[2024-01-25 18:04:05,483] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:04:05,484] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:04:05,484] [INFO] DQC Reference Directory: /var/lib/cwl/stg99c7e0ec-63e3-4d66-bbb9-e70908dbb80a/dqc_reference
[2024-01-25 18:04:06,625] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:04:06,626] [INFO] Task started: Prodigal
[2024-01-25 18:04:06,626] [INFO] Running command: gunzip -c /var/lib/cwl/stga5024cfc-44fb-44f7-a4bd-4c58902a3ac1/GCF_016836705.1_ASM1683670v1_genomic.fna.gz | prodigal -d GCF_016836705.1_ASM1683670v1_genomic.fna/cds.fna -a GCF_016836705.1_ASM1683670v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:04:26,247] [INFO] Task succeeded: Prodigal
[2024-01-25 18:04:26,248] [INFO] Task started: HMMsearch
[2024-01-25 18:04:26,248] [INFO] Running command: hmmsearch --tblout GCF_016836705.1_ASM1683670v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99c7e0ec-63e3-4d66-bbb9-e70908dbb80a/dqc_reference/reference_markers.hmm GCF_016836705.1_ASM1683670v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:04:26,526] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:04:26,527] [INFO] Found 6/6 markers.
[2024-01-25 18:04:26,580] [INFO] Query marker FASTA was written to GCF_016836705.1_ASM1683670v1_genomic.fna/markers.fasta
[2024-01-25 18:04:26,581] [INFO] Task started: Blastn
[2024-01-25 18:04:26,581] [INFO] Running command: blastn -query GCF_016836705.1_ASM1683670v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99c7e0ec-63e3-4d66-bbb9-e70908dbb80a/dqc_reference/reference_markers.fasta -out GCF_016836705.1_ASM1683670v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:04:27,579] [INFO] Task succeeded: Blastn
[2024-01-25 18:04:27,581] [INFO] Selected 19 target genomes.
[2024-01-25 18:04:27,582] [INFO] Target genome list was writen to GCF_016836705.1_ASM1683670v1_genomic.fna/target_genomes.txt
[2024-01-25 18:04:27,598] [INFO] Task started: fastANI
[2024-01-25 18:04:27,598] [INFO] Running command: fastANI --query /var/lib/cwl/stga5024cfc-44fb-44f7-a4bd-4c58902a3ac1/GCF_016836705.1_ASM1683670v1_genomic.fna.gz --refList GCF_016836705.1_ASM1683670v1_genomic.fna/target_genomes.txt --output GCF_016836705.1_ASM1683670v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:04:59,342] [INFO] Task succeeded: fastANI
[2024-01-25 18:04:59,343] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99c7e0ec-63e3-4d66-bbb9-e70908dbb80a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:04:59,343] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99c7e0ec-63e3-4d66-bbb9-e70908dbb80a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:04:59,354] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:04:59,354] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:04:59,355] [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 caraganae	strain=LMG 24397	GCA_016836705.1	483206	483206	type	True	100.0	2365	2371	95	conclusive
Mesorhizobium neociceri	strain=CCANP35	GCA_013520985.1	1307853	1307853	type	True	91.6275	1744	2371	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	86.3688	1645	2371	95	below_threshold
Mesorhizobium norvegicum	strain=10.2.2	GCA_004919685.1	1085774	1085774	type	True	86.3074	1535	2371	95	below_threshold
Mesorhizobium jarvisii	strain=LMG 28313	GCA_003601985.1	1777867	1777867	type	True	86.2781	1485	2371	95	below_threshold
Mesorhizobium jarvisii	strain=ATCC 33669	GCA_013170785.1	1777867	1777867	type	True	86.1346	1561	2371	95	below_threshold
Mesorhizobium loti	strain=DSM 2626	GCA_003148495.1	381	381	suspected-type	True	86.1201	1537	2371	95	below_threshold
Mesorhizobium opportunistum	strain=WSM2075	GCA_000176035.2	593909	593909	type	True	86.0854	1505	2371	95	below_threshold
Mesorhizobium helmanticense	strain=CSLC115N	GCA_003034915.1	1776423	1776423	type	True	85.956	1437	2371	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	85.9526	1368	2371	95	below_threshold
Mesorhizobium sophorae	strain=ICMP 19535	GCA_002270415.1	1300294	1300294	type	True	85.9521	1587	2371	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	85.6731	1275	2371	95	below_threshold
Mesorhizobium temperatum	strain=SDW018	GCA_002284575.1	241416	241416	type	True	85.2986	1444	2371	95	below_threshold
