[2023-06-05 12:46:23,471] [INFO] DFAST_QC pipeline started.
[2023-06-05 12:46:23,475] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 12:46:23,476] [INFO] DQC Reference Directory: /var/lib/cwl/stg08bb065e-b8a3-4c61-8c10-6a122622cf84/dqc_reference
[2023-06-05 12:46:26,963] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 12:46:26,964] [INFO] Task started: Prodigal
[2023-06-05 12:46:26,964] [INFO] Running command: gunzip -c /var/lib/cwl/stgaee5e62b-68c5-4384-a90f-7123c41a5816/GCA_004018815.1_ASM401881v1_genomic.fna.gz | prodigal -d GCA_004018815.1_ASM401881v1_genomic.fna/cds.fna -a GCA_004018815.1_ASM401881v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 12:46:43,685] [INFO] Task succeeded: Prodigal
[2023-06-05 12:46:43,685] [INFO] Task started: HMMsearch
[2023-06-05 12:46:43,685] [INFO] Running command: hmmsearch --tblout GCA_004018815.1_ASM401881v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg08bb065e-b8a3-4c61-8c10-6a122622cf84/dqc_reference/reference_markers.hmm GCA_004018815.1_ASM401881v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 12:46:43,945] [INFO] Task succeeded: HMMsearch
[2023-06-05 12:46:43,946] [INFO] Found 6/6 markers.
[2023-06-05 12:46:43,996] [INFO] Query marker FASTA was written to GCA_004018815.1_ASM401881v1_genomic.fna/markers.fasta
[2023-06-05 12:46:43,996] [INFO] Task started: Blastn
[2023-06-05 12:46:43,997] [INFO] Running command: blastn -query GCA_004018815.1_ASM401881v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08bb065e-b8a3-4c61-8c10-6a122622cf84/dqc_reference/reference_markers.fasta -out GCA_004018815.1_ASM401881v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 12:46:45,016] [INFO] Task succeeded: Blastn
[2023-06-05 12:46:45,020] [INFO] Selected 16 target genomes.
[2023-06-05 12:46:45,020] [INFO] Target genome list was writen to GCA_004018815.1_ASM401881v1_genomic.fna/target_genomes.txt
[2023-06-05 12:46:45,021] [INFO] Task started: fastANI
[2023-06-05 12:46:45,021] [INFO] Running command: fastANI --query /var/lib/cwl/stgaee5e62b-68c5-4384-a90f-7123c41a5816/GCA_004018815.1_ASM401881v1_genomic.fna.gz --refList GCA_004018815.1_ASM401881v1_genomic.fna/target_genomes.txt --output GCA_004018815.1_ASM401881v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 12:47:09,394] [INFO] Task succeeded: fastANI
[2023-06-05 12:47:09,394] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg08bb065e-b8a3-4c61-8c10-6a122622cf84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 12:47:09,395] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg08bb065e-b8a3-4c61-8c10-6a122622cf84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 12:47:09,408] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 12:47:09,408] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 12:47:09,408] [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 waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	87.2817	1415	1888	95	below_threshold
Mesorhizobium silamurunense	strain=CCBAU 01550	GCA_014843825.1	499528	499528	type	True	86.6079	1277	1888	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	86.5682	1368	1888	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	86.5061	1369	1888	95	below_threshold
Mesorhizobium caraganae	strain=LMG 24397	GCA_016836705.1	483206	483206	type	True	86.253	1347	1888	95	below_threshold
Mesorhizobium muleiense	strain=CGMCC 1.11022	GCA_900099905.1	1004279	1004279	type	True	86.2327	1215	1888	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	86.1464	1295	1888	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	85.941	1179	1888	95	below_threshold
Mesorhizobium helmanticense	strain=CSLC115N	GCA_003034915.1	1776423	1776423	type	True	85.9267	1220	1888	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	85.7817	1122	1888	95	below_threshold
Mesorhizobium loti	strain=DSM 2626	GCA_003148495.1	381	381	suspected-type	True	85.4195	1287	1888	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	85.055	1169	1888	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	84.969	1236	1888	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	79.7719	650	1888	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	79.7354	653	1888	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	79.2677	583	1888	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 12:47:09,411] [INFO] DFAST Taxonomy check result was written to GCA_004018815.1_ASM401881v1_genomic.fna/tc_result.tsv
[2023-06-05 12:47:09,411] [INFO] ===== Taxonomy check completed =====
