[2023-06-27 18:26:12,922] [INFO] DFAST_QC pipeline started.
[2023-06-27 18:26:12,925] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 18:26:12,925] [INFO] DQC Reference Directory: /var/lib/cwl/stg16c9d232-1304-4d0c-9cfe-bc29fd27caca/dqc_reference
[2023-06-27 18:26:14,390] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 18:26:14,391] [INFO] Task started: Prodigal
[2023-06-27 18:26:14,392] [INFO] Running command: gunzip -c /var/lib/cwl/stgb50d0fcb-e8f3-49d5-809d-874263ba16b8/GCA_026169115.1_ASM2616911v1_genomic.fna.gz | prodigal -d GCA_026169115.1_ASM2616911v1_genomic.fna/cds.fna -a GCA_026169115.1_ASM2616911v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 18:26:21,734] [INFO] Task succeeded: Prodigal
[2023-06-27 18:26:21,734] [INFO] Task started: HMMsearch
[2023-06-27 18:26:21,734] [INFO] Running command: hmmsearch --tblout GCA_026169115.1_ASM2616911v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg16c9d232-1304-4d0c-9cfe-bc29fd27caca/dqc_reference/reference_markers.hmm GCA_026169115.1_ASM2616911v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 18:26:22,005] [INFO] Task succeeded: HMMsearch
[2023-06-27 18:26:22,006] [INFO] Found 6/6 markers.
[2023-06-27 18:26:22,056] [INFO] Query marker FASTA was written to GCA_026169115.1_ASM2616911v1_genomic.fna/markers.fasta
[2023-06-27 18:26:22,056] [INFO] Task started: Blastn
[2023-06-27 18:26:22,056] [INFO] Running command: blastn -query GCA_026169115.1_ASM2616911v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16c9d232-1304-4d0c-9cfe-bc29fd27caca/dqc_reference/reference_markers.fasta -out GCA_026169115.1_ASM2616911v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 18:26:22,728] [INFO] Task succeeded: Blastn
[2023-06-27 18:26:22,732] [INFO] Selected 17 target genomes.
[2023-06-27 18:26:22,732] [INFO] Target genome list was writen to GCA_026169115.1_ASM2616911v1_genomic.fna/target_genomes.txt
[2023-06-27 18:26:22,734] [INFO] Task started: fastANI
[2023-06-27 18:26:22,735] [INFO] Running command: fastANI --query /var/lib/cwl/stgb50d0fcb-e8f3-49d5-809d-874263ba16b8/GCA_026169115.1_ASM2616911v1_genomic.fna.gz --refList GCA_026169115.1_ASM2616911v1_genomic.fna/target_genomes.txt --output GCA_026169115.1_ASM2616911v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 18:26:33,489] [INFO] Task succeeded: fastANI
[2023-06-27 18:26:33,489] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg16c9d232-1304-4d0c-9cfe-bc29fd27caca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 18:26:33,489] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg16c9d232-1304-4d0c-9cfe-bc29fd27caca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 18:26:33,499] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 18:26:33,499] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 18:26:33,499] [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
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	81.1617	357	805	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	81.1054	397	805	95	below_threshold
Intestinimonas butyriciproducens	strain=SRB-521-5-I	GCA_004154955.1	1297617	1297617	type	True	80.5289	388	805	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	80.4775	388	805	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	80.4214	395	805	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	80.2402	321	805	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	80.1278	200	805	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	79.0623	266	805	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.6284	141	805	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	76.0196	53	805	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 18:26:33,510] [INFO] DFAST Taxonomy check result was written to GCA_026169115.1_ASM2616911v1_genomic.fna/tc_result.tsv
[2023-06-27 18:26:33,511] [INFO] ===== Taxonomy check completed =====
[2023-06-27 18:26:33,511] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 18:26:33,511] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg16c9d232-1304-4d0c-9cfe-bc29fd27caca/dqc_reference/checkm_data
[2023-06-27 18:26:33,513] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 18:26:33,544] [INFO] Task started: CheckM
[2023-06-27 18:26:33,544] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026169115.1_ASM2616911v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026169115.1_ASM2616911v1_genomic.fna/checkm_input GCA_026169115.1_ASM2616911v1_genomic.fna/checkm_result
[2023-06-27 18:27:00,424] [INFO] Task succeeded: CheckM
[2023-06-27 18:27:00,426] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 18:27:00,447] [INFO] ===== Completeness check finished =====
[2023-06-27 18:27:00,448] [INFO] ===== Start GTDB Search =====
[2023-06-27 18:27:00,448] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026169115.1_ASM2616911v1_genomic.fna/markers.fasta)
[2023-06-27 18:27:00,449] [INFO] Task started: Blastn
[2023-06-27 18:27:00,449] [INFO] Running command: blastn -query GCA_026169115.1_ASM2616911v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16c9d232-1304-4d0c-9cfe-bc29fd27caca/dqc_reference/reference_markers_gtdb.fasta -out GCA_026169115.1_ASM2616911v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 18:27:01,649] [INFO] Task succeeded: Blastn
[2023-06-27 18:27:01,653] [INFO] Selected 11 target genomes.
[2023-06-27 18:27:01,654] [INFO] Target genome list was writen to GCA_026169115.1_ASM2616911v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 18:27:01,707] [INFO] Task started: fastANI
[2023-06-27 18:27:01,708] [INFO] Running command: fastANI --query /var/lib/cwl/stgb50d0fcb-e8f3-49d5-809d-874263ba16b8/GCA_026169115.1_ASM2616911v1_genomic.fna.gz --refList GCA_026169115.1_ASM2616911v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026169115.1_ASM2616911v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 18:27:08,306] [INFO] Task succeeded: fastANI
[2023-06-27 18:27:08,322] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 18:27:08,322] [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_900626145.1	s__Intestinimonas timonensis	87.3516	542	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019115345.1	s__Intestinimonas stercorigallinarum	86.9708	358	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019115785.1	s__Intestinimonas merdavium	85.1866	433	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	98.39	98.39	0.88	0.88	2	-
GCA_019119795.1	s__Intestinimonas pullistercoris	83.4476	377	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	99.29	99.15	0.85	0.82	4	-
GCA_019117605.1	s__Intestinimonas stercoravium	82.4376	388	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	98.97	98.96	0.85	0.84	3	-
GCA_900540545.1	s__Intestinimonas sp900540545	81.6631	410	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002161215.1	s__Flavonifractor avistercoris	81.2096	366	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	96.82	96.45	0.91	0.89	7	-
GCF_002159265.1	s__Flavonifractor sp002159265	81.1525	345	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001244995.1	s__Intestinimonas massiliensis	81.1282	386	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	99.15	98.60	0.93	0.82	6	-
GCF_002159175.1	s__An92 sp002159175	80.8475	341	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	98.91	98.91	0.91	0.91	2	-
GCA_905205085.1	s__Lawsonibacter sp900766145	79.1427	205	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	99.79	99.79	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-06-27 18:27:08,324] [INFO] GTDB search result was written to GCA_026169115.1_ASM2616911v1_genomic.fna/result_gtdb.tsv
[2023-06-27 18:27:08,325] [INFO] ===== GTDB Search completed =====
[2023-06-27 18:27:08,329] [INFO] DFAST_QC result json was written to GCA_026169115.1_ASM2616911v1_genomic.fna/dqc_result.json
[2023-06-27 18:27:08,330] [INFO] DFAST_QC completed!
[2023-06-27 18:27:08,330] [INFO] Total running time: 0h0m55s