[2024-01-24 13:55:25,790] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:25,791] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:25,792] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f824b66-b52e-42d4-999d-1649fcae0f4d/dqc_reference
[2024-01-24 13:55:26,993] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:26,994] [INFO] Task started: Prodigal
[2024-01-24 13:55:26,994] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2aa617d-d4b9-4b11-9cfd-252c25df7f5c/GCF_021044795.1_ASM2104479v1_genomic.fna.gz | prodigal -d GCF_021044795.1_ASM2104479v1_genomic.fna/cds.fna -a GCF_021044795.1_ASM2104479v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:34,142] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:34,143] [INFO] Task started: HMMsearch
[2024-01-24 13:55:34,143] [INFO] Running command: hmmsearch --tblout GCF_021044795.1_ASM2104479v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f824b66-b52e-42d4-999d-1649fcae0f4d/dqc_reference/reference_markers.hmm GCF_021044795.1_ASM2104479v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:34,387] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:34,388] [INFO] Found 6/6 markers.
[2024-01-24 13:55:34,416] [INFO] Query marker FASTA was written to GCF_021044795.1_ASM2104479v1_genomic.fna/markers.fasta
[2024-01-24 13:55:34,416] [INFO] Task started: Blastn
[2024-01-24 13:55:34,416] [INFO] Running command: blastn -query GCF_021044795.1_ASM2104479v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f824b66-b52e-42d4-999d-1649fcae0f4d/dqc_reference/reference_markers.fasta -out GCF_021044795.1_ASM2104479v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:35,030] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:35,034] [INFO] Selected 10 target genomes.
[2024-01-24 13:55:35,035] [INFO] Target genome list was writen to GCF_021044795.1_ASM2104479v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:35,058] [INFO] Task started: fastANI
[2024-01-24 13:55:35,059] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2aa617d-d4b9-4b11-9cfd-252c25df7f5c/GCF_021044795.1_ASM2104479v1_genomic.fna.gz --refList GCF_021044795.1_ASM2104479v1_genomic.fna/target_genomes.txt --output GCF_021044795.1_ASM2104479v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:40,811] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:40,811] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f824b66-b52e-42d4-999d-1649fcae0f4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:40,812] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f824b66-b52e-42d4-999d-1649fcae0f4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:40,818] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:55:40,818] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:40,818] [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
Acidaminococcus provencensis	strain=Marseille-P4266	GCA_900291475.1	2058289	2058289	type	True	99.2716	743	828	95	conclusive
Acidaminococcus fermentans	strain=DSM 20731	GCA_000025305.1	905	905	type	True	80.3118	384	828	95	below_threshold
Acidaminococcus timonensis	strain=Marseille-P2764	GCA_900106585.1	1871002	1871002	type	True	79.9234	353	828	95	below_threshold
Acidaminococcus massiliensis	strain=Marseille-P2828	GCA_900095825.1	1852375	1852375	type	True	79.7783	348	828	95	below_threshold
Acidaminococcus intestini	strain=DSM 21505	GCA_000425045.1	187327	187327	type	True	77.8863	124	828	95	below_threshold
Succiniclasticum ruminis	strain=DSM 9236	GCA_900112895.1	40841	40841	suspected-type	True	76.2311	51	828	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:40,820] [INFO] DFAST Taxonomy check result was written to GCF_021044795.1_ASM2104479v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:40,821] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:40,821] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:40,822] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f824b66-b52e-42d4-999d-1649fcae0f4d/dqc_reference/checkm_data
[2024-01-24 13:55:40,824] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:40,857] [INFO] Task started: CheckM
[2024-01-24 13:55:40,857] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021044795.1_ASM2104479v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021044795.1_ASM2104479v1_genomic.fna/checkm_input GCF_021044795.1_ASM2104479v1_genomic.fna/checkm_result
[2024-01-24 13:56:07,353] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:07,355] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:07,375] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:07,375] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:07,376] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021044795.1_ASM2104479v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:07,376] [INFO] Task started: Blastn
[2024-01-24 13:56:07,376] [INFO] Running command: blastn -query GCF_021044795.1_ASM2104479v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f824b66-b52e-42d4-999d-1649fcae0f4d/dqc_reference/reference_markers_gtdb.fasta -out GCF_021044795.1_ASM2104479v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:08,224] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:08,228] [INFO] Selected 8 target genomes.
[2024-01-24 13:56:08,228] [INFO] Target genome list was writen to GCF_021044795.1_ASM2104479v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:08,307] [INFO] Task started: fastANI
[2024-01-24 13:56:08,307] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2aa617d-d4b9-4b11-9cfd-252c25df7f5c/GCF_021044795.1_ASM2104479v1_genomic.fna.gz --refList GCF_021044795.1_ASM2104479v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021044795.1_ASM2104479v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:12,723] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:12,734] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:12,734] [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_900291475.1	s__Acidaminococcus provencensis	99.2693	743	828	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Acidaminococcus	95.0	99.37	99.31	0.92	0.88	6	conclusive
GCF_009696675.1	s__Acidaminococcus sp000437815	80.5964	376	828	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Acidaminococcus	95.0	98.16	97.76	0.92	0.89	4	-
GCF_000025305.1	s__Acidaminococcus fermentans	80.3203	383	828	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Acidaminococcus	95.0	98.69	98.27	0.92	0.87	11	-
GCA_900770265.1	s__Acidaminococcus sp900770265	80.003	296	828	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Acidaminococcus	95.0	96.61	96.61	0.81	0.81	2	-
GCF_900106585.1	s__Acidaminococcus timonensis	79.9426	351	828	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Acidaminococcus	95.0	97.46	97.46	0.95	0.94	3	-
GCF_900095825.1	s__Acidaminococcus massiliensis	79.7709	349	828	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Acidaminococcus	95.0	98.55	97.11	0.93	0.86	3	-
GCA_905215645.1	s__Acidaminococcus sp905215645	79.513	340	828	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Acidaminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004555735.1	s__Acidaminococcus fermentans_A	79.242	289	828	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Acidaminococcus	95.0	95.98	95.98	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:56:12,736] [INFO] GTDB search result was written to GCF_021044795.1_ASM2104479v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:12,737] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:12,739] [INFO] DFAST_QC result json was written to GCF_021044795.1_ASM2104479v1_genomic.fna/dqc_result.json
[2024-01-24 13:56:12,740] [INFO] DFAST_QC completed!
[2024-01-24 13:56:12,740] [INFO] Total running time: 0h0m47s