[2024-01-24 13:22:02,468] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:02,471] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:02,472] [INFO] DQC Reference Directory: /var/lib/cwl/stgcfd55ce8-4eba-467d-9143-44c8f9cf612a/dqc_reference
[2024-01-24 13:22:03,815] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:03,816] [INFO] Task started: Prodigal
[2024-01-24 13:22:03,816] [INFO] Running command: gunzip -c /var/lib/cwl/stg7612312c-79fd-4a6c-9f88-29c968aa2e90/GCF_002270415.1_ASM227041v1_genomic.fna.gz | prodigal -d GCF_002270415.1_ASM227041v1_genomic.fna/cds.fna -a GCF_002270415.1_ASM227041v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:29,375] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:29,376] [INFO] Task started: HMMsearch
[2024-01-24 13:22:29,376] [INFO] Running command: hmmsearch --tblout GCF_002270415.1_ASM227041v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcfd55ce8-4eba-467d-9143-44c8f9cf612a/dqc_reference/reference_markers.hmm GCF_002270415.1_ASM227041v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:29,783] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:29,784] [INFO] Found 6/6 markers.
[2024-01-24 13:22:29,845] [INFO] Query marker FASTA was written to GCF_002270415.1_ASM227041v1_genomic.fna/markers.fasta
[2024-01-24 13:22:29,845] [INFO] Task started: Blastn
[2024-01-24 13:22:29,845] [INFO] Running command: blastn -query GCF_002270415.1_ASM227041v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfd55ce8-4eba-467d-9143-44c8f9cf612a/dqc_reference/reference_markers.fasta -out GCF_002270415.1_ASM227041v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:31,007] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:31,010] [INFO] Selected 12 target genomes.
[2024-01-24 13:22:31,011] [INFO] Target genome list was writen to GCF_002270415.1_ASM227041v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:31,019] [INFO] Task started: fastANI
[2024-01-24 13:22:31,019] [INFO] Running command: fastANI --query /var/lib/cwl/stg7612312c-79fd-4a6c-9f88-29c968aa2e90/GCF_002270415.1_ASM227041v1_genomic.fna.gz --refList GCF_002270415.1_ASM227041v1_genomic.fna/target_genomes.txt --output GCF_002270415.1_ASM227041v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:53,590] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:53,591] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcfd55ce8-4eba-467d-9143-44c8f9cf612a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:53,591] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcfd55ce8-4eba-467d-9143-44c8f9cf612a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:53,603] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:53,603] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:53,603] [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 sophorae	strain=ICMP 19535	GCA_002270415.1	1300294	1300294	type	True	100.0	2668	2673	95	conclusive
Mesorhizobium sangaii	strain=DSM 100039	GCA_014207355.1	505389	505389	type	True	94.3641	1981	2673	95	below_threshold
Mesorhizobium norvegicum	strain=10.2.2	GCA_004919685.1	1085774	1085774	type	True	89.6886	1676	2673	95	below_threshold
Mesorhizobium loti	strain=DSM 2626	GCA_003148495.1	381	381	suspected-type	True	89.421	1677	2673	95	below_threshold
Mesorhizobium qingshengii	strain=CGMCC 1.12097	GCA_900103325.1	1165689	1165689	type	True	88.7316	1608	2673	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	86.8729	1691	2673	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	85.961	1517	2673	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	85.8833	1349	2673	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	84.9414	1472	2673	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	78.9862	638	2673	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	78.9183	716	2673	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	78.9108	715	2673	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:53,605] [INFO] DFAST Taxonomy check result was written to GCF_002270415.1_ASM227041v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:53,606] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:53,606] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:53,606] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcfd55ce8-4eba-467d-9143-44c8f9cf612a/dqc_reference/checkm_data
[2024-01-24 13:22:53,607] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:53,688] [INFO] Task started: CheckM
[2024-01-24 13:22:53,688] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002270415.1_ASM227041v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002270415.1_ASM227041v1_genomic.fna/checkm_input GCF_002270415.1_ASM227041v1_genomic.fna/checkm_result
[2024-01-24 13:24:04,244] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:04,246] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:04,270] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:04,270] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:04,270] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002270415.1_ASM227041v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:04,271] [INFO] Task started: Blastn
[2024-01-24 13:24:04,271] [INFO] Running command: blastn -query GCF_002270415.1_ASM227041v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfd55ce8-4eba-467d-9143-44c8f9cf612a/dqc_reference/reference_markers_gtdb.fasta -out GCF_002270415.1_ASM227041v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:06,400] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:06,404] [INFO] Selected 13 target genomes.
[2024-01-24 13:24:06,404] [INFO] Target genome list was writen to GCF_002270415.1_ASM227041v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:06,420] [INFO] Task started: fastANI
[2024-01-24 13:24:06,420] [INFO] Running command: fastANI --query /var/lib/cwl/stg7612312c-79fd-4a6c-9f88-29c968aa2e90/GCF_002270415.1_ASM227041v1_genomic.fna.gz --refList GCF_002270415.1_ASM227041v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002270415.1_ASM227041v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:31,106] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:31,129] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:31,129] [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_002270415.1	s__Mesorhizobium sophorae	100.0	2665	2673	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_014207355.1	s__Mesorhizobium sangaii	94.379	1979	2673	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	92.3152	1858	2673	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004919685.1	s__Mesorhizobium norvegicum	89.6461	1681	2673	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.97	99.97	0.98	0.98	2	-
GCF_001425625.1	s__Mesorhizobium sp001425625	89.4249	1612	2673	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.21	99.21	0.90	0.90	2	-
GCA_014189435.1	s__Mesorhizobium loti_G	89.4159	1763	2673	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004017275.1	s__Mesorhizobium sp004017275	89.0446	1599	2673	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.13	97.50	0.90	0.85	4	-
GCF_000185905.1	s__Mesorhizobium ciceri	88.7875	1570	2673	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.42	98.05	0.90	0.85	36	-
GCF_900103325.1	s__Mesorhizobium qingshengii	88.7152	1610	2673	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000519305.1	s__Mesorhizobium ciceri_B	88.663	1605	2673	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000502955.1	s__Mesorhizobium sp000502955	88.3608	1578	2673	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003601975.1	s__Mesorhizobium waimense	86.8682	1693	2673	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001686985.1	s__Mesorhizobium amorphae_B	86.0116	1607	2673	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0866	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:31,131] [INFO] GTDB search result was written to GCF_002270415.1_ASM227041v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:31,131] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:31,136] [INFO] DFAST_QC result json was written to GCF_002270415.1_ASM227041v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:31,136] [INFO] DFAST_QC completed!
[2024-01-24 13:24:31,136] [INFO] Total running time: 0h2m29s