[2024-01-24 11:51:36,522] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:36,525] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:36,525] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd056bcf-07fa-4d63-8482-50d1c51b89c5/dqc_reference
[2024-01-24 11:51:37,787] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:37,787] [INFO] Task started: Prodigal
[2024-01-24 11:51:37,787] [INFO] Running command: gunzip -c /var/lib/cwl/stga866b7ca-b523-4855-b01c-59c6115e9962/GCF_900445265.1_51765_E01_genomic.fna.gz | prodigal -d GCF_900445265.1_51765_E01_genomic.fna/cds.fna -a GCF_900445265.1_51765_E01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:41,017] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:41,018] [INFO] Task started: HMMsearch
[2024-01-24 11:51:41,018] [INFO] Running command: hmmsearch --tblout GCF_900445265.1_51765_E01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd056bcf-07fa-4d63-8482-50d1c51b89c5/dqc_reference/reference_markers.hmm GCF_900445265.1_51765_E01_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:41,251] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:41,253] [INFO] Found 6/6 markers.
[2024-01-24 11:51:41,276] [INFO] Query marker FASTA was written to GCF_900445265.1_51765_E01_genomic.fna/markers.fasta
[2024-01-24 11:51:41,276] [INFO] Task started: Blastn
[2024-01-24 11:51:41,277] [INFO] Running command: blastn -query GCF_900445265.1_51765_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd056bcf-07fa-4d63-8482-50d1c51b89c5/dqc_reference/reference_markers.fasta -out GCF_900445265.1_51765_E01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:41,861] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:41,865] [INFO] Selected 10 target genomes.
[2024-01-24 11:51:41,865] [INFO] Target genome list was writen to GCF_900445265.1_51765_E01_genomic.fna/target_genomes.txt
[2024-01-24 11:51:41,875] [INFO] Task started: fastANI
[2024-01-24 11:51:41,875] [INFO] Running command: fastANI --query /var/lib/cwl/stga866b7ca-b523-4855-b01c-59c6115e9962/GCF_900445265.1_51765_E01_genomic.fna.gz --refList GCF_900445265.1_51765_E01_genomic.fna/target_genomes.txt --output GCF_900445265.1_51765_E01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:45,746] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:45,747] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd056bcf-07fa-4d63-8482-50d1c51b89c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:45,747] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd056bcf-07fa-4d63-8482-50d1c51b89c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:45,763] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:45,763] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:45,764] [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
Anaerococcus octavius	strain=NCTC9810	GCA_900445265.1	54007	54007	type	True	100.0	636	637	95	conclusive
Anaerococcus provencensis	strain=9402080	GCA_000312365.2	938293	938293	type	True	81.8342	276	637	95	below_threshold
Anaerococcus nagyae	strain=DSM 101193	GCA_017874535.1	1755241	1755241	type	True	81.7923	302	637	95	below_threshold
Anaerococcus urinomassiliensis	strain=Marseille-P2143	GCA_900128425.1	1745712	1745712	type	True	80.7563	270	637	95	below_threshold
Anaerococcus prevotii	strain=DSM 20548	GCA_000024105.1	33034	33034	type	True	80.4014	120	637	95	below_threshold
Anaerococcus prevotii	strain=NCTC11806	GCA_900445285.1	33034	33034	type	True	80.0358	123	637	95	below_threshold
Anaerococcus marasmi	strain=Marseille-P3557	GCA_900290195.1	2057797	2057797	type	True	79.9523	117	637	95	below_threshold
Anaerococcus vaginimassiliensis	strain=Marseille-P4512	GCA_900626155.1	2042308	2042308	type	True	79.8578	162	637	95	below_threshold
Anaerococcus vaginalis	strain=FDAARGOS_988	GCA_016127475.1	33037	33037	type	True	79.5035	139	637	95	below_threshold
Anaerococcus hydrogenalis	strain=DSM 7454	GCA_000173355.1	33029	33029	type	True	79.1643	126	637	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:45,765] [INFO] DFAST Taxonomy check result was written to GCF_900445265.1_51765_E01_genomic.fna/tc_result.tsv
[2024-01-24 11:51:45,766] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:45,766] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:45,766] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd056bcf-07fa-4d63-8482-50d1c51b89c5/dqc_reference/checkm_data
[2024-01-24 11:51:45,768] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:45,794] [INFO] Task started: CheckM
[2024-01-24 11:51:45,795] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900445265.1_51765_E01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900445265.1_51765_E01_genomic.fna/checkm_input GCF_900445265.1_51765_E01_genomic.fna/checkm_result
[2024-01-24 11:52:03,446] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:03,449] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:03,470] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:03,471] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:03,471] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900445265.1_51765_E01_genomic.fna/markers.fasta)
[2024-01-24 11:52:03,472] [INFO] Task started: Blastn
[2024-01-24 11:52:03,472] [INFO] Running command: blastn -query GCF_900445265.1_51765_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd056bcf-07fa-4d63-8482-50d1c51b89c5/dqc_reference/reference_markers_gtdb.fasta -out GCF_900445265.1_51765_E01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:04,361] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:04,365] [INFO] Selected 12 target genomes.
[2024-01-24 11:52:04,365] [INFO] Target genome list was writen to GCF_900445265.1_51765_E01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:04,377] [INFO] Task started: fastANI
[2024-01-24 11:52:04,378] [INFO] Running command: fastANI --query /var/lib/cwl/stga866b7ca-b523-4855-b01c-59c6115e9962/GCF_900445265.1_51765_E01_genomic.fna.gz --refList GCF_900445265.1_51765_E01_genomic.fna/target_genomes_gtdb.txt --output GCF_900445265.1_51765_E01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:10,145] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:10,154] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:10,155] [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_900445265.1	s__Anaerococcus octavius	100.0	636	637	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	98.32	98.32	0.89	0.88	3	conclusive
GCF_016798225.1	s__Anaerococcus sp900541365	83.4519	425	637	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	99.32	99.29	0.94	0.94	3	-
GCF_017874535.1	s__Anaerococcus nagyae	81.8165	301	637	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	99.14	98.91	0.93	0.91	5	-
GCF_000312365.2	s__Anaerococcus provencensis	81.8004	277	637	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128425.1	s__Anaerococcus urinomassiliensis	80.7426	271	637	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000308255.3	s__Anaerococcus pacaensis	79.5997	204	637	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	99.91	99.91	0.98	0.98	2	-
GCF_900232825.1	s__Anaerococcus sp900232825	79.5901	234	637	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	95.02	95.02	0.81	0.81	2	-
GCF_000307225.1	s__Anaerococcus vaginalis_B	78.8577	135	637	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000321005.1	s__Anaerococcus senegalensis	77.8344	149	637	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:10,156] [INFO] GTDB search result was written to GCF_900445265.1_51765_E01_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:10,157] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:10,160] [INFO] DFAST_QC result json was written to GCF_900445265.1_51765_E01_genomic.fna/dqc_result.json
[2024-01-24 11:52:10,160] [INFO] DFAST_QC completed!
[2024-01-24 11:52:10,160] [INFO] Total running time: 0h0m34s