[2024-01-25 20:27:20,862] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:27:20,863] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:27:20,863] [INFO] DQC Reference Directory: /var/lib/cwl/stg34a05aae-c62b-4cec-938c-03602ec84e5c/dqc_reference
[2024-01-25 20:27:21,988] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:27:21,989] [INFO] Task started: Prodigal
[2024-01-25 20:27:21,989] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f3e3ad9-8778-4e66-b8d7-ef3a4e053164/GCF_900232945.1_PRJEB22715_genomic.fna.gz | prodigal -d GCF_900232945.1_PRJEB22715_genomic.fna/cds.fna -a GCF_900232945.1_PRJEB22715_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:27:25,872] [INFO] Task succeeded: Prodigal
[2024-01-25 20:27:25,873] [INFO] Task started: HMMsearch
[2024-01-25 20:27:25,873] [INFO] Running command: hmmsearch --tblout GCF_900232945.1_PRJEB22715_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34a05aae-c62b-4cec-938c-03602ec84e5c/dqc_reference/reference_markers.hmm GCF_900232945.1_PRJEB22715_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:27:26,041] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:27:26,042] [INFO] Found 6/6 markers.
[2024-01-25 20:27:26,067] [INFO] Query marker FASTA was written to GCF_900232945.1_PRJEB22715_genomic.fna/markers.fasta
[2024-01-25 20:27:26,067] [INFO] Task started: Blastn
[2024-01-25 20:27:26,067] [INFO] Running command: blastn -query GCF_900232945.1_PRJEB22715_genomic.fna/markers.fasta -db /var/lib/cwl/stg34a05aae-c62b-4cec-938c-03602ec84e5c/dqc_reference/reference_markers.fasta -out GCF_900232945.1_PRJEB22715_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:27:26,589] [INFO] Task succeeded: Blastn
[2024-01-25 20:27:26,593] [INFO] Selected 15 target genomes.
[2024-01-25 20:27:26,593] [INFO] Target genome list was writen to GCF_900232945.1_PRJEB22715_genomic.fna/target_genomes.txt
[2024-01-25 20:27:26,608] [INFO] Task started: fastANI
[2024-01-25 20:27:26,608] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f3e3ad9-8778-4e66-b8d7-ef3a4e053164/GCF_900232945.1_PRJEB22715_genomic.fna.gz --refList GCF_900232945.1_PRJEB22715_genomic.fna/target_genomes.txt --output GCF_900232945.1_PRJEB22715_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:27:33,545] [INFO] Task succeeded: fastANI
[2024-01-25 20:27:33,545] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34a05aae-c62b-4cec-938c-03602ec84e5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:27:33,546] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34a05aae-c62b-4cec-938c-03602ec84e5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:27:33,550] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:27:33,550] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:27:33,550] [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
Urinicoccus timonensis	strain=Marseille-P3926	GCA_900232945.1	2024205	2024205	type	True	100.0	643	651	95	conclusive
Peptoniphilus grossensis	strain=ph5	GCA_000311825.1	1465756	1465756	type	True	86.6121	79	651	95	below_threshold
Peptoniphilus harei	strain=FDAARGOS_1136	GCA_016726485.1	54005	54005	suspected-type	True	84.8775	52	651	95	below_threshold
Peptoniphilus harei	strain=NCTC13076	GCA_900454685.1	54005	54005	suspected-type	True	84.7926	57	651	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:27:33,551] [INFO] DFAST Taxonomy check result was written to GCF_900232945.1_PRJEB22715_genomic.fna/tc_result.tsv
[2024-01-25 20:27:33,552] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:27:33,552] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:27:33,552] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34a05aae-c62b-4cec-938c-03602ec84e5c/dqc_reference/checkm_data
[2024-01-25 20:27:33,553] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:27:33,576] [INFO] Task started: CheckM
[2024-01-25 20:27:33,577] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900232945.1_PRJEB22715_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900232945.1_PRJEB22715_genomic.fna/checkm_input GCF_900232945.1_PRJEB22715_genomic.fna/checkm_result
[2024-01-25 20:27:51,424] [INFO] Task succeeded: CheckM
[2024-01-25 20:27:51,425] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:27:51,446] [INFO] ===== Completeness check finished =====
[2024-01-25 20:27:51,447] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:27:51,447] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900232945.1_PRJEB22715_genomic.fna/markers.fasta)
[2024-01-25 20:27:51,447] [INFO] Task started: Blastn
[2024-01-25 20:27:51,447] [INFO] Running command: blastn -query GCF_900232945.1_PRJEB22715_genomic.fna/markers.fasta -db /var/lib/cwl/stg34a05aae-c62b-4cec-938c-03602ec84e5c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900232945.1_PRJEB22715_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:27:52,195] [INFO] Task succeeded: Blastn
[2024-01-25 20:27:52,198] [INFO] Selected 16 target genomes.
[2024-01-25 20:27:52,198] [INFO] Target genome list was writen to GCF_900232945.1_PRJEB22715_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:27:52,216] [INFO] Task started: fastANI
[2024-01-25 20:27:52,217] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f3e3ad9-8778-4e66-b8d7-ef3a4e053164/GCF_900232945.1_PRJEB22715_genomic.fna.gz --refList GCF_900232945.1_PRJEB22715_genomic.fna/target_genomes_gtdb.txt --output GCF_900232945.1_PRJEB22715_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:27:59,329] [INFO] Task succeeded: fastANI
[2024-01-25 20:27:59,334] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:27:59,334] [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
GCF_900232945.1	s__Urinicoccus timonensis	100.0	640	651	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Urinicoccus	95.0	97.46	97.28	0.88	0.85	3	conclusive
GCF_900120405.1	s__Urinicoccus massiliensis	90.8446	520	651	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Urinicoccus	95.0	97.19	97.19	0.83	0.83	2	-
GCF_000311825.1	s__Peptoniphilus_A grossensis	86.6121	79	651	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	95.0	97.39	95.38	0.93	0.87	4	-
GCF_900454685.1	s__Peptoniphilus_A harei	84.9038	57	651	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	95.0	97.43	96.58	0.91	0.87	7	-
GCA_001299455.1	s__Urinicoccus sp001299455	80.3329	224	651	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Urinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:27:59,336] [INFO] GTDB search result was written to GCF_900232945.1_PRJEB22715_genomic.fna/result_gtdb.tsv
[2024-01-25 20:27:59,336] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:27:59,338] [INFO] DFAST_QC result json was written to GCF_900232945.1_PRJEB22715_genomic.fna/dqc_result.json
[2024-01-25 20:27:59,338] [INFO] DFAST_QC completed!
[2024-01-25 20:27:59,338] [INFO] Total running time: 0h0m38s