[2023-06-19 00:04:45,387] [INFO] DFAST_QC pipeline started.
[2023-06-19 00:04:45,390] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 00:04:45,390] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ab39caf-8688-4da8-8556-a3a9b45ab3e7/dqc_reference
[2023-06-19 00:04:46,610] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 00:04:46,611] [INFO] Task started: Prodigal
[2023-06-19 00:04:46,611] [INFO] Running command: gunzip -c /var/lib/cwl/stg32f3f56e-b338-4fef-8fae-121d2e2d30e9/GCA_018375895.1_ASM1837589v1_genomic.fna.gz | prodigal -d GCA_018375895.1_ASM1837589v1_genomic.fna/cds.fna -a GCA_018375895.1_ASM1837589v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 00:04:51,950] [INFO] Task succeeded: Prodigal
[2023-06-19 00:04:51,951] [INFO] Task started: HMMsearch
[2023-06-19 00:04:51,951] [INFO] Running command: hmmsearch --tblout GCA_018375895.1_ASM1837589v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ab39caf-8688-4da8-8556-a3a9b45ab3e7/dqc_reference/reference_markers.hmm GCA_018375895.1_ASM1837589v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 00:04:52,258] [INFO] Task succeeded: HMMsearch
[2023-06-19 00:04:52,260] [INFO] Found 6/6 markers.
[2023-06-19 00:04:52,293] [INFO] Query marker FASTA was written to GCA_018375895.1_ASM1837589v1_genomic.fna/markers.fasta
[2023-06-19 00:04:52,293] [INFO] Task started: Blastn
[2023-06-19 00:04:52,293] [INFO] Running command: blastn -query GCA_018375895.1_ASM1837589v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ab39caf-8688-4da8-8556-a3a9b45ab3e7/dqc_reference/reference_markers.fasta -out GCA_018375895.1_ASM1837589v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 00:04:52,958] [INFO] Task succeeded: Blastn
[2023-06-19 00:04:52,961] [INFO] Selected 26 target genomes.
[2023-06-19 00:04:52,962] [INFO] Target genome list was writen to GCA_018375895.1_ASM1837589v1_genomic.fna/target_genomes.txt
[2023-06-19 00:04:52,963] [INFO] Task started: fastANI
[2023-06-19 00:04:52,963] [INFO] Running command: fastANI --query /var/lib/cwl/stg32f3f56e-b338-4fef-8fae-121d2e2d30e9/GCA_018375895.1_ASM1837589v1_genomic.fna.gz --refList GCA_018375895.1_ASM1837589v1_genomic.fna/target_genomes.txt --output GCA_018375895.1_ASM1837589v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 00:05:11,403] [INFO] Task succeeded: fastANI
[2023-06-19 00:05:11,404] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ab39caf-8688-4da8-8556-a3a9b45ab3e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 00:05:11,404] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ab39caf-8688-4da8-8556-a3a9b45ab3e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 00:05:11,412] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 00:05:11,412] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 00:05:11,413] [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=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	80.5322	77	375	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	80.1661	77	375	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	79.9169	68	375	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	77.3614	53	375	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.0317	57	375	95	below_threshold
Intestinimonas butyriciproducens	strain=SRB-521-5-I	GCA_004154955.1	1297617	1297617	type	True	76.6303	53	375	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	76.6303	53	375	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	76.5897	54	375	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 00:05:11,417] [INFO] DFAST Taxonomy check result was written to GCA_018375895.1_ASM1837589v1_genomic.fna/tc_result.tsv
[2023-06-19 00:05:11,418] [INFO] ===== Taxonomy check completed =====
[2023-06-19 00:05:11,418] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 00:05:11,418] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ab39caf-8688-4da8-8556-a3a9b45ab3e7/dqc_reference/checkm_data
[2023-06-19 00:05:11,420] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 00:05:11,447] [INFO] Task started: CheckM
[2023-06-19 00:05:11,447] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018375895.1_ASM1837589v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018375895.1_ASM1837589v1_genomic.fna/checkm_input GCA_018375895.1_ASM1837589v1_genomic.fna/checkm_result
[2023-06-19 00:05:33,616] [INFO] Task succeeded: CheckM
[2023-06-19 00:05:33,618] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.74%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 00:05:33,675] [INFO] ===== Completeness check finished =====
[2023-06-19 00:05:33,675] [INFO] ===== Start GTDB Search =====
[2023-06-19 00:05:33,676] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018375895.1_ASM1837589v1_genomic.fna/markers.fasta)
[2023-06-19 00:05:33,676] [INFO] Task started: Blastn
[2023-06-19 00:05:33,676] [INFO] Running command: blastn -query GCA_018375895.1_ASM1837589v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ab39caf-8688-4da8-8556-a3a9b45ab3e7/dqc_reference/reference_markers_gtdb.fasta -out GCA_018375895.1_ASM1837589v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 00:05:34,789] [INFO] Task succeeded: Blastn
[2023-06-19 00:05:34,796] [INFO] Selected 30 target genomes.
[2023-06-19 00:05:34,796] [INFO] Target genome list was writen to GCA_018375895.1_ASM1837589v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 00:05:34,828] [INFO] Task started: fastANI
[2023-06-19 00:05:34,829] [INFO] Running command: fastANI --query /var/lib/cwl/stg32f3f56e-b338-4fef-8fae-121d2e2d30e9/GCA_018375895.1_ASM1837589v1_genomic.fna.gz --refList GCA_018375895.1_ASM1837589v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018375895.1_ASM1837589v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 00:05:45,774] [INFO] Task succeeded: fastANI
[2023-06-19 00:05:45,797] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 00:05:45,798] [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_002159265.1	s__Flavonifractor sp002159265	78.7601	81	375	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018713205.1	s__Avoscillospira stercorigallinarum	77.6353	57	375	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Avoscillospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904395865.1	s__Avoscillospira_A sp904395865	77.5813	63	375	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Avoscillospira_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018712245.1	s__Avoscillospira avicola	77.2479	59	375	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Avoscillospira	95.0	96.26	96.26	0.82	0.82	2	-
GCA_904395905.1	s__Avoscillospira_A sp904395905	77.1985	63	375	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Avoscillospira_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543935.1	s__Marseille-P3106 sp900543935	77.1469	54	375	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Marseille-P3106	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001244995.1	s__Intestinimonas massiliensis	77.1469	55	375	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_900626145.1	s__Intestinimonas timonensis	77.1125	59	375	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_018917965.1	s__An92 sp018917965	77.0587	65	375	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549565.1	s__UMGS1202 sp900549565	76.9705	61	375	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UMGS1202	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018710845.1	s__Onthomonas avicola	76.9632	51	375	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Onthomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 00:05:45,801] [INFO] GTDB search result was written to GCA_018375895.1_ASM1837589v1_genomic.fna/result_gtdb.tsv
[2023-06-19 00:05:45,807] [INFO] ===== GTDB Search completed =====
[2023-06-19 00:05:45,813] [INFO] DFAST_QC result json was written to GCA_018375895.1_ASM1837589v1_genomic.fna/dqc_result.json
[2023-06-19 00:05:45,813] [INFO] DFAST_QC completed!
[2023-06-19 00:05:45,813] [INFO] Total running time: 0h1m0s