[2024-01-24 12:29:18,889] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:18,891] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:18,891] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf5e9c3a-674f-46a0-b20b-7a3db13910aa/dqc_reference
[2024-01-24 12:29:20,091] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:20,092] [INFO] Task started: Prodigal
[2024-01-24 12:29:20,092] [INFO] Running command: gunzip -c /var/lib/cwl/stg79b0e4ac-7950-4a8d-bffa-ee8b5ae626ff/GCF_003289945.1_ASM328994v1_genomic.fna.gz | prodigal -d GCF_003289945.1_ASM328994v1_genomic.fna/cds.fna -a GCF_003289945.1_ASM328994v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:41,934] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:41,935] [INFO] Task started: HMMsearch
[2024-01-24 12:29:41,935] [INFO] Running command: hmmsearch --tblout GCF_003289945.1_ASM328994v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf5e9c3a-674f-46a0-b20b-7a3db13910aa/dqc_reference/reference_markers.hmm GCF_003289945.1_ASM328994v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:42,261] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:42,264] [INFO] Found 6/6 markers.
[2024-01-24 12:29:42,322] [INFO] Query marker FASTA was written to GCF_003289945.1_ASM328994v1_genomic.fna/markers.fasta
[2024-01-24 12:29:42,323] [INFO] Task started: Blastn
[2024-01-24 12:29:42,323] [INFO] Running command: blastn -query GCF_003289945.1_ASM328994v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf5e9c3a-674f-46a0-b20b-7a3db13910aa/dqc_reference/reference_markers.fasta -out GCF_003289945.1_ASM328994v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:43,412] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:43,416] [INFO] Selected 13 target genomes.
[2024-01-24 12:29:43,416] [INFO] Target genome list was writen to GCF_003289945.1_ASM328994v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:43,441] [INFO] Task started: fastANI
[2024-01-24 12:29:43,441] [INFO] Running command: fastANI --query /var/lib/cwl/stg79b0e4ac-7950-4a8d-bffa-ee8b5ae626ff/GCF_003289945.1_ASM328994v1_genomic.fna.gz --refList GCF_003289945.1_ASM328994v1_genomic.fna/target_genomes.txt --output GCF_003289945.1_ASM328994v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:04,473] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:04,474] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf5e9c3a-674f-46a0-b20b-7a3db13910aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:04,474] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf5e9c3a-674f-46a0-b20b-7a3db13910aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:04,485] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:30:04,485] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:04,486] [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 hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	100.0	2404	2411	95	conclusive
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	89.7377	1728	2411	95	below_threshold
Mesorhizobium silamurunense	strain=CCBAU 01550	GCA_014843825.1	499528	499528	type	True	87.4021	1495	2411	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	87.2584	1582	2411	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	84.532	1314	2411	95	below_threshold
Mesorhizobium norvegicum	strain=10.2.2	GCA_004919685.1	1085774	1085774	type	True	84.4958	1488	2411	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	84.391	1282	2411	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	84.3874	1413	2411	95	below_threshold
Mesorhizobium helmanticense	strain=CSLC115N	GCA_003034915.1	1776423	1776423	type	True	84.3819	1408	2411	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	83.604	1341	2411	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	79.3377	667	2411	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	79.3314	737	2411	95	below_threshold
Chelativorans intermedius	strain=LMG 28482	GCA_025398255.1	515947	515947	type	True	78.4903	550	2411	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:04,490] [INFO] DFAST Taxonomy check result was written to GCF_003289945.1_ASM328994v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:04,491] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:04,491] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:04,491] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf5e9c3a-674f-46a0-b20b-7a3db13910aa/dqc_reference/checkm_data
[2024-01-24 12:30:04,492] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:04,562] [INFO] Task started: CheckM
[2024-01-24 12:30:04,563] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003289945.1_ASM328994v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003289945.1_ASM328994v1_genomic.fna/checkm_input GCF_003289945.1_ASM328994v1_genomic.fna/checkm_result
[2024-01-24 12:31:05,647] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:05,648] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:05,676] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:05,676] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:05,677] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003289945.1_ASM328994v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:05,677] [INFO] Task started: Blastn
[2024-01-24 12:31:05,677] [INFO] Running command: blastn -query GCF_003289945.1_ASM328994v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf5e9c3a-674f-46a0-b20b-7a3db13910aa/dqc_reference/reference_markers_gtdb.fasta -out GCF_003289945.1_ASM328994v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:07,953] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:07,957] [INFO] Selected 13 target genomes.
[2024-01-24 12:31:07,957] [INFO] Target genome list was writen to GCF_003289945.1_ASM328994v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:07,969] [INFO] Task started: fastANI
[2024-01-24 12:31:07,969] [INFO] Running command: fastANI --query /var/lib/cwl/stg79b0e4ac-7950-4a8d-bffa-ee8b5ae626ff/GCF_003289945.1_ASM328994v1_genomic.fna.gz --refList GCF_003289945.1_ASM328994v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003289945.1_ASM328994v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:32,680] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:32,698] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:32,698] [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_003289945.1	s__Mesorhizobium hawassense	100.0	2404	2411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_019091085.1	s__Mesorhizobium sp019091085	92.2175	1730	2411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004022705.2	s__Mesorhizobium sp004022705	90.8788	1722	2411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.85	98.91	0.98	0.93	18	-
GCF_006440735.1	s__Mesorhizobium sp006440735	90.2296	1596	2411	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	90.0539	1613	2411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_006440675.1	s__Mesorhizobium sp006440675	89.9799	1618	2411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.39	95.73	0.91	0.84	9	-
GCF_004016445.2	s__Mesorhizobium sp004016445	89.8105	1759	2411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.24	96.92	0.94	0.90	3	-
GCF_002294725.1	s__Mesorhizobium sp002294725	89.3172	1629	2411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.90	96.90	0.87	0.87	2	-
GCA_004017535.1	s__Mesorhizobium sp004017535	89.2203	1709	2411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.05	98.03	0.89	0.85	7	-
GCF_016591715.1	s__Mesorhizobium sp016591715	89.2187	1684	2411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006440775.1	s__Mesorhizobium sp006440775	89.216	1626	2411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.82	97.16	0.94	0.92	4	-
GCF_006442965.1	s__Mesorhizobium sp006442965	88.5362	1656	2411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003952465.1	s__Mesorhizobium sp003952465	87.4607	1672	2411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.37	98.09	0.92	0.88	6	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:32,700] [INFO] GTDB search result was written to GCF_003289945.1_ASM328994v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:32,701] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:32,706] [INFO] DFAST_QC result json was written to GCF_003289945.1_ASM328994v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:32,706] [INFO] DFAST_QC completed!
[2024-01-24 12:31:32,706] [INFO] Total running time: 0h2m14s