[2024-01-24 15:17:49,199] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:17:49,226] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:17:49,227] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c17ce83-57d6-4f8c-880b-988000b8447d/dqc_reference
[2024-01-24 15:17:51,533] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:17:51,535] [INFO] Task started: Prodigal
[2024-01-24 15:17:51,535] [INFO] Running command: gunzip -c /var/lib/cwl/stg08e06bc5-fcdc-483f-89be-29907bff69c0/GCF_002204185.1_ASM220418v1_genomic.fna.gz | prodigal -d GCF_002204185.1_ASM220418v1_genomic.fna/cds.fna -a GCF_002204185.1_ASM220418v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:09,536] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:09,537] [INFO] Task started: HMMsearch
[2024-01-24 15:18:09,537] [INFO] Running command: hmmsearch --tblout GCF_002204185.1_ASM220418v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c17ce83-57d6-4f8c-880b-988000b8447d/dqc_reference/reference_markers.hmm GCF_002204185.1_ASM220418v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:09,914] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:09,916] [INFO] Found 6/6 markers.
[2024-01-24 15:18:09,974] [INFO] Query marker FASTA was written to GCF_002204185.1_ASM220418v1_genomic.fna/markers.fasta
[2024-01-24 15:18:09,974] [INFO] Task started: Blastn
[2024-01-24 15:18:09,975] [INFO] Running command: blastn -query GCF_002204185.1_ASM220418v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c17ce83-57d6-4f8c-880b-988000b8447d/dqc_reference/reference_markers.fasta -out GCF_002204185.1_ASM220418v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:10,989] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:10,993] [INFO] Selected 17 target genomes.
[2024-01-24 15:18:10,994] [INFO] Target genome list was writen to GCF_002204185.1_ASM220418v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:11,002] [INFO] Task started: fastANI
[2024-01-24 15:18:11,002] [INFO] Running command: fastANI --query /var/lib/cwl/stg08e06bc5-fcdc-483f-89be-29907bff69c0/GCF_002204185.1_ASM220418v1_genomic.fna.gz --refList GCF_002204185.1_ASM220418v1_genomic.fna/target_genomes.txt --output GCF_002204185.1_ASM220418v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:37,063] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:37,063] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c17ce83-57d6-4f8c-880b-988000b8447d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:37,064] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c17ce83-57d6-4f8c-880b-988000b8447d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:37,078] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:18:37,078] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:37,078] [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 esperanzae	strain=CNPSo 668	GCA_002204185.1	1967781	1967781	suspected-type	True	100.0	2060	2063	95	conclusive
Rhizobium etli	strain=CFN 42	GCA_000092045.1	29449	29449	suspected-type	True	93.4099	1806	2063	95	below_threshold
Rhizobium aethiopicum	strain=HBR26	GCA_900094625.1	1138170	1138170	type	True	89.9027	1683	2063	95	below_threshold
Rhizobium bangladeshense	strain=BLR175	GCA_019684215.1	1138189	1138189	type	True	89.8868	1658	2063	95	below_threshold
Rhizobium bangladeshense	strain=BLR175	GCA_017357245.1	1138189	1138189	type	True	89.8472	1657	2063	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	89.4097	1654	2063	95	below_threshold
Rhizobium phaseoli	strain=ATCC 14482	GCA_003985125.1	396	396	type	True	89.3701	1685	2063	95	below_threshold
Rhizobium lentis	strain=BLR27	GCA_019684715.1	1138194	1138194	type	True	89.061	1621	2063	95	below_threshold
Rhizobium sophoriradicis	strain=CCBAU 03470	GCA_003939025.1	1535245	1535245	type	True	88.9659	1683	2063	95	below_threshold
Rhizobium binae	strain=BLR195	GCA_017357225.1	1138190	1138190	type	True	88.6617	1587	2063	95	below_threshold
Rhizobium binae	strain=BLR195	GCA_019684455.1	1138190	1138190	type	True	88.6391	1597	2063	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	87.9649	1631	2063	95	below_threshold
Rhizobium sophorae	strain=CCBAU 03386	GCA_013087515.1	1535242	1535242	type	True	87.7925	1604	2063	95	below_threshold
Rhizobium anhuiense	strain=CGMCC 1.12621	GCA_014638185.1	1184720	1184720	type	True	87.6897	1580	2063	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	81.2579	1096	2063	95	below_threshold
