[2023-06-29 14:43:29,667] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:43:29,669] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:43:29,669] [INFO] DQC Reference Directory: /var/lib/cwl/stge07a0617-baaf-4c00-9c69-1bc23e90383a/dqc_reference
[2023-06-29 14:43:30,885] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:43:30,885] [INFO] Task started: Prodigal
[2023-06-29 14:43:30,886] [INFO] Running command: gunzip -c /var/lib/cwl/stg9f51ea5d-e246-4df7-b90f-ba61b025543f/GCA_023708245.1_ASM2370824v1_genomic.fna.gz | prodigal -d GCA_023708245.1_ASM2370824v1_genomic.fna/cds.fna -a GCA_023708245.1_ASM2370824v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:43:36,738] [INFO] Task succeeded: Prodigal
[2023-06-29 14:43:36,739] [INFO] Task started: HMMsearch
[2023-06-29 14:43:36,739] [INFO] Running command: hmmsearch --tblout GCA_023708245.1_ASM2370824v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge07a0617-baaf-4c00-9c69-1bc23e90383a/dqc_reference/reference_markers.hmm GCA_023708245.1_ASM2370824v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:43:36,993] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:43:36,994] [INFO] Found 6/6 markers.
[2023-06-29 14:43:37,015] [INFO] Query marker FASTA was written to GCA_023708245.1_ASM2370824v1_genomic.fna/markers.fasta
[2023-06-29 14:43:37,015] [INFO] Task started: Blastn
[2023-06-29 14:43:37,015] [INFO] Running command: blastn -query GCA_023708245.1_ASM2370824v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge07a0617-baaf-4c00-9c69-1bc23e90383a/dqc_reference/reference_markers.fasta -out GCA_023708245.1_ASM2370824v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:43:37,599] [INFO] Task succeeded: Blastn
[2023-06-29 14:43:37,602] [INFO] Selected 18 target genomes.
[2023-06-29 14:43:37,603] [INFO] Target genome list was writen to GCA_023708245.1_ASM2370824v1_genomic.fna/target_genomes.txt
[2023-06-29 14:43:37,605] [INFO] Task started: fastANI
[2023-06-29 14:43:37,605] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f51ea5d-e246-4df7-b90f-ba61b025543f/GCA_023708245.1_ASM2370824v1_genomic.fna.gz --refList GCA_023708245.1_ASM2370824v1_genomic.fna/target_genomes.txt --output GCA_023708245.1_ASM2370824v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:43:44,818] [INFO] Task succeeded: fastANI
[2023-06-29 14:43:44,819] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge07a0617-baaf-4c00-9c69-1bc23e90383a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:43:44,820] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge07a0617-baaf-4c00-9c69-1bc23e90383a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:43:44,829] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2023-06-29 14:43:44,830] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 14:43:44,830] [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 intestini	strain=DSM 21505	GCA_000425045.1	187327	187327	type	True	99.3731	623	679	95	conclusive
Acidaminococcus massiliensis	strain=Marseille-P2828	GCA_900095825.1	1852375	1852375	type	True	78.145	120	679	95	below_threshold
Acidaminococcus fermentans	strain=DSM 20731	GCA_000025305.1	905	905	type	True	78.083	124	679	95	below_threshold
Acidaminococcus provencensis	strain=Marseille-P4266	GCA_900291475.1	2058289	2058289	type	True	77.9171	123	679	95	below_threshold
Acidaminococcus timonensis	strain=Marseille-P2764	GCA_900106585.1	1871002	1871002	type	True	77.8425	126	679	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 14:43:44,832] [INFO] DFAST Taxonomy check result was written to GCA_023708245.1_ASM2370824v1_genomic.fna/tc_result.tsv
[2023-06-29 14:43:44,833] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:43:44,833] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:43:44,833] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge07a0617-baaf-4c00-9c69-1bc23e90383a/dqc_reference/checkm_data
[2023-06-29 14:43:44,834] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:43:44,863] [INFO] Task started: CheckM
[2023-06-29 14:43:44,863] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023708245.1_ASM2370824v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023708245.1_ASM2370824v1_genomic.fna/checkm_input GCA_023708245.1_ASM2370824v1_genomic.fna/checkm_result
[2023-06-29 14:44:08,966] [INFO] Task succeeded: CheckM
[2023-06-29 14:44:08,968] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 14:44:08,993] [INFO] ===== Completeness check finished =====
[2023-06-29 14:44:08,993] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:44:08,994] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023708245.1_ASM2370824v1_genomic.fna/markers.fasta)
[2023-06-29 14:44:08,994] [INFO] Task started: Blastn
[2023-06-29 14:44:08,994] [INFO] Running command: blastn -query GCA_023708245.1_ASM2370824v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge07a0617-baaf-4c00-9c69-1bc23e90383a/dqc_reference/reference_markers_gtdb.fasta -out GCA_023708245.1_ASM2370824v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:44:09,818] [INFO] Task succeeded: Blastn
[2023-06-29 14:44:09,822] [INFO] Selected 15 target genomes.
[2023-06-29 14:44:09,822] [INFO] Target genome list was writen to GCA_023708245.1_ASM2370824v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:44:09,828] [INFO] Task started: fastANI
[2023-06-29 14:44:09,828] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f51ea5d-e246-4df7-b90f-ba61b025543f/GCA_023708245.1_ASM2370824v1_genomic.fna.gz --refList GCA_023708245.1_ASM2370824v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023708245.1_ASM2370824v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:44:16,485] [INFO] Task succeeded: fastANI
[2023-06-29 14:44:16,497] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 14:44:16,497] [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_000425045.1	s__Acidaminococcus intestini	99.3731	623	679	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Acidaminococcus	95.0	99.60	99.25	0.93	0.88	13	conclusive
GCA_900538365.1	s__Acidaminococcus sp900538365	92.2076	561	679	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Acidaminococcus	95.0	98.99	97.67	0.93	0.89	4	-
GCF_009696675.1	s__Acidaminococcus sp000437815	78.6481	132	679	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_900095825.1	s__Acidaminococcus massiliensis	78.145	120	679	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_902796945.1	s__Acidaminococcus sp902796945	78.0954	209	679	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_900315205.1	s__Acidaminococcus sp900315205	78.0837	167	679	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Acidaminococcus	95.0	99.22	98.84	0.89	0.88	6	-
GCF_000025305.1	s__Acidaminococcus fermentans	78.083	124	679	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	77.893	91	679	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Acidaminococcus	95.0	96.61	96.61	0.81	0.81	2	-
GCA_905215645.1	s__Acidaminococcus sp905215645	77.7457	121	679	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_900314165.1	s__Acidaminococcus sp900314165	77.2028	100	679	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Acidaminococcus	95.0	100.00	100.00	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2023-06-29 14:44:16,499] [INFO] GTDB search result was written to GCA_023708245.1_ASM2370824v1_genomic.fna/result_gtdb.tsv
[2023-06-29 14:44:16,500] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:44:16,502] [INFO] DFAST_QC result json was written to GCA_023708245.1_ASM2370824v1_genomic.fna/dqc_result.json
[2023-06-29 14:44:16,503] [INFO] DFAST_QC completed!
[2023-06-29 14:44:16,503] [INFO] Total running time: 0h0m47s