[2024-01-24 12:15:20,405] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:20,407] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:20,407] [INFO] DQC Reference Directory: /var/lib/cwl/stg68cd16b5-8788-429a-b411-cbb6316fcbd2/dqc_reference
[2024-01-24 12:15:21,742] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:21,743] [INFO] Task started: Prodigal
[2024-01-24 12:15:21,744] [INFO] Running command: gunzip -c /var/lib/cwl/stg51bcc425-f7e9-4bcb-8899-3453f7526d89/GCF_014873945.1_ASM1487394v1_genomic.fna.gz | prodigal -d GCF_014873945.1_ASM1487394v1_genomic.fna/cds.fna -a GCF_014873945.1_ASM1487394v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:42,579] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:42,580] [INFO] Task started: HMMsearch
[2024-01-24 12:15:42,580] [INFO] Running command: hmmsearch --tblout GCF_014873945.1_ASM1487394v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68cd16b5-8788-429a-b411-cbb6316fcbd2/dqc_reference/reference_markers.hmm GCF_014873945.1_ASM1487394v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:42,935] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:42,936] [INFO] Found 6/6 markers.
[2024-01-24 12:15:42,998] [INFO] Query marker FASTA was written to GCF_014873945.1_ASM1487394v1_genomic.fna/markers.fasta
[2024-01-24 12:15:42,999] [INFO] Task started: Blastn
[2024-01-24 12:15:42,999] [INFO] Running command: blastn -query GCF_014873945.1_ASM1487394v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68cd16b5-8788-429a-b411-cbb6316fcbd2/dqc_reference/reference_markers.fasta -out GCF_014873945.1_ASM1487394v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:44,019] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:44,023] [INFO] Selected 24 target genomes.
[2024-01-24 12:15:44,024] [INFO] Target genome list was writen to GCF_014873945.1_ASM1487394v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:44,034] [INFO] Task started: fastANI
[2024-01-24 12:15:44,035] [INFO] Running command: fastANI --query /var/lib/cwl/stg51bcc425-f7e9-4bcb-8899-3453f7526d89/GCF_014873945.1_ASM1487394v1_genomic.fna.gz --refList GCF_014873945.1_ASM1487394v1_genomic.fna/target_genomes.txt --output GCF_014873945.1_ASM1487394v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:16:17,078] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:17,078] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68cd16b5-8788-429a-b411-cbb6316fcbd2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:16:17,079] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68cd16b5-8788-429a-b411-cbb6316fcbd2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:16:17,099] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:16:17,100] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:16:17,100] [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 viscosum	strain=DSM 7307	GCA_014873945.1	1673	1673	type	True	100.0	2353	2355	95	conclusive
Rhizobium fabae	strain=CCBAU 33202	GCA_003985135.1	573179	573179	type	True	83.4893	1328	2355	95	below_threshold
Rhizobium fabae	strain=DSM 19331	GCA_014196235.1	573179	573179	type	True	83.4837	1334	2355	95	below_threshold
Rhizobium pisi	strain=DSM 30132	GCA_003938655.1	574561	574561	type	True	83.3543	1328	2355	95	below_threshold
Rhizobium chutanense	strain=C5	GCA_002531935.1	2035448	2035448	type	True	83.2908	1337	2355	95	below_threshold
Rhizobium anhuiense	strain=CCBAU 23252	GCA_003985145.1	1184720	1184720	type	True	83.2276	1350	2355	95	below_threshold
Rhizobium anhuiense	strain=CGMCC 1.12621	GCA_014638185.1	1184720	1184720	type	True	83.2155	1343	2355	95	below_threshold
Rhizobium ecuadorense	strain=CNPSO 671	GCA_001187535.1	1671795	1671795	type	True	83.1373	1283	2355	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	83.0838	1285	2355	95	below_threshold
Rhizobium hidalgonense	strain=FH14	GCA_002914525.1	1538159	1538159	type	True	83.0623	1290	2355	95	below_threshold
Rhizobium phaseoli	strain=ATCC 14482	GCA_003985125.1	396	396	type	True	83.0516	1282	2355	95	below_threshold
Rhizobium hidalgonense	strain=FH14	GCA_002531855.1	1538159	1538159	type	True	83.0497	1292	2355	95	below_threshold
Rhizobium ruizarguesonis	strain=UPM1133	GCA_012349115.1	2081791	2081791	type	True	83.0245	1362	2355	95	below_threshold
Rhizobium leguminosarum	strain=USDA 2370	GCA_003058385.1	384	384	suspected-type	True	82.9661	1363	2355	95	below_threshold
Rhizobium indigoferae	strain=CCBAU 71042	GCA_013087605.1	158891	158891	type	True	82.9373	1364	2355	95	below_threshold
Rhizobium esperanzae	strain=CNPSo 668	GCA_002204185.1	1967781	1967781	suspected-type	True	82.9322	1234	2355	95	below_threshold
