[2024-01-24 11:06:04,654] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:06:04,657] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:06:04,657] [INFO] DQC Reference Directory: /var/lib/cwl/stg453e8577-4574-4bf2-99fa-fb2574ff1b4d/dqc_reference
[2024-01-24 11:06:07,010] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:06:07,011] [INFO] Task started: Prodigal
[2024-01-24 11:06:07,011] [INFO] Running command: gunzip -c /var/lib/cwl/stg010b7d84-726c-4cc9-874a-9d585ef789a8/GCF_030160895.1_ASM3016089v1_genomic.fna.gz | prodigal -d GCF_030160895.1_ASM3016089v1_genomic.fna/cds.fna -a GCF_030160895.1_ASM3016089v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:06:30,019] [INFO] Task succeeded: Prodigal
[2024-01-24 11:06:30,019] [INFO] Task started: HMMsearch
[2024-01-24 11:06:30,019] [INFO] Running command: hmmsearch --tblout GCF_030160895.1_ASM3016089v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg453e8577-4574-4bf2-99fa-fb2574ff1b4d/dqc_reference/reference_markers.hmm GCF_030160895.1_ASM3016089v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:06:30,354] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:06:30,356] [INFO] Found 6/6 markers.
[2024-01-24 11:06:30,416] [INFO] Query marker FASTA was written to GCF_030160895.1_ASM3016089v1_genomic.fna/markers.fasta
[2024-01-24 11:06:30,416] [INFO] Task started: Blastn
[2024-01-24 11:06:30,416] [INFO] Running command: blastn -query GCF_030160895.1_ASM3016089v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg453e8577-4574-4bf2-99fa-fb2574ff1b4d/dqc_reference/reference_markers.fasta -out GCF_030160895.1_ASM3016089v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:31,467] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:31,470] [INFO] Selected 12 target genomes.
[2024-01-24 11:06:31,471] [INFO] Target genome list was writen to GCF_030160895.1_ASM3016089v1_genomic.fna/target_genomes.txt
[2024-01-24 11:06:31,488] [INFO] Task started: fastANI
[2024-01-24 11:06:31,488] [INFO] Running command: fastANI --query /var/lib/cwl/stg010b7d84-726c-4cc9-874a-9d585ef789a8/GCF_030160895.1_ASM3016089v1_genomic.fna.gz --refList GCF_030160895.1_ASM3016089v1_genomic.fna/target_genomes.txt --output GCF_030160895.1_ASM3016089v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:49,839] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:49,840] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg453e8577-4574-4bf2-99fa-fb2574ff1b4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:49,840] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg453e8577-4574-4bf2-99fa-fb2574ff1b4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:49,854] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:06:49,855] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:06:49,855] [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 temperatum	strain=SDW018	GCA_002284575.1	241416	241416	type	True	91.1498	1703	2540	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	90.871	1711	2540	95	below_threshold
Mesorhizobium wenxiniae	strain=WYCCWR 10195	GCA_002284535.1	2014805	2014805	type	True	90.494	1573	2540	95	below_threshold
Mesorhizobium muleiense	strain=CGMCC 1.11022	GCA_900099905.1	1004279	1004279	type	True	90.1011	1598	2540	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	87.8131	1415	2540	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	87.6921	1354	2540	95	below_threshold
Mesorhizobium helmanticense	strain=CSLC115N	GCA_003034915.1	1776423	1776423	type	True	87.5404	1510	2540	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	85.9794	1520	2540	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	84.1897	1275	2540	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	79.2781	658	2540	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	79.2245	634	2540	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	78.9722	721	2540	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:49,856] [INFO] DFAST Taxonomy check result was written to GCF_030160895.1_ASM3016089v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:49,857] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:49,857] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:49,857] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg453e8577-4574-4bf2-99fa-fb2574ff1b4d/dqc_reference/checkm_data
[2024-01-24 11:06:49,858] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:49,932] [INFO] Task started: CheckM
[2024-01-24 11:06:49,932] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030160895.1_ASM3016089v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030160895.1_ASM3016089v1_genomic.fna/checkm_input GCF_030160895.1_ASM3016089v1_genomic.fna/checkm_result
[2024-01-24 11:07:55,088] [INFO] Task succeeded: CheckM
[2024-01-24 11:07:55,090] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:07:55,112] [INFO] ===== Completeness check finished =====
[2024-01-24 11:07:55,113] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:07:55,113] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030160895.1_ASM3016089v1_genomic.fna/markers.fasta)
[2024-01-24 11:07:55,113] [INFO] Task started: Blastn
[2024-01-24 11:07:55,114] [INFO] Running command: blastn -query GCF_030160895.1_ASM3016089v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg453e8577-4574-4bf2-99fa-fb2574ff1b4d/dqc_reference/reference_markers_gtdb.fasta -out GCF_030160895.1_ASM3016089v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:07:57,286] [INFO] Task succeeded: Blastn
[2024-01-24 11:07:57,290] [INFO] Selected 12 target genomes.
[2024-01-24 11:07:57,290] [INFO] Target genome list was writen to GCF_030160895.1_ASM3016089v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:07:57,305] [INFO] Task started: fastANI
[2024-01-24 11:07:57,305] [INFO] Running command: fastANI --query /var/lib/cwl/stg010b7d84-726c-4cc9-874a-9d585ef789a8/GCF_030160895.1_ASM3016089v1_genomic.fna.gz --refList GCF_030160895.1_ASM3016089v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030160895.1_ASM3016089v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:08:18,668] [INFO] Task succeeded: fastANI
[2024-01-24 11:08:18,683] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:08:18,684] [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_007830515.1	s__Mesorhizobium tianshanense	99.9818	2508	2540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004962245.1	s__Mesorhizobium sp004962245	93.4139	1798	2540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.59	99.49	0.95	0.95	3	-
GCF_003952365.1	s__Mesorhizobium sp003952365	93.3318	1738	2540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002284575.1	s__Mesorhizobium temperatum	91.156	1701	2540	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	90.7669	1664	2540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.16	97.72	0.92	0.89	20	-
GCA_004962925.1	s__Mesorhizobium sp004962925	90.488	1476	2540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004020315.1	s__Mesorhizobium sp004020315	90.4598	1588	2540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.08	99.08	0.89	0.89	2	-
GCA_004020645.1	s__Mesorhizobium sp004020645	90.3287	1681	2540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.46	97.82	0.90	0.85	20	-
GCF_900156895.1	s__Mesorhizobium prunaredense	90.2632	1588	2540	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	89.7973	1606	2540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.38	95.83	0.84	0.81	7	-
GCF_000359125.1	s__Mesorhizobium sp000359125	88.0648	1423	2540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253745.1	s__Mesorhizobium kowhaii	85.9245	1472	2540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:08:18,685] [INFO] GTDB search result was written to GCF_030160895.1_ASM3016089v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:08:18,686] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:08:18,692] [INFO] DFAST_QC result json was written to GCF_030160895.1_ASM3016089v1_genomic.fna/dqc_result.json
[2024-01-24 11:08:18,693] [INFO] DFAST_QC completed!
[2024-01-24 11:08:18,693] [INFO] Total running time: 0h2m14s