[2023-06-05 14:48:43,985] [INFO] DFAST_QC pipeline started.
[2023-06-05 14:48:43,987] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 14:48:43,987] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf54feee-4a20-40e9-9e6f-eeeca0ed5c2e/dqc_reference
[2023-06-05 14:48:45,078] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 14:48:45,079] [INFO] Task started: Prodigal
[2023-06-05 14:48:45,079] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ed692e5-090e-47d5-9c35-d61a2a9ef96c/GCA_004965045.1_ASM496504v1_genomic.fna.gz | prodigal -d GCA_004965045.1_ASM496504v1_genomic.fna/cds.fna -a GCA_004965045.1_ASM496504v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 14:48:54,797] [INFO] Task succeeded: Prodigal
[2023-06-05 14:48:54,798] [INFO] Task started: HMMsearch
[2023-06-05 14:48:54,798] [INFO] Running command: hmmsearch --tblout GCA_004965045.1_ASM496504v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf54feee-4a20-40e9-9e6f-eeeca0ed5c2e/dqc_reference/reference_markers.hmm GCA_004965045.1_ASM496504v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 14:48:54,994] [INFO] Task succeeded: HMMsearch
[2023-06-05 14:48:54,995] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg3ed692e5-090e-47d5-9c35-d61a2a9ef96c/GCA_004965045.1_ASM496504v1_genomic.fna.gz]
[2023-06-05 14:48:55,041] [INFO] Query marker FASTA was written to GCA_004965045.1_ASM496504v1_genomic.fna/markers.fasta
[2023-06-05 14:48:55,041] [INFO] Task started: Blastn
[2023-06-05 14:48:55,041] [INFO] Running command: blastn -query GCA_004965045.1_ASM496504v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf54feee-4a20-40e9-9e6f-eeeca0ed5c2e/dqc_reference/reference_markers.fasta -out GCA_004965045.1_ASM496504v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 14:48:55,623] [INFO] Task succeeded: Blastn
[2023-06-05 14:48:55,626] [INFO] Selected 13 target genomes.
[2023-06-05 14:48:55,626] [INFO] Target genome list was writen to GCA_004965045.1_ASM496504v1_genomic.fna/target_genomes.txt
[2023-06-05 14:48:55,628] [INFO] Task started: fastANI
[2023-06-05 14:48:55,628] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ed692e5-090e-47d5-9c35-d61a2a9ef96c/GCA_004965045.1_ASM496504v1_genomic.fna.gz --refList GCA_004965045.1_ASM496504v1_genomic.fna/target_genomes.txt --output GCA_004965045.1_ASM496504v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 14:49:09,081] [INFO] Task succeeded: fastANI
[2023-06-05 14:49:09,081] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf54feee-4a20-40e9-9e6f-eeeca0ed5c2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 14:49:09,082] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf54feee-4a20-40e9-9e6f-eeeca0ed5c2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 14:49:09,091] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 14:49:09,091] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 14:49:09,091] [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
Mesorhizobium wenxiniae	strain=WYCCWR 10195	GCA_002284535.1	2014805	2014805	type	True	94.1253	402	528	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	91.9938	413	528	95	below_threshold
Mesorhizobium temperatum	strain=SDW018	GCA_002284575.1	241416	241416	type	True	91.7931	398	528	95	below_threshold
Mesorhizobium muleiense	strain=CGMCC 1.11022	GCA_900099905.1	1004279	1004279	type	True	90.9836	396	528	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	86.3417	315	528	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	84.6786	327	528	95	below_threshold
Mesorhizobium sangaii	strain=DSM 100039	GCA_014207355.1	505389	505389	type	True	84.0269	300	528	95	below_threshold
Mesorhizobium erdmanii	strain=USDA 3471	GCA_000472705.1	1777866	1777866	type	True	83.6572	280	528	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	83.497	290	528	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	83.1306	240	528	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	79.4216	140	528	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	79.4216	140	528	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	79.1372	125	528	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 14:49:09,093] [INFO] DFAST Taxonomy check result was written to GCA_004965045.1_ASM496504v1_genomic.fna/tc_result.tsv