Rhizobium dioscoreae	strain=S-93	GCA_009176305.1	2653122	2653122	type	True	80.4745	928	2063	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	79.8872	698	2063	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:37,080] [INFO] DFAST Taxonomy check result was written to GCF_002204185.1_ASM220418v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:37,080] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:37,081] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:37,081] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c17ce83-57d6-4f8c-880b-988000b8447d/dqc_reference/checkm_data
[2024-01-24 15:18:37,082] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:37,146] [INFO] Task started: CheckM
[2024-01-24 15:18:37,147] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002204185.1_ASM220418v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002204185.1_ASM220418v1_genomic.fna/checkm_input GCF_002204185.1_ASM220418v1_genomic.fna/checkm_result
[2024-01-24 15:19:29,650] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:29,651] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:29,675] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:29,675] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:29,676] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002204185.1_ASM220418v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:29,676] [INFO] Task started: Blastn
[2024-01-24 15:19:29,677] [INFO] Running command: blastn -query GCF_002204185.1_ASM220418v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c17ce83-57d6-4f8c-880b-988000b8447d/dqc_reference/reference_markers_gtdb.fasta -out GCF_002204185.1_ASM220418v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:31,718] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:31,723] [INFO] Selected 12 target genomes.
[2024-01-24 15:19:31,723] [INFO] Target genome list was writen to GCF_002204185.1_ASM220418v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:31,734] [INFO] Task started: fastANI
[2024-01-24 15:19:31,734] [INFO] Running command: fastANI --query /var/lib/cwl/stg08e06bc5-fcdc-483f-89be-29907bff69c0/GCF_002204185.1_ASM220418v1_genomic.fna.gz --refList GCF_002204185.1_ASM220418v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002204185.1_ASM220418v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:51,605] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:51,618] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:51,618] [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_002204185.1	s__Rhizobium esperanzae	100.0	2060	2063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.10	96.05	0.88	0.87	12	conclusive
GCF_014197535.1	s__Rhizobium aethiopicum_A	93.516	1738	2063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.98	99.98	0.98	0.98	2	-
GCF_000092045.1	s__Rhizobium etli	93.4042	1807	2063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.53	98.53	0.90	0.89	3	-
GCF_017948245.1	s__Rhizobium sp017948245	92.455	1724	2063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002117485.1	s__Rhizobium sp002117485	91.8708	1739	2063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.28	97.20	0.87	0.86	3	-
GCF_900094625.1	s__Rhizobium aethiopicum	89.9006	1683	2063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.33	98.33	0.89	0.89	2	-
GCF_002531955.1	s__Rhizobium sp002531955	89.6125	1706	2063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.59	95.76	0.89	0.85	5	-
GCF_003939025.1	s__Rhizobium sophoriradicis	88.9729	1681	2063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.45	97.30	0.92	0.88	16	-
GCF_001662075.1	s__Rhizobium bangladeshense_B	88.9451	1616	2063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002211285.1	s__Rhizobium sp002211285	88.8949	1517	2063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000172795.2	s__Rhizobium sp000172795	88.489	1567	2063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002531825.1	s__Rhizobium sp002531825	88.4329	1590	2063	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 15:19:51,622] [INFO] GTDB search result was written to GCF_002204185.1_ASM220418v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:51,622] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:51,626] [INFO] DFAST_QC result json was written to GCF_002204185.1_ASM220418v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:51,626] [INFO] DFAST_QC completed!
[2024-01-24 15:19:51,626] [INFO] Total running time: 0h2m2s