[2024-01-24 13:46:01,727] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:01,729] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:01,729] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b905e19-8773-4821-b7ae-39efc72c7553/dqc_reference
[2024-01-24 13:46:03,068] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:03,069] [INFO] Task started: Prodigal
[2024-01-24 13:46:03,069] [INFO] Running command: gunzip -c /var/lib/cwl/stg2b5dfd89-1a96-4b4c-8389-51aeaf2b5b83/GCF_013283645.1_ASM1328364v1_genomic.fna.gz | prodigal -d GCF_013283645.1_ASM1328364v1_genomic.fna/cds.fna -a GCF_013283645.1_ASM1328364v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:26,275] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:26,276] [INFO] Task started: HMMsearch
[2024-01-24 13:46:26,276] [INFO] Running command: hmmsearch --tblout GCF_013283645.1_ASM1328364v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b905e19-8773-4821-b7ae-39efc72c7553/dqc_reference/reference_markers.hmm GCF_013283645.1_ASM1328364v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:26,673] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:26,674] [INFO] Found 6/6 markers.
[2024-01-24 13:46:26,740] [INFO] Query marker FASTA was written to GCF_013283645.1_ASM1328364v1_genomic.fna/markers.fasta
[2024-01-24 13:46:26,740] [INFO] Task started: Blastn
[2024-01-24 13:46:26,740] [INFO] Running command: blastn -query GCF_013283645.1_ASM1328364v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b905e19-8773-4821-b7ae-39efc72c7553/dqc_reference/reference_markers.fasta -out GCF_013283645.1_ASM1328364v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:27,856] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:27,859] [INFO] Selected 14 target genomes.
[2024-01-24 13:46:27,860] [INFO] Target genome list was writen to GCF_013283645.1_ASM1328364v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:27,867] [INFO] Task started: fastANI
[2024-01-24 13:46:27,867] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b5dfd89-1a96-4b4c-8389-51aeaf2b5b83/GCF_013283645.1_ASM1328364v1_genomic.fna.gz --refList GCF_013283645.1_ASM1328364v1_genomic.fna/target_genomes.txt --output GCF_013283645.1_ASM1328364v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:48,804] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:48,804] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b905e19-8773-4821-b7ae-39efc72c7553/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:48,804] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b905e19-8773-4821-b7ae-39efc72c7553/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:48,816] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:48,816] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:48,817] [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
Ensifer psoraleae	strain=CCBAU 65732	GCA_013283645.1	520838	520838	type	True	100.0	2442	2446	95	conclusive
Ensifer mexicanus	strain=ITTG R7	GCA_013488225.1	375549	375549	type	True	87.6137	1591	2446	95	below_threshold
Ensifer mexicanus	strain=DSM 18446	GCA_017873105.1	375549	375549	type	True	87.568	1586	2446	95	below_threshold
Sinorhizobium fredii	strain=USDA 205	GCA_001461695.1	380	380	type	True	83.0112	1305	2446	95	below_threshold
Sinorhizobium fredii	strain=NBRC 14780	GCA_006539605.1	380	380	type	True	82.9612	1284	2446	95	below_threshold
Sinorhizobium meliloti	strain=USDA 1002	GCA_017876815.1	382	382	type	True	82.4888	1362	2446	95	below_threshold
Sinorhizobium meliloti	strain=NBRC 14782	GCA_006539625.1	382	382	type	True	82.4394	1283	2446	95	below_threshold
Sinorhizobium meliloti	strain=USDA1002	GCA_009601385.1	382	382	type	True	82.4353	1329	2446	95	below_threshold
Ensifer sesbaniae	strain=CCBAU 65729	GCA_013283665.1	1214071	1214071	type	True	82.2619	1280	2446	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	80.1661	767	2446	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	80.0966	878	2446	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	79.6268	714	2446	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	79.5899	768	2446	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	79.5806	702	2446	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:48,818] [INFO] DFAST Taxonomy check result was written to GCF_013283645.1_ASM1328364v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:48,819] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:48,819] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:48,819] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b905e19-8773-4821-b7ae-39efc72c7553/dqc_reference/checkm_data
[2024-01-24 13:46:48,821] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:48,891] [INFO] Task started: CheckM
[2024-01-24 13:46:48,891] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013283645.1_ASM1328364v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013283645.1_ASM1328364v1_genomic.fna/checkm_input GCF_013283645.1_ASM1328364v1_genomic.fna/checkm_result
[2024-01-24 13:47:50,062] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:50,064] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:50,088] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:50,088] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:50,089] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013283645.1_ASM1328364v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:50,089] [INFO] Task started: Blastn
[2024-01-24 13:47:50,089] [INFO] Running command: blastn -query GCF_013283645.1_ASM1328364v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b905e19-8773-4821-b7ae-39efc72c7553/dqc_reference/reference_markers_gtdb.fasta -out GCF_013283645.1_ASM1328364v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:52,019] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:52,022] [INFO] Selected 10 target genomes.
[2024-01-24 13:47:52,023] [INFO] Target genome list was writen to GCF_013283645.1_ASM1328364v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:52,031] [INFO] Task started: fastANI
[2024-01-24 13:47:52,031] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b5dfd89-1a96-4b4c-8389-51aeaf2b5b83/GCF_013283645.1_ASM1328364v1_genomic.fna.gz --refList GCF_013283645.1_ASM1328364v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013283645.1_ASM1328364v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:08,646] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:08,655] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:08,655] [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_013283645.1	s__Sinorhizobium psoraleae	100.0	2442	2446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004827385.1	s__Sinorhizobium sp004827385	88.0549	1752	2446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009601505.1	s__Sinorhizobium terangae	87.8534	1677	2446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	99.98	99.98	0.98	0.98	2	-
GCF_013488225.1	s__Sinorhizobium mexicanum	87.6196	1589	2446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000513895.1	s__Sinorhizobium sp000513895	83.2107	1360	2446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001461695.1	s__Sinorhizobium fredii	83.0124	1305	2446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	98.55	96.82	0.88	0.82	17	-
GCF_000018545.1	s__Sinorhizobium fredii_A	82.9643	1331	2446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378985.1	s__Sinorhizobium sp000378985	82.7795	1344	2446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013283665.1	s__Ensifer sesbaniae	82.2463	1282	2446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	98.93	98.93	0.89	0.89	2	-
GCF_013283195.1	s__Ensifer adhaerens_G	81.4268	1104	2446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	98.31	98.31	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:48:08,657] [INFO] GTDB search result was written to GCF_013283645.1_ASM1328364v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:08,657] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:08,661] [INFO] DFAST_QC result json was written to GCF_013283645.1_ASM1328364v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:08,661] [INFO] DFAST_QC completed!
[2024-01-24 13:48:08,661] [INFO] Total running time: 0h2m7s