succeeded: Prodigal
[2023-06-27 13:29:02,340] [INFO] Task started: HMMsearch
[2023-06-27 13:29:02,340] [INFO] Running command: hmmsearch --tblout GCA_026399635.1_ASM2639963v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf6685a43-bb3b-4820-8a13-804463585269/dqc_reference/reference_markers.hmm GCA_026399635.1_ASM2639963v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 13:29:02,554] [INFO] Task succeeded: HMMsearch
[2023-06-27 13:29:02,556] [INFO] Found 6/6 markers.
[2023-06-27 13:29:02,575] [INFO] Query marker FASTA was written to GCA_026399635.1_ASM2639963v1_genomic.fna/markers.fasta
[2023-06-27 13:29:02,575] [INFO] Task started: Blastn
[2023-06-27 13:29:02,575] [INFO] Running command: blastn -query GCA_026399635.1_ASM2639963v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6685a43-bb3b-4820-8a13-804463585269/dqc_reference/reference_markers.fasta -out GCA_026399635.1_ASM2639963v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 13:29:04,187] [INFO] Task succeeded: Blastn
[2023-06-27 13:29:04,192] [INFO] Selected 23 target genomes.
[2023-06-27 13:29:04,192] [INFO] Target genome list was writen to GCA_026399635.1_ASM2639963v1_genomic.fna/target_genomes.txt
[2023-06-27 13:29:04,197] [INFO] Task started: fastANI
[2023-06-27 13:29:04,198] [INFO] Running command: fastANI --query /var/lib/cwl/stgb405c7c3-027e-44d0-b527-2b3e2bfa9a24/GCA_026399635.1_ASM2639963v1_genomic.fna.gz --refList GCA_026399635.1_ASM2639963v1_genomic.fna/target_genomes.txt --output GCA_026399635.1_ASM2639963v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 13:29:14,853] [INFO] Task succeeded: fastANI
[2023-06-27 13:29:14,853] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf6685a43-bb3b-4820-8a13-804463585269/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 13:29:14,854] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf6685a43-bb3b-4820-8a13-804463585269/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 13:29:14,856] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 13:29:14,856] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 13:29:14,856] [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
--------------------------------------------------------------------------------
[2023-06-27 13:29:14,859] [INFO] DFAST Taxonomy check result was written to GCA_026399635.1_ASM2639963v1_genomic.fna/tc_result.tsv
[2023-06-27 13:29:14,859] [INFO] ===== Taxonomy check completed =====
[2023-06-27 13:29:14,860] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 13:29:14,860] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf6685a43-bb3b-4820-8a13-804463585269/dqc_reference/checkm_data
[2023-06-27 13:29:14,864] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 13:29:14,879] [INFO] Task started: CheckM
[2023-06-27 13:29:14,879] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026399635.1_ASM2639963v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026399635.1_ASM2639963v1_genomic.fna/checkm_input GCA_026399635.1_ASM2639963v1_genomic.fna/checkm_result
[2023-06-27 13:29:29,724] [INFO] Task succeeded: CheckM
[2023-06-27 13:29:29,726] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-27 13:29:29,746] [INFO] ===== Completeness check finished =====
[2023-06-27 13:29:29,747] [INFO] ===== Start GTDB Search =====
[2023-06-27 13:29:29,748] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026399635.1_ASM2639963v1_genomic.fna/markers.fasta)
[2023-06-27 13:29:29,748] [INFO] Task started: Blastn
[2023-06-27 13:29:29,748] [INFO] Running command: blastn -query GCA_026399635.1_ASM2639963v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6685a43-bb3b-4820-8a13-804463585269/dqc_reference/reference_markers_gtdb.fasta -out GCA_026399635.1_ASM2639963v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 13:29:30,639] [INFO] Task succeeded: Blastn
[2023-06-27 13:29:30,644] [INFO] Selected 10 target genomes.
[2023-06-27 13:29:30,645] [INFO] Target genome list was writen to GCA_026399635.1_ASM2639963v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 13:29:30,645] [INFO] Task started: fastANI
[2023-06-27 13:29:30,646] [INFO] Running command: fastANI --query /var/lib/cwl/stgb405c7c3-027e-44d0-b527-2b3e2bfa9a24/GCA_026399635.1_ASM2639963v1_genomic.fna.gz --refList GCA_026399635.1_ASM2639963v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026399635.1_ASM2639963v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 13:29:33,190] [INFO] Task succeeded: fastANI
[2023-06-27 13:29:33,206] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 13:29:33,207] [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_014190615.1	s__Methylopumilus sp014190615	98.4351	262	307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903914945.1	s__Methylopumilus sp903914945	91.1715	239	307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus	95.0	98.58	97.76	0.86	0.81	18	-
GCF_000981505.1	s__Methylopumilus planktonicus	84.9077	271	307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus	95.0	96.26	95.25	0.92	0.89	9	-
GCF_006365315.1	s__Methylopumilus universalis	84.6141	264	307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus	95.0	97.60	96.52	0.95	0.91	36	-
GCF_006364615.1	s__Methylopumilus rimovensis	83.3436	255	307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus	95.0	98.38	98.38	0.95	0.95	2	-
GCA_903849185.1	s__Methylopumilus sp903849185	83.2025	222	307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus	95.0	98.91	98.07	0.83	0.78	5	-
GCA_003533095.1	s__Methylopumilus sp003533095	82.8409	152	307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus	95.0	99.11	99.08	0.89	0.88	3	-
GCA_016868195.1	s__Methylopumilus sp016868195	82.718	248	307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009693175.1	s__Methylopumilus sp009693175	82.4451	226	307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009926035.1	s__Methylopumilus sp009926035	82.1394	170	307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 13:29:33,209] [INFO] GTDB search result was written to GCA_026399635.1_ASM2639963v1_genomic.fna/result_gtdb.tsv
[2023-06-27 13:29:33,209] [INFO] ===== GTDB Search completed =====
[2023-06-27 13:29:33,212] [INFO] DFAST_QC result json was written to GCA_026399635.1_ASM2639963v1_genomic.fna/dqc_result.json
[2023-06-27 13:29:33,212] [INFO] DFAST_QC completed!
[2023-06-27 13:29:33,212] [INFO] Total running time: 0h0m35s