[2023-06-05 14:49:09,093] [INFO] ===== Taxonomy check completed =====
[2023-06-05 14:49:09,093] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 14:49:09,094] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf54feee-4a20-40e9-9e6f-eeeca0ed5c2e/dqc_reference/checkm_data
[2023-06-05 14:49:09,094] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 14:49:09,141] [INFO] Task started: CheckM
[2023-06-05 14:49:09,141] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004965045.1_ASM496504v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004965045.1_ASM496504v1_genomic.fna/checkm_input GCA_004965045.1_ASM496504v1_genomic.fna/checkm_result
[2023-06-05 14:49:39,526] [INFO] Task succeeded: CheckM
[2023-06-05 14:49:39,527] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.52%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 14:49:39,546] [INFO] ===== Completeness check finished =====
[2023-06-05 14:49:39,546] [INFO] ===== Start GTDB Search =====
[2023-06-05 14:49:39,546] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004965045.1_ASM496504v1_genomic.fna/markers.fasta)
[2023-06-05 14:49:39,546] [INFO] Task started: Blastn
[2023-06-05 14:49:39,546] [INFO] Running command: blastn -query GCA_004965045.1_ASM496504v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf54feee-4a20-40e9-9e6f-eeeca0ed5c2e/dqc_reference/reference_markers_gtdb.fasta -out GCA_004965045.1_ASM496504v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 14:49:40,420] [INFO] Task succeeded: Blastn
[2023-06-05 14:49:40,422] [INFO] Selected 10 target genomes.
[2023-06-05 14:49:40,423] [INFO] Target genome list was writen to GCA_004965045.1_ASM496504v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 14:49:40,429] [INFO] Task started: fastANI
[2023-06-05 14:49:40,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ed692e5-090e-47d5-9c35-d61a2a9ef96c/GCA_004965045.1_ASM496504v1_genomic.fna.gz --refList GCA_004965045.1_ASM496504v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004965045.1_ASM496504v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 14:49:50,691] [INFO] Task succeeded: fastANI
[2023-06-05 14:49:50,698] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 14:49:50,698] [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_002284535.1	s__Mesorhizobium wenxiniae	94.1253	402	528	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.50	95.53	0.83	0.79	62	-
GCA_004020645.1	s__Mesorhizobium sp004020645	93.8172	455	528	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.46	97.82	0.90	0.85	20	-
GCA_004020315.1	s__Mesorhizobium sp004020315	91.9158	400	528	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.08	99.08	0.89	0.89	2	-
GCF_002284575.1	s__Mesorhizobium temperatum	91.7931	398	528	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	95.74	95.09	0.81	0.81	3	-
GCF_002284565.1	s__Mesorhizobium mediterraneum_A	91.0346	375	528	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.16	97.72	0.92	0.89	20	-
GCF_900099905.1	s__Mesorhizobium muleiense	90.9836	396	528	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.77	96.33	0.85	0.80	57	-
GCF_900156895.1	s__Mesorhizobium prunaredense	90.8329	378	528	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016756595.1	s__Mesorhizobium sp004020105	90.1872	394	528	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.38	95.83	0.84	0.81	7	-
GCA_004962245.1	s__Mesorhizobium sp004962245	89.7875	358	528	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.59	99.49	0.95	0.95	3	-
GCA_005063415.1	s__Mesorhizobium sp005063415	86.0376	341	528	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 14:49:50,699] [INFO] GTDB search result was written to GCA_004965045.1_ASM496504v1_genomic.fna/result_gtdb.tsv
[2023-06-05 14:49:50,700] [INFO] ===== GTDB Search completed =====
[2023-06-05 14:49:50,703] [INFO] DFAST_QC result json was written to GCA_004965045.1_ASM496504v1_genomic.fna/dqc_result.json
[2023-06-05 14:49:50,703] [INFO] DFAST_QC completed!
[2023-06-05 14:49:50,703] [INFO] Total running time: 0h1m7s