[2024-01-25 19:53:35,523] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:53:35,525] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:53:35,525] [INFO] DQC Reference Directory: /var/lib/cwl/stgb189a15c-289f-4435-903a-04c80d9d5262/dqc_reference
[2024-01-25 19:53:36,667] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:53:36,668] [INFO] Task started: Prodigal
[2024-01-25 19:53:36,668] [INFO] Running command: gunzip -c /var/lib/cwl/stg20747b7c-57e5-4d24-990f-6c48f4870bc9/GCF_003938655.1_ASM393865v1_genomic.fna.gz | prodigal -d GCF_003938655.1_ASM393865v1_genomic.fna/cds.fna -a GCF_003938655.1_ASM393865v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:53:54,032] [INFO] Task succeeded: Prodigal
[2024-01-25 19:53:54,032] [INFO] Task started: HMMsearch
[2024-01-25 19:53:54,032] [INFO] Running command: hmmsearch --tblout GCF_003938655.1_ASM393865v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb189a15c-289f-4435-903a-04c80d9d5262/dqc_reference/reference_markers.hmm GCF_003938655.1_ASM393865v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:53:54,307] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:53:54,308] [INFO] Found 6/6 markers.
[2024-01-25 19:53:54,362] [INFO] Query marker FASTA was written to GCF_003938655.1_ASM393865v1_genomic.fna/markers.fasta
[2024-01-25 19:53:54,362] [INFO] Task started: Blastn
[2024-01-25 19:53:54,362] [INFO] Running command: blastn -query GCF_003938655.1_ASM393865v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb189a15c-289f-4435-903a-04c80d9d5262/dqc_reference/reference_markers.fasta -out GCF_003938655.1_ASM393865v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:53:55,348] [INFO] Task succeeded: Blastn
[2024-01-25 19:53:55,350] [INFO] Selected 17 target genomes.
[2024-01-25 19:53:55,351] [INFO] Target genome list was writen to GCF_003938655.1_ASM393865v1_genomic.fna/target_genomes.txt
[2024-01-25 19:53:55,359] [INFO] Task started: fastANI
[2024-01-25 19:53:55,360] [INFO] Running command: fastANI --query /var/lib/cwl/stg20747b7c-57e5-4d24-990f-6c48f4870bc9/GCF_003938655.1_ASM393865v1_genomic.fna.gz --refList GCF_003938655.1_ASM393865v1_genomic.fna/target_genomes.txt --output GCF_003938655.1_ASM393865v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:54:22,831] [INFO] Task succeeded: fastANI
[2024-01-25 19:54:22,832] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb189a15c-289f-4435-903a-04c80d9d5262/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:54:22,833] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb189a15c-289f-4435-903a-04c80d9d5262/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:54:22,843] [INFO] Found 17 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 19:54:22,843] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 19:54:22,843] [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 pisi	strain=DSM 30132	GCA_003938655.1	574561	574561	type	True	100.0	2185	2189	95	inconclusive
Rhizobium fabae	strain=CCBAU 33202	GCA_003985135.1	573179	573179	type	True	97.5622	1973	2189	95	inconclusive
Rhizobium fabae	strain=DSM 19331	GCA_014196235.1	573179	573179	type	True	97.5545	1967	2189	95	inconclusive
Rhizobium vallis	strain=CCBAU 65647	GCA_003985155.1	634290	634290	type	True	91.1073	1814	2189	95	below_threshold
Rhizobium anhuiense	strain=CGMCC 1.12621	GCA_014638185.1	1184720	1184720	type	True	88.9076	1686	2189	95	below_threshold
Rhizobium ruizarguesonis	strain=UPM1133	GCA_012349115.1	2081791	2081791	type	True	88.7096	1683	2189	95	below_threshold
Rhizobium indicum	strain=JKLM 12A2	GCA_005862305.2	2583231	2583231	type	True	88.6459	1667	2189	95	below_threshold
Rhizobium sophorae	strain=CCBAU 03386	GCA_013087515.1	1535242	1535242	type	True	88.5408	1688	2189	95	below_threshold
Rhizobium ecuadorense	strain=CNPSO 671	GCA_001187535.1	1671795	1671795	type	True	88.1646	1533	2189	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	87.9334	1611	2189	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	87.8224	1534	2189	95	below_threshold
Rhizobium lentis	strain=BLR27	GCA_019684715.1	1138194	1138194	type	True	87.5396	1566	2189	95	below_threshold
Rhizobium lentis	strain=BLR27	GCA_017352135.1	1138194	1138194	type	True	87.4875	1562	2189	95	below_threshold
Rhizobium viscosum	strain=DSM 7307	GCA_014873945.1	1673	1673	type	True	83.2888	1342	2189	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	81.5294	1119	2189	95	below_threshold
Rhizobium dioscoreae	strain=S-93	GCA_009176305.1	2653122	2653122	type	True	80.5632	968	2189	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	80.1386	729	2189	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:54:22,844] [INFO] DFAST Taxonomy check result was written to GCF_003938655.1_ASM393865v1_genomic.fna/tc_result.tsv
[2024-01-25 19:54:22,845] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:54:22,845] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:54:22,845] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb189a15c-289f-4435-903a-04c80d9d5262/dqc_reference/checkm_data
