[2024-01-24 13:40:57,650] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:57,651] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:57,651] [INFO] DQC Reference Directory: /var/lib/cwl/stg667c035c-e43d-4d54-9e53-8fd4ffa27e51/dqc_reference
[2024-01-24 13:40:58,880] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:58,881] [INFO] Task started: Prodigal
[2024-01-24 13:40:58,881] [INFO] Running command: gunzip -c /var/lib/cwl/stgf22193be-28d5-47e4-9a8f-251bc7622526/GCF_009696575.1_ASM969657v1_genomic.fna.gz | prodigal -d GCF_009696575.1_ASM969657v1_genomic.fna/cds.fna -a GCF_009696575.1_ASM969657v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:01,963] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:01,963] [INFO] Task started: HMMsearch
[2024-01-24 13:41:01,963] [INFO] Running command: hmmsearch --tblout GCF_009696575.1_ASM969657v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg667c035c-e43d-4d54-9e53-8fd4ffa27e51/dqc_reference/reference_markers.hmm GCF_009696575.1_ASM969657v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:02,185] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:02,186] [INFO] Found 6/6 markers.
[2024-01-24 13:41:02,207] [INFO] Query marker FASTA was written to GCF_009696575.1_ASM969657v1_genomic.fna/markers.fasta
[2024-01-24 13:41:02,208] [INFO] Task started: Blastn
[2024-01-24 13:41:02,208] [INFO] Running command: blastn -query GCF_009696575.1_ASM969657v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg667c035c-e43d-4d54-9e53-8fd4ffa27e51/dqc_reference/reference_markers.fasta -out GCF_009696575.1_ASM969657v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:02,746] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:02,748] [INFO] Selected 8 target genomes.
[2024-01-24 13:41:02,749] [INFO] Target genome list was writen to GCF_009696575.1_ASM969657v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:02,754] [INFO] Task started: fastANI
[2024-01-24 13:41:02,754] [INFO] Running command: fastANI --query /var/lib/cwl/stgf22193be-28d5-47e4-9a8f-251bc7622526/GCF_009696575.1_ASM969657v1_genomic.fna.gz --refList GCF_009696575.1_ASM969657v1_genomic.fna/target_genomes.txt --output GCF_009696575.1_ASM969657v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:05,925] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:05,925] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg667c035c-e43d-4d54-9e53-8fd4ffa27e51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:05,926] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg667c035c-e43d-4d54-9e53-8fd4ffa27e51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:05,931] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:41:05,931] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:41:05,932] [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 vaginalis	strain=ATCC 51170	GCA_000163295.1	33037	33037	type	True	81.0186	322	725	95	below_threshold
Anaerococcus vaginalis	strain=FDAARGOS_988	GCA_016127475.1	33037	33037	type	True	80.988	322	725	95	below_threshold
Anaerococcus ihuae	strain=Marseille-Q5893	GCA_928368155.1	2899519	2899519	type	True	80.6095	300	725	95	below_threshold
Anaerococcus hydrogenalis	strain=DSM 7454	GCA_000173355.1	33029	33029	type	True	80.3486	311	725	95	below_threshold
Anaerococcus obesiensis	strain=ph10	GCA_000311745.1	1287640	1287640	type	True	80.3436	314	725	95	below_threshold
Anaerococcus jeddahensis	strain=SB3	GCA_001182725.1	1673719	1673719	type	True	80.3237	307	725	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:05,933] [INFO] DFAST Taxonomy check result was written to GCF_009696575.1_ASM969657v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:05,933] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:05,934] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:05,934] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg667c035c-e43d-4d54-9e53-8fd4ffa27e51/dqc_reference/checkm_data
[2024-01-24 13:41:05,934] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:05,959] [INFO] Task started: CheckM
[2024-01-24 13:41:05,959] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009696575.1_ASM969657v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009696575.1_ASM969657v1_genomic.fna/checkm_input GCF_009696575.1_ASM969657v1_genomic.fna/checkm_result
[2024-01-24 13:41:22,164] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:22,165] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:22,179] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:22,180] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:22,180] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009696575.1_ASM969657v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:22,180] [INFO] Task started: Blastn
[2024-01-24 13:41:22,180] [INFO] Running command: blastn -query GCF_009696575.1_ASM969657v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg667c035c-e43d-4d54-9e53-8fd4ffa27e51/dqc_reference/reference_markers_gtdb.fasta -out GCF_009696575.1_ASM969657v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:22,958] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:22,961] [INFO] Selected 13 target genomes.
[2024-01-24 13:41:22,961] [INFO] Target genome list was writen to GCF_009696575.1_ASM969657v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:22,978] [INFO] Task started: fastANI
[2024-01-24 13:41:22,978] [INFO] Running command: fastANI --query /var/lib/cwl/stgf22193be-28d5-47e4-9a8f-251bc7622526/GCF_009696575.1_ASM969657v1_genomic.fna.gz --refList GCF_009696575.1_ASM969657v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009696575.1_ASM969657v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:27,935] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:27,942] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:27,942] [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_009696575.1	s__Anaerococcus porci	100.0	723	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	99.45	99.45	0.91	0.91	2	conclusive
GCF_000163295.1	s__Anaerococcus vaginalis	80.9979	323	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	96.6984	98.39	96.80	0.93	0.86	3	-
GCF_000321005.1	s__Anaerococcus senegalensis	80.6166	311	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018363915.1	s__Anaerococcus vaginalis_C	80.5392	298	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	96.5262	96.79	96.79	0.85	0.85	2	-
GCA_900550345.1	s__Anaerococcus sp900550345	80.4839	214	725	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_000311745.1	s__Anaerococcus obesiensis	80.3626	313	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	96.6984	97.99	96.80	0.92	0.85	6	-
GCF_000173355.1	s__Anaerococcus hydrogenalis	80.3486	311	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	97.52	96.64	0.89	0.85	5	-
GCF_001182725.1	s__Anaerococcus jeddahensis	80.3237	307	725	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_001487145.1	s__Anaerococcus rubeinfantis	80.3164	293	725	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_900106845.1	s__Romboutsia timonensis	75.0652	50	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia	95.0	98.20	98.12	0.88	0.86	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:27,943] [INFO] GTDB search result was written to GCF_009696575.1_ASM969657v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:27,944] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:27,946] [INFO] DFAST_QC result json was written to GCF_009696575.1_ASM969657v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:27,947] [INFO] DFAST_QC completed!
[2024-01-24 13:41:27,947] [INFO] Total running time: 0h0m30s