[2023-06-27 05:39:14,219] [INFO] DFAST_QC pipeline started.
[2023-06-27 05:39:14,224] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 05:39:14,224] [INFO] DQC Reference Directory: /var/lib/cwl/stg25f2bd56-325d-43a8-8138-192c03794ea1/dqc_reference
[2023-06-27 05:39:17,349] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 05:39:17,350] [INFO] Task started: Prodigal
[2023-06-27 05:39:17,350] [INFO] Running command: gunzip -c /var/lib/cwl/stg071852a9-f4f3-413a-ab56-23b00be65fca/GCA_002457355.1_ASM245735v1_genomic.fna.gz | prodigal -d GCA_002457355.1_ASM245735v1_genomic.fna/cds.fna -a GCA_002457355.1_ASM245735v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 05:39:20,813] [INFO] Task succeeded: Prodigal
[2023-06-27 05:39:20,813] [INFO] Task started: HMMsearch
[2023-06-27 05:39:20,813] [INFO] Running command: hmmsearch --tblout GCA_002457355.1_ASM245735v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25f2bd56-325d-43a8-8138-192c03794ea1/dqc_reference/reference_markers.hmm GCA_002457355.1_ASM245735v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 05:39:20,952] [INFO] Task succeeded: HMMsearch
[2023-06-27 05:39:20,953] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg071852a9-f4f3-413a-ab56-23b00be65fca/GCA_002457355.1_ASM245735v1_genomic.fna.gz]
[2023-06-27 05:39:20,965] [INFO] Query marker FASTA was written to GCA_002457355.1_ASM245735v1_genomic.fna/markers.fasta
[2023-06-27 05:39:20,966] [INFO] Task started: Blastn
[2023-06-27 05:39:20,966] [INFO] Running command: blastn -query GCA_002457355.1_ASM245735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25f2bd56-325d-43a8-8138-192c03794ea1/dqc_reference/reference_markers.fasta -out GCA_002457355.1_ASM245735v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:39:21,447] [INFO] Task succeeded: Blastn
[2023-06-27 05:39:21,450] [INFO] Selected 15 target genomes.
[2023-06-27 05:39:21,450] [INFO] Target genome list was writen to GCA_002457355.1_ASM245735v1_genomic.fna/target_genomes.txt
[2023-06-27 05:39:21,453] [INFO] Task started: fastANI
[2023-06-27 05:39:21,453] [INFO] Running command: fastANI --query /var/lib/cwl/stg071852a9-f4f3-413a-ab56-23b00be65fca/GCA_002457355.1_ASM245735v1_genomic.fna.gz --refList GCA_002457355.1_ASM245735v1_genomic.fna/target_genomes.txt --output GCA_002457355.1_ASM245735v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 05:39:28,232] [INFO] Task succeeded: fastANI
[2023-06-27 05:39:28,233] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25f2bd56-325d-43a8-8138-192c03794ea1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 05:39:28,233] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25f2bd56-325d-43a8-8138-192c03794ea1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 05:39:28,235] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 05:39:28,235] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 05:39:28,235] [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 05:39:28,237] [INFO] DFAST Taxonomy check result was written to GCA_002457355.1_ASM245735v1_genomic.fna/tc_result.tsv
[2023-06-27 05:39:28,237] [INFO] ===== Taxonomy check completed =====
[2023-06-27 05:39:28,237] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 05:39:28,237] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25f2bd56-325d-43a8-8138-192c03794ea1/dqc_reference/checkm_data
[2023-06-27 05:39:28,241] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 05:39:28,255] [INFO] Task started: CheckM
[2023-06-27 05:39:28,255] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002457355.1_ASM245735v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002457355.1_ASM245735v1_genomic.fna/checkm_input GCA_002457355.1_ASM245735v1_genomic.fna/checkm_result
[2023-06-27 05:39:45,504] [INFO] Task succeeded: CheckM
[2023-06-27 05:39:45,505] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 05:39:45,530] [INFO] ===== Completeness check finished =====
[2023-06-27 05:39:45,531] [INFO] ===== Start GTDB Search =====
[2023-06-27 05:39:45,531] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002457355.1_ASM245735v1_genomic.fna/markers.fasta)
[2023-06-27 05:39:45,531] [INFO] Task started: Blastn
[2023-06-27 05:39:45,531] [INFO] Running command: blastn -query GCA_002457355.1_ASM245735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25f2bd56-325d-43a8-8138-192c03794ea1/dqc_reference/reference_markers_gtdb.fasta -out GCA_002457355.1_ASM245735v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:39:45,957] [INFO] Task succeeded: Blastn
[2023-06-27 05:39:45,960] [INFO] Selected 19 target genomes.
[2023-06-27 05:39:45,960] [INFO] Target genome list was writen to GCA_002457355.1_ASM245735v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 05:39:45,984] [INFO] Task started: fastANI
[2023-06-27 05:39:45,985] [INFO] Running command: fastANI --query /var/lib/cwl/stg071852a9-f4f3-413a-ab56-23b00be65fca/GCA_002457355.1_ASM245735v1_genomic.fna.gz --refList GCA_002457355.1_ASM245735v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002457355.1_ASM245735v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 05:39:52,156] [INFO] Task succeeded: fastANI
[2023-06-27 05:39:52,164] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 05:39:52,164] [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_902584445.1	s__UBA8316 sp902584445	78.6466	130	281	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002171295.2	s__UBA8316 sp002171295	78.638	90	281	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902515395.1	s__UBA8316 sp902515395	78.6311	110	281	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	96.55	96.55	0.73	0.73	2	-
GCA_902590705.1	s__UBA8316 sp902590705	78.3821	119	281	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.92	99.92	0.88	0.88	2	-
GCA_002695445.1	s__UBA8316 sp002695445	76.9473	78	281	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	97.71	97.71	0.68	0.68	2	-
GCA_002364535.1	s__UBA8316 sp002364535	76.9264	62	281	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.85	99.85	0.95	0.95	2	-
GCA_018647605.1	s__UBA8316 sp018647605	76.754	68	281	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009936675.1	s__UBA8316 sp009936675	76.4881	56	281	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.40	99.39	0.87	0.79	3	-
--------------------------------------------------------------------------------
[2023-06-27 05:39:52,166] [INFO] GTDB search result was written to GCA_002457355.1_ASM245735v1_genomic.fna/result_gtdb.tsv
[2023-06-27 05:39:52,166] [INFO] ===== GTDB Search completed =====
[2023-06-27 05:39:52,189] [INFO] DFAST_QC result json was written to GCA_002457355.1_ASM245735v1_genomic.fna/dqc_result.json
[2023-06-27 05:39:52,189] [INFO] DFAST_QC completed!
[2023-06-27 05:39:52,189] [INFO] Total running time: 0h0m38s