[2024-01-25 19:54:22,846] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:54:22,905] [INFO] Task started: CheckM
[2024-01-25 19:54:22,905] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003938655.1_ASM393865v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003938655.1_ASM393865v1_genomic.fna/checkm_input GCF_003938655.1_ASM393865v1_genomic.fna/checkm_result
[2024-01-25 19:55:11,829] [INFO] Task succeeded: CheckM
[2024-01-25 19:55:11,830] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:55:11,863] [INFO] ===== Completeness check finished =====
[2024-01-25 19:55:11,864] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:55:11,864] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003938655.1_ASM393865v1_genomic.fna/markers.fasta)
[2024-01-25 19:55:11,864] [INFO] Task started: Blastn
[2024-01-25 19:55:11,864] [INFO] Running command: blastn -query GCF_003938655.1_ASM393865v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb189a15c-289f-4435-903a-04c80d9d5262/dqc_reference/reference_markers_gtdb.fasta -out GCF_003938655.1_ASM393865v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:55:13,915] [INFO] Task succeeded: Blastn
[2024-01-25 19:55:13,917] [INFO] Selected 22 target genomes.
[2024-01-25 19:55:13,917] [INFO] Target genome list was writen to GCF_003938655.1_ASM393865v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:55:13,930] [INFO] Task started: fastANI
[2024-01-25 19:55:13,931] [INFO] Running command: fastANI --query /var/lib/cwl/stg20747b7c-57e5-4d24-990f-6c48f4870bc9/GCF_003938655.1_ASM393865v1_genomic.fna.gz --refList GCF_003938655.1_ASM393865v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003938655.1_ASM393865v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:55:51,474] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:51,487] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:55:51,488] [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_003938655.1	s__Rhizobium pisi	100.0	2185	2189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.78	97.55	0.94	0.90	5	conclusive
GCF_003985155.1	s__Rhizobium vallis	91.1073	1814	2189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014198335.1	s__Rhizobium leguminosarum_N	89.1849	1524	2189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.95	99.93	0.95	0.91	10	-
GCF_002531725.1	s__Rhizobium sp002531725	89.0151	1651	2189	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	88.9045	1562	2189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002953715.1	s__Rhizobium leguminosarum_K	88.7075	1678	2189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	95.64	95.51	0.85	0.83	10	-
GCF_012349115.1	s__Rhizobium ruizarguesonis	88.6929	1685	2189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.01	96.15	0.89	0.84	170	-
GCF_004123835.1	s__Rhizobium leguminosarum_M	88.69	1642	2189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001657485.1	s__Rhizobium sp001657485	88.5468	1646	2189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.95	97.95	0.90	0.90	2	-
GCF_013087515.1	s__Rhizobium sophorae	88.5413	1688	2189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.85	95.49	0.87	0.83	6	-
GCF_000009265.1	s__Rhizobium leguminosarum_L	88.4962	1655	2189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.59	95.46	0.90	0.82	60	-
GCF_002531825.1	s__Rhizobium sp002531825	88.4897	1575	2189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000769405.2	s__Rhizobium leguminosarum_E	88.4522	1642	2189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.71	96.49	0.91	0.87	37	-
GCF_014193025.1	s__Rhizobium sp014193025	88.4164	1565	2189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002008165.1	s__Rhizobium laguerreae	88.3311	1620	2189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.33	95.04	0.87	0.82	51	-
GCF_001187535.1	s__Rhizobium ecuadorense	88.1673	1532	2189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.51	98.31	0.89	0.89	4	-
GCF_017876795.1	s__Rhizobium leguminosarum_P	88.1276	1620	2189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001664485.1	s__Rhizobium sp001664485	88.0778	1590	2189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.08	96.02	0.91	0.83	8	-
GCF_000271845.1	s__Rhizobium leguminosarum_G	87.9638	1692	2189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017352135.1	s__Rhizobium lentis	87.4791	1563	2189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017357245.1	s__Rhizobium bangladeshense	86.8143	1520	2189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.42	98.08	0.93	0.91	5	-
GCA_900470965.1	s__Rhizobium sp900470965	83.4184	1258	2189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:55:51,489] [INFO] GTDB search result was written to GCF_003938655.1_ASM393865v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:55:51,490] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:55:51,493] [INFO] DFAST_QC result json was written to GCF_003938655.1_ASM393865v1_genomic.fna/dqc_result.json
[2024-01-25 19:55:51,493] [INFO] DFAST_QC completed!
[2024-01-25 19:55:51,493] [INFO] Total running time: 0h2m16s