[2024-01-24 12:14:09,822] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:09,828] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:09,828] [INFO] DQC Reference Directory: /var/lib/cwl/stga428c75c-8385-422d-862a-feff456f832b/dqc_reference
[2024-01-24 12:14:11,193] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:11,194] [INFO] Task started: Prodigal
[2024-01-24 12:14:11,194] [INFO] Running command: gunzip -c /var/lib/cwl/stge0d2e19a-ff15-40de-886b-fa15e1c13e1f/GCF_000521505.1_ASM52150v1_genomic.fna.gz | prodigal -d GCF_000521505.1_ASM52150v1_genomic.fna/cds.fna -a GCF_000521505.1_ASM52150v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:27,047] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:27,048] [INFO] Task started: HMMsearch
[2024-01-24 12:14:27,048] [INFO] Running command: hmmsearch --tblout GCF_000521505.1_ASM52150v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga428c75c-8385-422d-862a-feff456f832b/dqc_reference/reference_markers.hmm GCF_000521505.1_ASM52150v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:27,425] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:27,426] [INFO] Found 6/6 markers.
[2024-01-24 12:14:27,479] [INFO] Query marker FASTA was written to GCF_000521505.1_ASM52150v1_genomic.fna/markers.fasta
[2024-01-24 12:14:27,479] [INFO] Task started: Blastn
[2024-01-24 12:14:27,479] [INFO] Running command: blastn -query GCF_000521505.1_ASM52150v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga428c75c-8385-422d-862a-feff456f832b/dqc_reference/reference_markers.fasta -out GCF_000521505.1_ASM52150v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:28,197] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:28,200] [INFO] Selected 20 target genomes.
[2024-01-24 12:14:28,200] [INFO] Target genome list was writen to GCF_000521505.1_ASM52150v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:28,208] [INFO] Task started: fastANI
[2024-01-24 12:14:28,209] [INFO] Running command: fastANI --query /var/lib/cwl/stge0d2e19a-ff15-40de-886b-fa15e1c13e1f/GCF_000521505.1_ASM52150v1_genomic.fna.gz --refList GCF_000521505.1_ASM52150v1_genomic.fna/target_genomes.txt --output GCF_000521505.1_ASM52150v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:44,367] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:44,368] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga428c75c-8385-422d-862a-feff456f832b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:44,369] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga428c75c-8385-422d-862a-feff456f832b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:44,384] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:44,384] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:44,384] [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
Advenella mimigardefordensis	strain=DPN7	GCA_000521505.1	302406	302406	type	True	100.0	1586	1587	95	conclusive
Advenella incenata	strain=DSM 23814	GCA_004217095.1	267800	267800	type	True	84.5492	1147	1587	95	below_threshold
Advenella kashmirensis	strain=WT001	GCA_000219915.3	310575	310575	type	True	84.3936	1093	1587	95	below_threshold
Advenella faeciporci	strain=KCTC 23732	GCA_014652395.1	797535	797535	type	True	77.4884	187	1587	95	below_threshold
Advenella mandrilli	strain=WQ 585	GCA_016595155.1	2800330	2800330	type	True	77.4805	158	1587	95	below_threshold
Bordetella trematum	strain=NCTC12995	GCA_900445945.1	123899	123899	type	True	77.4651	113	1587	95	below_threshold
Advenella alkanexedens	strain=LAM0050	GCA_019132845.1	1481665	1481665	type	True	77.3779	175	1587	95	below_threshold
Pusillimonas minor	strain=YC-7-48	GCA_014237865.1	2697024	2697024	type	True	77.197	96	1587	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	77.0779	99	1587	95	below_threshold
Pusillimonas ginsengisoli	strain=KCTC 22046	GCA_004153455.1	453575	453575	type	True	76.4274	110	1587	95	below_threshold
Achromobacter aegrifaciens	strain=LMG 26852	GCA_902859735.1	1287736	1287736	type	True	76.3669	140	1587	95	below_threshold
Pusillimonas soli	strain=KCTC 22455	GCA_004153445.1	659016	659016	type	True	76.352	97	1587	95	below_threshold
Candidimonas humi	strain=DSM 25336	GCA_019166065.1	683355	683355	type	True	76.2769	115	1587	95	below_threshold
Achromobacter mucicolens	strain=LMG 26685	GCA_902859725.1	1389922	1389922	type	True	76.2569	134	1587	95	below_threshold
Candidimonas nitroreducens	strain=SC-089	GCA_002209565.1	683354	683354	type	True	76.2166	129	1587	95	below_threshold
Achromobacter deleyi	strain=LMG 3458	GCA_902859705.1	1353891	1353891	type	True	76.0721	163	1587	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	75.2978	54	1587	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:44,395] [INFO] DFAST Taxonomy check result was written to GCF_000521505.1_ASM52150v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:44,398] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:44,398] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:44,399] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga428c75c-8385-422d-862a-feff456f832b/dqc_reference/checkm_data
[2024-01-24 12:14:44,401] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:44,456] [INFO] Task started: CheckM
[2024-01-24 12:14:44,457] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000521505.1_ASM52150v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000521505.1_ASM52150v1_genomic.fna/checkm_input GCF_000521505.1_ASM52150v1_genomic.fna/checkm_result
[2024-01-24 12:15:33,116] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:33,118] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:33,135] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:33,135] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:33,135] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000521505.1_ASM52150v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:33,136] [INFO] Task started: Blastn
[2024-01-24 12:15:33,136] [INFO] Running command: blastn -query GCF_000521505.1_ASM52150v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga428c75c-8385-422d-862a-feff456f832b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000521505.1_ASM52150v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:34,017] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:34,020] [INFO] Selected 7 target genomes.
[2024-01-24 12:15:34,021] [INFO] Target genome list was writen to GCF_000521505.1_ASM52150v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:34,026] [INFO] Task started: fastANI
[2024-01-24 12:15:34,026] [INFO] Running command: fastANI --query /var/lib/cwl/stge0d2e19a-ff15-40de-886b-fa15e1c13e1f/GCF_000521505.1_ASM52150v1_genomic.fna.gz --refList GCF_000521505.1_ASM52150v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000521505.1_ASM52150v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:41,423] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:41,430] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:41,430] [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_000521505.1	s__Advenella mimigardefordensis	100.0	1586	1587	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Advenella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014897675.1	s__Advenella sp003533245	84.8961	1056	1587	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Advenella	95.0	98.87	98.87	0.91	0.91	2	-
GCF_004217095.1	s__Advenella incenata	84.5511	1146	1587	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Advenella	95.0	99.05	99.05	0.92	0.92	2	-
GCF_000219915.2	s__Advenella kashmirensis	84.3971	1095	1587	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Advenella	95.0	98.94	98.94	0.95	0.95	2	-
GCF_002810445.1	s__Advenella sp002810445	81.6775	878	1587	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Advenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000506985.1	s__Advenella kashmirensis_A	80.5567	797	1587	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Advenella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:41,432] [INFO] GTDB search result was written to GCF_000521505.1_ASM52150v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:41,432] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:41,435] [INFO] DFAST_QC result json was written to GCF_000521505.1_ASM52150v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:41,436] [INFO] DFAST_QC completed!
[2024-01-24 12:15:41,436] [INFO] Total running time: 0h1m32s