[2023-06-29 15:27:28,409] [INFO] DFAST_QC pipeline started.
[2023-06-29 15:27:28,411] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 15:27:28,411] [INFO] DQC Reference Directory: /var/lib/cwl/stgfaa33c8a-c792-4f4a-8fd4-a2b07ca29b29/dqc_reference
[2023-06-29 15:27:29,578] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 15:27:29,579] [INFO] Task started: Prodigal
[2023-06-29 15:27:29,579] [INFO] Running command: gunzip -c /var/lib/cwl/stge2b70fe3-ecb1-4de5-bc1a-5a20e7d337a2/GCA_021206435.1_ASM2120643v1_genomic.fna.gz | prodigal -d GCA_021206435.1_ASM2120643v1_genomic.fna/cds.fna -a GCA_021206435.1_ASM2120643v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 15:27:34,940] [INFO] Task succeeded: Prodigal
[2023-06-29 15:27:34,940] [INFO] Task started: HMMsearch
[2023-06-29 15:27:34,940] [INFO] Running command: hmmsearch --tblout GCA_021206435.1_ASM2120643v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfaa33c8a-c792-4f4a-8fd4-a2b07ca29b29/dqc_reference/reference_markers.hmm GCA_021206435.1_ASM2120643v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 15:27:35,077] [INFO] Task succeeded: HMMsearch
[2023-06-29 15:27:35,078] [WARNING] Found 3/6 markers. [/var/lib/cwl/stge2b70fe3-ecb1-4de5-bc1a-5a20e7d337a2/GCA_021206435.1_ASM2120643v1_genomic.fna.gz]
[2023-06-29 15:27:35,093] [INFO] Query marker FASTA was written to GCA_021206435.1_ASM2120643v1_genomic.fna/markers.fasta
[2023-06-29 15:27:35,093] [INFO] Task started: Blastn
[2023-06-29 15:27:35,093] [INFO] Running command: blastn -query GCA_021206435.1_ASM2120643v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfaa33c8a-c792-4f4a-8fd4-a2b07ca29b29/dqc_reference/reference_markers.fasta -out GCA_021206435.1_ASM2120643v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:27:35,603] [INFO] Task succeeded: Blastn
[2023-06-29 15:27:35,606] [INFO] Selected 9 target genomes.
[2023-06-29 15:27:35,607] [INFO] Target genome list was writen to GCA_021206435.1_ASM2120643v1_genomic.fna/target_genomes.txt
[2023-06-29 15:27:35,608] [INFO] Task started: fastANI
[2023-06-29 15:27:35,609] [INFO] Running command: fastANI --query /var/lib/cwl/stge2b70fe3-ecb1-4de5-bc1a-5a20e7d337a2/GCA_021206435.1_ASM2120643v1_genomic.fna.gz --refList GCA_021206435.1_ASM2120643v1_genomic.fna/target_genomes.txt --output GCA_021206435.1_ASM2120643v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 15:27:41,597] [INFO] Task succeeded: fastANI
[2023-06-29 15:27:41,598] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfaa33c8a-c792-4f4a-8fd4-a2b07ca29b29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 15:27:41,598] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfaa33c8a-c792-4f4a-8fd4-a2b07ca29b29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 15:27:41,603] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 15:27:41,603] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 15:27:41,603] [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
Parabacteroides faecis	strain=DSM 102983	GCA_014199665.1	1217282	1217282	type	True	77.0175	50	362	95	below_threshold
Parabacteroides gordonii	strain=FDAARGOS_1522	GCA_020297465.1	574930	574930	type	True	76.7838	55	362	95	below_threshold
Parabacteroides gordonii	strain=MS-1	GCA_000969825.1	574930	574930	type	True	76.7484	58	362	95	below_threshold
Parabacteroides gordonii	strain=DSM 23371	GCA_000428565.1	574930	574930	type	True	76.7479	58	362	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 15:27:41,605] [INFO] DFAST Taxonomy check result was written to GCA_021206435.1_ASM2120643v1_genomic.fna/tc_result.tsv
[2023-06-29 15:27:41,605] [INFO] ===== Taxonomy check completed =====
[2023-06-29 15:27:41,606] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 15:27:41,606] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfaa33c8a-c792-4f4a-8fd4-a2b07ca29b29/dqc_reference/checkm_data
[2023-06-29 15:27:41,607] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 15:27:41,620] [INFO] Task started: CheckM
[2023-06-29 15:27:41,620] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021206435.1_ASM2120643v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021206435.1_ASM2120643v1_genomic.fna/checkm_input GCA_021206435.1_ASM2120643v1_genomic.fna/checkm_result
[2023-06-29 15:28:02,291] [INFO] Task succeeded: CheckM
[2023-06-29 15:28:02,292] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 29.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 15:28:02,307] [INFO] ===== Completeness check finished =====
[2023-06-29 15:28:02,307] [INFO] ===== Start GTDB Search =====
[2023-06-29 15:28:02,307] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021206435.1_ASM2120643v1_genomic.fna/markers.fasta)
[2023-06-29 15:28:02,307] [INFO] Task started: Blastn
[2023-06-29 15:28:02,308] [INFO] Running command: blastn -query GCA_021206435.1_ASM2120643v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfaa33c8a-c792-4f4a-8fd4-a2b07ca29b29/dqc_reference/reference_markers_gtdb.fasta -out GCA_021206435.1_ASM2120643v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:28:02,900] [INFO] Task succeeded: Blastn
[2023-06-29 15:28:02,904] [INFO] Selected 13 target genomes.
[2023-06-29 15:28:02,904] [INFO] Target genome list was writen to GCA_021206435.1_ASM2120643v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 15:28:02,910] [INFO] Task started: fastANI
[2023-06-29 15:28:02,910] [INFO] Running command: fastANI --query /var/lib/cwl/stge2b70fe3-ecb1-4de5-bc1a-5a20e7d337a2/GCA_021206435.1_ASM2120643v1_genomic.fna.gz --refList GCA_021206435.1_ASM2120643v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021206435.1_ASM2120643v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 15:28:10,009] [INFO] Task succeeded: fastANI
[2023-06-29 15:28:10,013] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 15:28:10,013] [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_013409575.1	s__Macellibacteroides fermentans	97.7683	340	362	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Macellibacteroides	95.0	96.90	95.56	0.80	0.74	5	conclusive
GCA_018054455.1	s__Macellibacteroides sp018054455	79.4127	174	362	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Macellibacteroides	95.0	98.91	97.71	0.78	0.74	5	-
GCF_000969825.1	s__Parabacteroides gordonii	76.7108	55	362	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.64	96.69	0.92	0.81	6	-
--------------------------------------------------------------------------------
[2023-06-29 15:28:10,015] [INFO] GTDB search result was written to GCA_021206435.1_ASM2120643v1_genomic.fna/result_gtdb.tsv
[2023-06-29 15:28:10,015] [INFO] ===== GTDB Search completed =====
[2023-06-29 15:28:10,017] [INFO] DFAST_QC result json was written to GCA_021206435.1_ASM2120643v1_genomic.fna/dqc_result.json
[2023-06-29 15:28:10,017] [INFO] DFAST_QC completed!
[2023-06-29 15:28:10,017] [INFO] Total running time: 0h0m42s