Mesorhizobium australicum	strain=WSM2073	GCA_000230995.3	536018	536018	type	True	85.2774	1423	2371	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	85.2454	1383	2371	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	84.9853	1429	2371	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	79.3898	640	2371	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	79.2207	698	2371	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	79.1971	701	2371	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:04:59,356] [INFO] DFAST Taxonomy check result was written to GCF_016836705.1_ASM1683670v1_genomic.fna/tc_result.tsv
[2024-01-25 18:04:59,356] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:04:59,356] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:04:59,357] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99c7e0ec-63e3-4d66-bbb9-e70908dbb80a/dqc_reference/checkm_data
[2024-01-25 18:04:59,357] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:04:59,426] [INFO] Task started: CheckM
[2024-01-25 18:04:59,427] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016836705.1_ASM1683670v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016836705.1_ASM1683670v1_genomic.fna/checkm_input GCF_016836705.1_ASM1683670v1_genomic.fna/checkm_result
[2024-01-25 18:05:54,719] [INFO] Task succeeded: CheckM
[2024-01-25 18:05:54,720] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:05:54,742] [INFO] ===== Completeness check finished =====
[2024-01-25 18:05:54,742] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:05:54,743] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016836705.1_ASM1683670v1_genomic.fna/markers.fasta)
[2024-01-25 18:05:54,744] [INFO] Task started: Blastn
[2024-01-25 18:05:54,744] [INFO] Running command: blastn -query GCF_016836705.1_ASM1683670v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99c7e0ec-63e3-4d66-bbb9-e70908dbb80a/dqc_reference/reference_markers_gtdb.fasta -out GCF_016836705.1_ASM1683670v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:05:56,878] [INFO] Task succeeded: Blastn
[2024-01-25 18:05:56,881] [INFO] Selected 9 target genomes.
[2024-01-25 18:05:56,881] [INFO] Target genome list was writen to GCF_016836705.1_ASM1683670v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:05:56,897] [INFO] Task started: fastANI
[2024-01-25 18:05:56,897] [INFO] Running command: fastANI --query /var/lib/cwl/stga5024cfc-44fb-44f7-a4bd-4c58902a3ac1/GCF_016836705.1_ASM1683670v1_genomic.fna.gz --refList GCF_016836705.1_ASM1683670v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016836705.1_ASM1683670v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:06:14,271] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:14,278] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:06:14,278] [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_016836705.1	s__Mesorhizobium caraganae	100.0	2365	2371	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.40	96.20	0.88	0.86	3	conclusive
GCF_007003975.1	s__Mesorhizobium sp007003975	93.6051	1750	2371	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.98	99.98	0.98	0.98	2	-
GCF_013520985.1	s__Mesorhizobium sp013520985	91.6128	1746	2371	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000502715.1	s__Mesorhizobium sp000502715	90.6837	1578	2371	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.12	97.73	0.92	0.90	39	-
GCA_900472295.1	s__Mesorhizobium sp900472295	90.2664	1589	2371	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.35	97.33	0.92	0.92	3	-
GCF_014843845.1	s__Mesorhizobium amorphae_A	87.021	1629	2371	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0866	97.39	97.39	0.88	0.88	2	-
GCF_003253745.1	s__Mesorhizobium kowhaii	86.4314	1610	2371	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176035.2	s__Mesorhizobium opportunistum	86.0981	1504	2371	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.26	95.55	0.85	0.80	10	-
GCF_000230995.2	s__Mesorhizobium australicum	85.2897	1421	2371	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.45	95.19	0.87	0.83	12	-
--------------------------------------------------------------------------------
[2024-01-25 18:06:14,281] [INFO] GTDB search result was written to GCF_016836705.1_ASM1683670v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:06:14,281] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:06:14,284] [INFO] DFAST_QC result json was written to GCF_016836705.1_ASM1683670v1_genomic.fna/dqc_result.json
[2024-01-25 18:06:14,285] [INFO] DFAST_QC completed!
[2024-01-25 18:06:14,285] [INFO] Total running time: 0h2m9s