Rhizobium leguminosarum	strain=DSM 106839	GCA_014202125.1	384	384	suspected-type	True	82.9253	1377	2355	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	82.9235	1303	2355	95	below_threshold
Rhizobium leguminosarum	strain=USDA 2370	GCA_002008365.1	384	384	suspected-type	True	82.9116	1369	2355	95	below_threshold
Rhizobium lentis	strain=BLR27	GCA_017352135.1	1138194	1138194	type	True	82.8916	1296	2355	95	below_threshold
Rhizobium lentis	strain=BLR27	GCA_019684715.1	1138194	1138194	type	True	82.8865	1289	2355	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	81.0312	1094	2355	95	below_threshold
Rhizobium dioscoreae	strain=S-93	GCA_009176305.1	2653122	2653122	type	True	80.2225	981	2355	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	79.0884	626	2355	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:16:17,103] [INFO] DFAST Taxonomy check result was written to GCF_014873945.1_ASM1487394v1_genomic.fna/tc_result.tsv
[2024-01-24 12:16:17,103] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:16:17,103] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:16:17,104] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68cd16b5-8788-429a-b411-cbb6316fcbd2/dqc_reference/checkm_data
[2024-01-24 12:16:17,105] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:16:17,177] [INFO] Task started: CheckM
[2024-01-24 12:16:17,177] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014873945.1_ASM1487394v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014873945.1_ASM1487394v1_genomic.fna/checkm_input GCF_014873945.1_ASM1487394v1_genomic.fna/checkm_result
[2024-01-24 12:17:16,762] [INFO] Task succeeded: CheckM
[2024-01-24 12:17:16,763] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:17:16,789] [INFO] ===== Completeness check finished =====
[2024-01-24 12:17:16,789] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:17:16,790] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014873945.1_ASM1487394v1_genomic.fna/markers.fasta)
[2024-01-24 12:17:16,790] [INFO] Task started: Blastn
[2024-01-24 12:17:16,790] [INFO] Running command: blastn -query GCF_014873945.1_ASM1487394v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68cd16b5-8788-429a-b411-cbb6316fcbd2/dqc_reference/reference_markers_gtdb.fasta -out GCF_014873945.1_ASM1487394v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:17:18,767] [INFO] Task succeeded: Blastn
[2024-01-24 12:17:18,772] [INFO] Selected 10 target genomes.
[2024-01-24 12:17:18,772] [INFO] Target genome list was writen to GCF_014873945.1_ASM1487394v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:17:18,789] [INFO] Task started: fastANI
[2024-01-24 12:17:18,790] [INFO] Running command: fastANI --query /var/lib/cwl/stg51bcc425-f7e9-4bcb-8899-3453f7526d89/GCF_014873945.1_ASM1487394v1_genomic.fna.gz --refList GCF_014873945.1_ASM1487394v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014873945.1_ASM1487394v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:17:35,577] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:35,590] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:17:35,591] [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_014873945.1	s__Rhizobium viscosum	100.0	2352	2355	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000744505.1	s__Rhizobium alamii	91.7528	1916	2355	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.05	95.76	0.86	0.84	29	-
GCA_900470965.1	s__Rhizobium sp900470965	91.5247	1806	2355	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900466475.1	s__Rhizobium sp900466475	90.5943	1879	2355	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.15	97.80	0.95	0.94	17	-
GCF_014193255.1	s__Rhizobium sp014193255	90.3019	1688	2355	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.48	98.48	0.95	0.95	2	-
GCF_014193695.1	s__Rhizobium sp014193695	89.9718	1752	2355	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.81	98.81	0.97	0.97	2	-
GCF_018987265.1	s__Rhizobium sp018987265	89.2729	1743	2355	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900471515.1	s__Rhizobium sp900471515	88.5757	1595	2355	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.61	98.55	0.92	0.91	6	-
GCF_014195325.1	s__Rhizobium sp014195325	87.6012	1631	2355	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900471925.1	s__Rhizobium sp900471925	86.9359	1576	2355	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 12:17:35,592] [INFO] GTDB search result was written to GCF_014873945.1_ASM1487394v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:17:35,593] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:17:35,597] [INFO] DFAST_QC result json was written to GCF_014873945.1_ASM1487394v1_genomic.fna/dqc_result.json
[2024-01-24 12:17:35,597] [INFO] DFAST_QC completed!
[2024-01-24 12:17:35,597] [INFO] Total running time: 0h2m15s