[2024-01-24 10:47:11,666] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:11,668] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:11,668] [INFO] DQC Reference Directory: /var/lib/cwl/stg05f0783e-1a31-4479-aed1-9fad0ca4dc0c/dqc_reference
[2024-01-24 10:47:16,942] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:16,944] [INFO] Task started: Prodigal
[2024-01-24 10:47:16,944] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2e48a5a-f609-4c01-80af-dbce043e811a/GCF_016595155.1_ASM1659515v1_genomic.fna.gz | prodigal -d GCF_016595155.1_ASM1659515v1_genomic.fna/cds.fna -a GCF_016595155.1_ASM1659515v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:28,693] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:28,693] [INFO] Task started: HMMsearch
[2024-01-24 10:47:28,693] [INFO] Running command: hmmsearch --tblout GCF_016595155.1_ASM1659515v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05f0783e-1a31-4479-aed1-9fad0ca4dc0c/dqc_reference/reference_markers.hmm GCF_016595155.1_ASM1659515v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:28,990] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:28,992] [INFO] Found 6/6 markers.
[2024-01-24 10:47:29,027] [INFO] Query marker FASTA was written to GCF_016595155.1_ASM1659515v1_genomic.fna/markers.fasta
[2024-01-24 10:47:29,027] [INFO] Task started: Blastn
[2024-01-24 10:47:29,027] [INFO] Running command: blastn -query GCF_016595155.1_ASM1659515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05f0783e-1a31-4479-aed1-9fad0ca4dc0c/dqc_reference/reference_markers.fasta -out GCF_016595155.1_ASM1659515v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:29,642] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:29,646] [INFO] Selected 19 target genomes.
[2024-01-24 10:47:29,647] [INFO] Target genome list was writen to GCF_016595155.1_ASM1659515v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:05,619] [INFO] Task started: fastANI
[2024-01-24 10:48:05,619] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2e48a5a-f609-4c01-80af-dbce043e811a/GCF_016595155.1_ASM1659515v1_genomic.fna.gz --refList GCF_016595155.1_ASM1659515v1_genomic.fna/target_genomes.txt --output GCF_016595155.1_ASM1659515v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:18,649] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:18,651] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05f0783e-1a31-4479-aed1-9fad0ca4dc0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:18,652] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05f0783e-1a31-4479-aed1-9fad0ca4dc0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:18,664] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:18,664] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:18,664] [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 mandrilli	strain=WQ 585	GCA_016595155.1	2800330	2800330	type	True	100.0	1075	1075	95	conclusive
Advenella faeciporci	strain=KCTC 23732	GCA_014652395.1	797535	797535	type	True	87.2588	830	1075	95	below_threshold
Advenella alkanexedens	strain=LAM0050	GCA_019132845.1	1481665	1481665	type	True	87.1758	823	1075	95	below_threshold
Advenella mimigardefordensis	strain=DPN7	GCA_000521505.1	302406	302406	type	True	77.3888	177	1075	95	below_threshold
Advenella kashmirensis	strain=WT001	GCA_000219915.3	310575	310575	type	True	77.2512	169	1075	95	below_threshold
Advenella incenata	strain=DSM 23814	GCA_004217095.1	267800	267800	type	True	77.1385	176	1075	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	76.5582	90	1075	95	below_threshold
Pusillimonas noertemannii	strain=DSM 10065	GCA_003545825.1	305977	305977	type	True	76.4361	60	1075	95	below_threshold
Achromobacter anxifer	strain=LMG 26857	GCA_903652925.1	1287737	1287737	type	True	76.1839	63	1075	95	below_threshold
Pusillimonas faecipullorum	strain=CC-YST705	GCA_020539505.1	2755040	2755040	type	True	76.1019	69	1075	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:18,666] [INFO] DFAST Taxonomy check result was written to GCF_016595155.1_ASM1659515v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:18,667] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:18,667] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:18,667] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05f0783e-1a31-4479-aed1-9fad0ca4dc0c/dqc_reference/checkm_data
[2024-01-24 10:48:18,668] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:18,706] [INFO] Task started: CheckM
[2024-01-24 10:48:18,706] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016595155.1_ASM1659515v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016595155.1_ASM1659515v1_genomic.fna/checkm_input GCF_016595155.1_ASM1659515v1_genomic.fna/checkm_result
[2024-01-24 10:48:51,605] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:51,608] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:51,626] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:51,626] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:51,627] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016595155.1_ASM1659515v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:51,627] [INFO] Task started: Blastn
[2024-01-24 10:48:51,628] [INFO] Running command: blastn -query GCF_016595155.1_ASM1659515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05f0783e-1a31-4479-aed1-9fad0ca4dc0c/dqc_reference/reference_markers_gtdb.fasta -out GCF_016595155.1_ASM1659515v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:52,465] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:52,470] [INFO] Selected 14 target genomes.
[2024-01-24 10:48:52,470] [INFO] Target genome list was writen to GCF_016595155.1_ASM1659515v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:52,481] [INFO] Task started: fastANI
[2024-01-24 10:48:52,481] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2e48a5a-f609-4c01-80af-dbce043e811a/GCF_016595155.1_ASM1659515v1_genomic.fna.gz --refList GCF_016595155.1_ASM1659515v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016595155.1_ASM1659515v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:01,891] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:01,910] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:01,911] [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_016595155.1	s__Advenella sp016595155	100.0	1075	1075	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_014652395.1	s__Advenella faeciporci	87.2436	831	1075	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Advenella	95.0	97.16	97.10	0.89	0.86	3	-
GCF_019132845.1	s__Advenella alkanexedens	87.1758	823	1075	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Advenella	95.0	98.89	98.76	0.91	0.89	3	-
GCA_012735395.1	s__Advenella sp012735395	81.0852	442	1075	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	77.4108	162	1075	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	77.3913	176	1075	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	77.1385	176	1075	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Advenella	95.0	99.05	99.05	0.92	0.92	2	-
GCF_002810445.1	s__Advenella sp002810445	77.1309	133	1075	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	76.9361	164	1075	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Advenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000209655.1	s__Pusillimonas_C sp000209655	76.4165	88	1075	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003994415.1	s__Achromobacter spanius_C	76.3866	76	1075	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.60	98.60	0.94	0.94	2	-
GCA_012744285.1	s__Pusillimonas_A sp012744285	76.1688	65	1075	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:01,912] [INFO] GTDB search result was written to GCF_016595155.1_ASM1659515v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:01,913] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:01,916] [INFO] DFAST_QC result json was written to GCF_016595155.1_ASM1659515v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:01,916] [INFO] DFAST_QC completed!
[2024-01-24 10:49:01,916] [INFO] Total running time: 0h1m50s