[2024-01-24 13:41:19,854] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:19,858] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:19,859] [INFO] DQC Reference Directory: /var/lib/cwl/stg4640235d-5e5f-4870-ba35-cc7d17d5efc3/dqc_reference
[2024-01-24 13:41:21,275] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:21,276] [INFO] Task started: Prodigal
[2024-01-24 13:41:21,277] [INFO] Running command: gunzip -c /var/lib/cwl/stg8443487f-765a-45cd-8af9-0eca9e05cdda/GCF_000312365.2_ASM31236v2_genomic.fna.gz | prodigal -d GCF_000312365.2_ASM31236v2_genomic.fna/cds.fna -a GCF_000312365.2_ASM31236v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:25,696] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:25,696] [INFO] Task started: HMMsearch
[2024-01-24 13:41:25,696] [INFO] Running command: hmmsearch --tblout GCF_000312365.2_ASM31236v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4640235d-5e5f-4870-ba35-cc7d17d5efc3/dqc_reference/reference_markers.hmm GCF_000312365.2_ASM31236v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:25,998] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:26,000] [INFO] Found 6/6 markers.
[2024-01-24 13:41:26,021] [INFO] Query marker FASTA was written to GCF_000312365.2_ASM31236v2_genomic.fna/markers.fasta
[2024-01-24 13:41:26,022] [INFO] Task started: Blastn
[2024-01-24 13:41:26,022] [INFO] Running command: blastn -query GCF_000312365.2_ASM31236v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg4640235d-5e5f-4870-ba35-cc7d17d5efc3/dqc_reference/reference_markers.fasta -out GCF_000312365.2_ASM31236v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:26,671] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:26,674] [INFO] Selected 9 target genomes.
[2024-01-24 13:41:26,674] [INFO] Target genome list was writen to GCF_000312365.2_ASM31236v2_genomic.fna/target_genomes.txt
[2024-01-24 13:41:26,678] [INFO] Task started: fastANI
[2024-01-24 13:41:26,678] [INFO] Running command: fastANI --query /var/lib/cwl/stg8443487f-765a-45cd-8af9-0eca9e05cdda/GCF_000312365.2_ASM31236v2_genomic.fna.gz --refList GCF_000312365.2_ASM31236v2_genomic.fna/target_genomes.txt --output GCF_000312365.2_ASM31236v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:31,025] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:31,025] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4640235d-5e5f-4870-ba35-cc7d17d5efc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:31,026] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4640235d-5e5f-4870-ba35-cc7d17d5efc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:31,038] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:31,038] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:31,038] [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 provencensis	strain=9402080	GCA_000312365.2	938293	938293	type	True	99.9999	747	749	95	conclusive
Anaerococcus urinomassiliensis	strain=Marseille-P2143	GCA_900128425.1	1745712	1745712	type	True	91.1967	566	749	95	below_threshold
Anaerococcus octavius	strain=NCTC9810	GCA_900445265.1	54007	54007	type	True	81.7369	287	749	95	below_threshold
Anaerococcus mediterraneensis	strain=Marseille-P2765	GCA_900128415.1	1870984	1870984	type	True	81.3808	136	749	95	below_threshold
Anaerococcus prevotii	strain=DSM 20548	GCA_000024105.1	33034	33034	type	True	80.703	172	749	95	below_threshold
Anaerococcus prevotii	strain=NCTC11806	GCA_900445285.1	33034	33034	type	True	80.5728	171	749	95	below_threshold
Anaerococcus marasmi	strain=Marseille-P3557	GCA_900290195.1	2057797	2057797	type	True	80.5464	165	749	95	below_threshold
Anaerococcus tetradius	strain=ATCC 35098	GCA_000159095.1	33036	33036	type	True	79.8686	170	749	95	below_threshold
Anaerococcus nagyae	strain=DSM 101193	GCA_017874535.1	1755241	1755241	type	True	79.6964	235	749	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:31,040] [INFO] DFAST Taxonomy check result was written to GCF_000312365.2_ASM31236v2_genomic.fna/tc_result.tsv
[2024-01-24 13:41:31,041] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:31,041] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:31,041] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4640235d-5e5f-4870-ba35-cc7d17d5efc3/dqc_reference/checkm_data
[2024-01-24 13:41:31,043] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:31,072] [INFO] Task started: CheckM
[2024-01-24 13:41:31,072] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000312365.2_ASM31236v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000312365.2_ASM31236v2_genomic.fna/checkm_input GCF_000312365.2_ASM31236v2_genomic.fna/checkm_result
[2024-01-24 13:41:51,421] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:51,424] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:51,508] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:51,508] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:51,509] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000312365.2_ASM31236v2_genomic.fna/markers.fasta)
[2024-01-24 13:41:51,509] [INFO] Task started: Blastn
[2024-01-24 13:41:51,509] [INFO] Running command: blastn -query GCF_000312365.2_ASM31236v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg4640235d-5e5f-4870-ba35-cc7d17d5efc3/dqc_reference/reference_markers_gtdb.fasta -out GCF_000312365.2_ASM31236v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:52,380] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:52,384] [INFO] Selected 8 target genomes.
[2024-01-24 13:41:52,385] [INFO] Target genome list was writen to GCF_000312365.2_ASM31236v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:52,391] [INFO] Task started: fastANI
[2024-01-24 13:41:52,392] [INFO] Running command: fastANI --query /var/lib/cwl/stg8443487f-765a-45cd-8af9-0eca9e05cdda/GCF_000312365.2_ASM31236v2_genomic.fna.gz --refList GCF_000312365.2_ASM31236v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000312365.2_ASM31236v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:56,421] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:56,429] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:56,430] [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_000312365.2	s__Anaerococcus provencensis	99.9999	747	749	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900128425.1	s__Anaerococcus urinomassiliensis	91.2048	565	749	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_900445265.1	s__Anaerococcus octavius	81.7369	287	749	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	98.32	98.32	0.89	0.88	3	-
GCF_900232825.1	s__Anaerococcus sp900232825	81.2488	229	749	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	95.02	95.02	0.81	0.81	2	-
GCA_000308255.3	s__Anaerococcus pacaensis	81.0763	254	749	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_000159095.1	s__Anaerococcus tetradius	79.9372	167	749	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	98.20	98.20	0.90	0.90	2	-
GCF_016798225.1	s__Anaerococcus sp900541365	79.7282	218	749	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	79.6962	235	749	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	99.14	98.91	0.93	0.91	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:56,432] [INFO] GTDB search result was written to GCF_000312365.2_ASM31236v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:56,432] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:56,436] [INFO] DFAST_QC result json was written to GCF_000312365.2_ASM31236v2_genomic.fna/dqc_result.json
[2024-01-24 13:41:56,436] [INFO] DFAST_QC completed!
[2024-01-24 13:41:56,437] [INFO] Total running time: 0h0m37s