[2024-01-24 13:17:13,909] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:13,911] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:13,911] [INFO] DQC Reference Directory: /var/lib/cwl/stgecd15931-8307-478f-b9d5-3bd035e2c76b/dqc_reference
[2024-01-24 13:17:15,240] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:15,241] [INFO] Task started: Prodigal
[2024-01-24 13:17:15,242] [INFO] Running command: gunzip -c /var/lib/cwl/stg81c30f84-676f-44d3-8cf5-2297d42b165e/GCF_019793465.1_ASM1979346v1_genomic.fna.gz | prodigal -d GCF_019793465.1_ASM1979346v1_genomic.fna/cds.fna -a GCF_019793465.1_ASM1979346v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:33,497] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:33,498] [INFO] Task started: HMMsearch
[2024-01-24 13:17:33,498] [INFO] Running command: hmmsearch --tblout GCF_019793465.1_ASM1979346v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgecd15931-8307-478f-b9d5-3bd035e2c76b/dqc_reference/reference_markers.hmm GCF_019793465.1_ASM1979346v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:33,851] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:33,852] [INFO] Found 6/6 markers.
[2024-01-24 13:17:33,905] [INFO] Query marker FASTA was written to GCF_019793465.1_ASM1979346v1_genomic.fna/markers.fasta
[2024-01-24 13:17:33,905] [INFO] Task started: Blastn
[2024-01-24 13:17:33,905] [INFO] Running command: blastn -query GCF_019793465.1_ASM1979346v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgecd15931-8307-478f-b9d5-3bd035e2c76b/dqc_reference/reference_markers.fasta -out GCF_019793465.1_ASM1979346v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:34,962] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:34,966] [INFO] Selected 13 target genomes.
[2024-01-24 13:17:34,966] [INFO] Target genome list was writen to GCF_019793465.1_ASM1979346v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:34,972] [INFO] Task started: fastANI
[2024-01-24 13:17:34,973] [INFO] Running command: fastANI --query /var/lib/cwl/stg81c30f84-676f-44d3-8cf5-2297d42b165e/GCF_019793465.1_ASM1979346v1_genomic.fna.gz --refList GCF_019793465.1_ASM1979346v1_genomic.fna/target_genomes.txt --output GCF_019793465.1_ASM1979346v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:56,055] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:56,055] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgecd15931-8307-478f-b9d5-3bd035e2c76b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:56,056] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgecd15931-8307-478f-b9d5-3bd035e2c76b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:56,072] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:56,073] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:56,073] [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
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	100.0	2103	2103	95	conclusive
Rhizobium sophoriradicis	strain=CCBAU 03470	GCA_003939025.1	1535245	1535245	type	True	93.594	1861	2103	95	below_threshold
Rhizobium phaseoli	strain=ATCC 14482	GCA_003985125.1	396	396	type	True	92.4404	1761	2103	95	below_threshold
Rhizobium binae	strain=BLR195	GCA_017357225.1	1138190	1138190	type	True	91.3491	1647	2103	95	below_threshold
Rhizobium binae	strain=BLR195	GCA_019684455.1	1138190	1138190	type	True	91.303	1636	2103	95	below_threshold
Rhizobium etli	strain=CFN 42	GCA_000092045.1	29449	29449	suspected-type	True	90.0913	1727	2103	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	89.8196	1725	2103	95	below_threshold
Rhizobium esperanzae	strain=CNPSo 668	GCA_002204185.1	1967781	1967781	suspected-type	True	89.2893	1683	2103	95	below_threshold
Rhizobium anhuiense	strain=CGMCC 1.12621	GCA_014638185.1	1184720	1184720	type	True	88.3107	1635	2103	95	below_threshold
Rhizobium anhuiense	strain=CCBAU 23252	GCA_003985145.1	1184720	1184720	type	True	88.2622	1650	2103	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	81.4991	1163	2103	95	below_threshold
Rhizobium dioscoreae	strain=S-93	GCA_009176305.1	2653122	2653122	type	True	80.6119	945	2103	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	80.1306	746	2103	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:56,087] [INFO] DFAST Taxonomy check result was written to GCF_019793465.1_ASM1979346v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:56,088] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:56,088] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:56,089] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgecd15931-8307-478f-b9d5-3bd035e2c76b/dqc_reference/checkm_data
[2024-01-24 13:17:56,090] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:56,152] [INFO] Task started: CheckM
[2024-01-24 13:17:56,152] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019793465.1_ASM1979346v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019793465.1_ASM1979346v1_genomic.fna/checkm_input GCF_019793465.1_ASM1979346v1_genomic.fna/checkm_result
[2024-01-24 13:18:50,425] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:50,485] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:50,813] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:50,813] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:50,814] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019793465.1_ASM1979346v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:50,814] [INFO] Task started: Blastn
[2024-01-24 13:18:50,814] [INFO] Running command: blastn -query GCF_019793465.1_ASM1979346v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgecd15931-8307-478f-b9d5-3bd035e2c76b/dqc_reference/reference_markers_gtdb.fasta -out GCF_019793465.1_ASM1979346v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:52,928] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:52,932] [INFO] Selected 12 target genomes.
[2024-01-24 13:18:52,933] [INFO] Target genome list was writen to GCF_019793465.1_ASM1979346v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:52,943] [INFO] Task started: fastANI
[2024-01-24 13:18:52,943] [INFO] Running command: fastANI --query /var/lib/cwl/stg81c30f84-676f-44d3-8cf5-2297d42b165e/GCF_019793465.1_ASM1979346v1_genomic.fna.gz --refList GCF_019793465.1_ASM1979346v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019793465.1_ASM1979346v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:13,952] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:13,970] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:13,971] [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_002531955.1	s__Rhizobium sp002531955	95.8213	1852	2103	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.59	95.76	0.89	0.85	5	conclusive
GCF_001662075.1	s__Rhizobium bangladeshense_B	94.4494	1797	2103	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200175.1	s__Rhizobium lentis_A	93.6819	1768	2103	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.99	99.97	0.99	0.98	4	-
GCF_003939025.1	s__Rhizobium sophoriradicis	93.594	1861	2103	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.45	97.30	0.92	0.88	16	-
GCF_003985125.1	s__Rhizobium phaseoli	92.4426	1761	2103	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.51	96.92	0.91	0.87	41	-
GCF_017357225.1	s__Rhizobium binae	91.3467	1647	2103	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002531825.1	s__Rhizobium sp002531825	89.6439	1645	2103	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002531905.1	s__Rhizobium sp002531905	89.4182	1711	2103	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.24	98.93	0.89	0.86	4	-
GCF_002531755.2	s__Rhizobium acidisoli	89.1904	1692	2103	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.96	96.40	0.88	0.80	8	-
GCF_002211305.1	s__Rhizobium sp002211305	89.054	1613	2103	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.97	96.97	0.89	0.89	2	-
GCF_003985145.1	s__Rhizobium anhuiense	88.2943	1646	2103	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.85	98.46	0.91	0.88	19	-
GCF_014193025.1	s__Rhizobium sp014193025	87.3751	1435	2103	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:13,972] [INFO] GTDB search result was written to GCF_019793465.1_ASM1979346v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:13,973] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:13,977] [INFO] DFAST_QC result json was written to GCF_019793465.1_ASM1979346v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:13,977] [INFO] DFAST_QC completed!
[2024-01-24 13:19:13,977] [INFO] Total running time: 0h2m0s