[2023-06-05 12:47:09,412] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 12:47:09,412] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg08bb065e-b8a3-4c61-8c10-6a122622cf84/dqc_reference/checkm_data
[2023-06-05 12:47:09,413] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 12:47:09,474] [INFO] Task started: CheckM
[2023-06-05 12:47:09,475] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004018815.1_ASM401881v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004018815.1_ASM401881v1_genomic.fna/checkm_input GCA_004018815.1_ASM401881v1_genomic.fna/checkm_result
[2023-06-05 12:47:58,632] [INFO] Task succeeded: CheckM
[2023-06-05 12:47:58,633] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 12:47:58,668] [INFO] ===== Completeness check finished =====
[2023-06-05 12:47:58,669] [INFO] ===== Start GTDB Search =====
[2023-06-05 12:47:58,669] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004018815.1_ASM401881v1_genomic.fna/markers.fasta)
[2023-06-05 12:47:58,669] [INFO] Task started: Blastn
[2023-06-05 12:47:58,670] [INFO] Running command: blastn -query GCA_004018815.1_ASM401881v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08bb065e-b8a3-4c61-8c10-6a122622cf84/dqc_reference/reference_markers_gtdb.fasta -out GCA_004018815.1_ASM401881v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 12:48:00,699] [INFO] Task succeeded: Blastn
[2023-06-05 12:48:00,703] [INFO] Selected 16 target genomes.
[2023-06-05 12:48:00,703] [INFO] Target genome list was writen to GCA_004018815.1_ASM401881v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 12:48:00,708] [INFO] Task started: fastANI
[2023-06-05 12:48:00,708] [INFO] Running command: fastANI --query /var/lib/cwl/stgaee5e62b-68c5-4384-a90f-7123c41a5816/GCA_004018815.1_ASM401881v1_genomic.fna.gz --refList GCA_004018815.1_ASM401881v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004018815.1_ASM401881v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 12:48:25,049] [INFO] Task succeeded: fastANI
[2023-06-05 12:48:25,062] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 12:48:25,062] [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_004791025.1	s__Mesorhizobium sp004791025	98.0606	1727	1888	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.99	98.05	0.93	0.88	18	conclusive
GCF_003952505.1	s__Mesorhizobium sp003952505	93.3195	1570	1888	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.46	98.78	0.92	0.87	11	-
GCF_016756535.1	s__Mesorhizobium sp016756535	90.7899	1513	1888	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952385.1	s__Mesorhizobium sp003952385	87.8113	1424	1888	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.01	97.50	0.89	0.87	7	-
GCF_001686985.1	s__Mesorhizobium amorphae_B	87.6847	1420	1888	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0866	99.99	99.99	1.00	1.00	2	-
GCA_004963905.1	s__Mesorhizobium sp004963905	87.5722	1362	1888	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014843845.1	s__Mesorhizobium amorphae_A	87.4286	1391	1888	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0866	97.39	97.39	0.88	0.88	2	-
GCF_004016445.2	s__Mesorhizobium sp004016445	87.0494	1426	1888	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.24	96.92	0.94	0.90	3	-
GCF_003952525.1	s__Mesorhizobium sp002294945	86.9177	1314	1888	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.39	99.02	0.88	0.85	8	-
GCF_002294725.1	s__Mesorhizobium sp002294725	86.8649	1315	1888	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.90	96.90	0.87	0.87	2	-
GCF_019091085.1	s__Mesorhizobium sp019091085	86.7074	1236	1888	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006442815.1	s__Mesorhizobium sp006442815	86.4275	1223	1888	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_002294995.1	s__Mesorhizobium sp002294995	86.2454	1323	1888	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000427725.1	s__Mesorhizobium sp000427725	86.0237	1276	1888	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000350085.1	s__Mesorhizobium metallidurans	85.9754	1175	1888	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000824805.1	s__Mesorhizobium sp000824805	85.9218	1237	1888	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 12:48:25,064] [INFO] GTDB search result was written to GCA_004018815.1_ASM401881v1_genomic.fna/result_gtdb.tsv
[2023-06-05 12:48:25,064] [INFO] ===== GTDB Search completed =====
[2023-06-05 12:48:25,068] [INFO] DFAST_QC result json was written to GCA_004018815.1_ASM401881v1_genomic.fna/dqc_result.json
[2023-06-05 12:48:25,068] [INFO] DFAST_QC completed!
[2023-06-05 12:48:25,068] [INFO] Total running time: 0h2m2s