[2024-01-25 17:53:05,540] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:53:05,541] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:53:05,541] [INFO] DQC Reference Directory: /var/lib/cwl/stg9885a2f1-dc93-4711-8de8-32610bf1f7b9/dqc_reference
[2024-01-25 17:53:06,736] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:53:06,737] [INFO] Task started: Prodigal
[2024-01-25 17:53:06,737] [INFO] Running command: gunzip -c /var/lib/cwl/stg7e3c0a7f-cc86-47ba-b28b-a0e7045454e4/GCF_014652395.1_ASM1465239v1_genomic.fna.gz | prodigal -d GCF_014652395.1_ASM1465239v1_genomic.fna/cds.fna -a GCF_014652395.1_ASM1465239v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:53:14,891] [INFO] Task succeeded: Prodigal
[2024-01-25 17:53:14,892] [INFO] Task started: HMMsearch
[2024-01-25 17:53:14,892] [INFO] Running command: hmmsearch --tblout GCF_014652395.1_ASM1465239v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9885a2f1-dc93-4711-8de8-32610bf1f7b9/dqc_reference/reference_markers.hmm GCF_014652395.1_ASM1465239v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:53:15,115] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:53:15,117] [INFO] Found 6/6 markers.
[2024-01-25 17:53:15,143] [INFO] Query marker FASTA was written to GCF_014652395.1_ASM1465239v1_genomic.fna/markers.fasta
[2024-01-25 17:53:15,143] [INFO] Task started: Blastn
[2024-01-25 17:53:15,143] [INFO] Running command: blastn -query GCF_014652395.1_ASM1465239v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9885a2f1-dc93-4711-8de8-32610bf1f7b9/dqc_reference/reference_markers.fasta -out GCF_014652395.1_ASM1465239v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:53:15,783] [INFO] Task succeeded: Blastn
[2024-01-25 17:53:15,786] [INFO] Selected 16 target genomes.
[2024-01-25 17:53:15,786] [INFO] Target genome list was writen to GCF_014652395.1_ASM1465239v1_genomic.fna/target_genomes.txt
[2024-01-25 17:53:15,793] [INFO] Task started: fastANI
[2024-01-25 17:53:15,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e3c0a7f-cc86-47ba-b28b-a0e7045454e4/GCF_014652395.1_ASM1465239v1_genomic.fna.gz --refList GCF_014652395.1_ASM1465239v1_genomic.fna/target_genomes.txt --output GCF_014652395.1_ASM1465239v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:53:28,031] [INFO] Task succeeded: fastANI
[2024-01-25 17:53:28,031] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9885a2f1-dc93-4711-8de8-32610bf1f7b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:53:28,032] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9885a2f1-dc93-4711-8de8-32610bf1f7b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:53:28,039] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:53:28,039] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:53:28,039] [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 faeciporci	strain=KCTC 23732	GCA_014652395.1	797535	797535	type	True	100.0	1013	1015	95	conclusive
Advenella alkanexedens	strain=LAM0050	GCA_019132845.1	1481665	1481665	type	True	90.2609	835	1015	95	below_threshold
Advenella mandrilli	strain=WQ 585	GCA_016595155.1	2800330	2800330	type	True	87.3602	827	1015	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	78.2355	97	1015	95	below_threshold
Advenella mimigardefordensis	strain=DPN7	GCA_000521505.1	302406	302406	type	True	77.4555	188	1015	95	below_threshold
Advenella incenata	strain=DSM 23814	GCA_004217095.1	267800	267800	type	True	77.1936	146	1015	95	below_threshold
Advenella kashmirensis	strain=WT001	GCA_000219915.3	310575	310575	type	True	77.08	173	1015	95	below_threshold
Achromobacter insolitus	strain=LMG 6003	GCA_902859615.1	217204	217204	type	True	76.0645	50	1015	95	below_threshold
Achromobacter insolitus	strain=NCTC13520	GCA_900637265.1	217204	217204	type	True	76.031	51	1015	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:53:28,040] [INFO] DFAST Taxonomy check result was written to GCF_014652395.1_ASM1465239v1_genomic.fna/tc_result.tsv
[2024-01-25 17:53:28,041] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:53:28,041] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:53:28,041] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9885a2f1-dc93-4711-8de8-32610bf1f7b9/dqc_reference/checkm_data
[2024-01-25 17:53:28,042] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:53:28,072] [INFO] Task started: CheckM
[2024-01-25 17:53:28,072] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652395.1_ASM1465239v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652395.1_ASM1465239v1_genomic.fna/checkm_input GCF_014652395.1_ASM1465239v1_genomic.fna/checkm_result
[2024-01-25 17:53:56,035] [INFO] Task succeeded: CheckM
[2024-01-25 17:53:56,036] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:53:56,056] [INFO] ===== Completeness check finished =====
[2024-01-25 17:53:56,056] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:53:56,057] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652395.1_ASM1465239v1_genomic.fna/markers.fasta)
[2024-01-25 17:53:56,057] [INFO] Task started: Blastn
[2024-01-25 17:53:56,057] [INFO] Running command: blastn -query GCF_014652395.1_ASM1465239v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9885a2f1-dc93-4711-8de8-32610bf1f7b9/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652395.1_ASM1465239v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:53:57,164] [INFO] Task succeeded: Blastn
[2024-01-25 17:53:57,167] [INFO] Selected 15 target genomes.
[2024-01-25 17:53:57,167] [INFO] Target genome list was writen to GCF_014652395.1_ASM1465239v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:53:57,196] [INFO] Task started: fastANI
[2024-01-25 17:53:57,197] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e3c0a7f-cc86-47ba-b28b-a0e7045454e4/GCF_014652395.1_ASM1465239v1_genomic.fna.gz --refList GCF_014652395.1_ASM1465239v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652395.1_ASM1465239v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:54:09,010] [INFO] Task succeeded: fastANI
[2024-01-25 17:54:09,018] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:54:09,018] [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_014652395.1	s__Advenella faeciporci	100.0	1013	1015	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Advenella	95.0	97.16	97.10	0.89	0.86	3	conclusive
GCF_019132845.1	s__Advenella alkanexedens	90.2609	835	1015	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Advenella	95.0	98.89	98.76	0.91	0.89	3	-
GCF_016595155.1	s__Advenella sp016595155	87.3756	826	1015	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Advenella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012735395.1	s__Advenella sp012735395	80.3555	454	1015	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Advenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014897675.1	s__Advenella sp003533245	77.5201	156	1015	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Advenella	95.0	98.87	98.87	0.91	0.91	2	-
GCF_000521505.1	s__Advenella mimigardefordensis	77.4555	188	1015	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Advenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217095.1	s__Advenella incenata	77.1745	147	1015	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Advenella	95.0	99.05	99.05	0.92	0.92	2	-
GCF_017745595.1	s__Bordetella_A petrii_C	77.1565	87	1015	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000506985.1	s__Advenella kashmirensis_A	77.0349	164	1015	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Advenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002236805.1	s__Pusillimonas_A sp002236805	76.4712	81	1015	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	98.07	98.07	0.83	0.83	2	-
GCF_019218885.1	s__Bordetella_A sp019218885	76.2405	71	1015	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002261185.1	s__Bordetella_A sp002261185	75.8732	58	1015	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	98.69	98.69	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:54:09,019] [INFO] GTDB search result was written to GCF_014652395.1_ASM1465239v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:54:09,020] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:54:09,022] [INFO] DFAST_QC result json was written to GCF_014652395.1_ASM1465239v1_genomic.fna/dqc_result.json
[2024-01-25 17:54:09,022] [INFO] DFAST_QC completed!
[2024-01-25 17:54:09,023] [INFO] Total running time: 0h1m3s