[2024-01-24 12:31:50,883] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:50,891] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:50,892] [INFO] DQC Reference Directory: /var/lib/cwl/stg80b8ebd6-be78-4cd7-bf4b-7f1d26e424d1/dqc_reference
[2024-01-24 12:31:52,181] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:52,182] [INFO] Task started: Prodigal
[2024-01-24 12:31:52,182] [INFO] Running command: gunzip -c /var/lib/cwl/stgcd821d5a-f0ed-4114-9820-f087d9c0a21c/GCF_902162175.1_PRJEB33358_genomic.fna.gz | prodigal -d GCF_902162175.1_PRJEB33358_genomic.fna/cds.fna -a GCF_902162175.1_PRJEB33358_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:57,003] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:57,004] [INFO] Task started: HMMsearch
[2024-01-24 12:31:57,004] [INFO] Running command: hmmsearch --tblout GCF_902162175.1_PRJEB33358_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80b8ebd6-be78-4cd7-bf4b-7f1d26e424d1/dqc_reference/reference_markers.hmm GCF_902162175.1_PRJEB33358_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:57,241] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:57,242] [INFO] Found 6/6 markers.
[2024-01-24 12:31:57,265] [INFO] Query marker FASTA was written to GCF_902162175.1_PRJEB33358_genomic.fna/markers.fasta
[2024-01-24 12:31:57,266] [INFO] Task started: Blastn
[2024-01-24 12:31:57,266] [INFO] Running command: blastn -query GCF_902162175.1_PRJEB33358_genomic.fna/markers.fasta -db /var/lib/cwl/stg80b8ebd6-be78-4cd7-bf4b-7f1d26e424d1/dqc_reference/reference_markers.fasta -out GCF_902162175.1_PRJEB33358_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:57,854] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:57,860] [INFO] Selected 28 target genomes.
[2024-01-24 12:31:57,860] [INFO] Target genome list was writen to GCF_902162175.1_PRJEB33358_genomic.fna/target_genomes.txt
[2024-01-24 12:31:57,882] [INFO] Task started: fastANI
[2024-01-24 12:31:57,883] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd821d5a-f0ed-4114-9820-f087d9c0a21c/GCF_902162175.1_PRJEB33358_genomic.fna.gz --refList GCF_902162175.1_PRJEB33358_genomic.fna/target_genomes.txt --output GCF_902162175.1_PRJEB33358_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:11,860] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:11,861] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80b8ebd6-be78-4cd7-bf4b-7f1d26e424d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:11,862] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80b8ebd6-be78-4cd7-bf4b-7f1d26e424d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:11,884] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:11,884] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:11,884] [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
Bartonella saheliensis	strain=077	GCA_902162175.1	1457016	1457016	type	True	100.0	678	683	95	conclusive
Bartonella krasnovii	strain=OE 1-1	GCA_003606345.3	2267275	2267275	type	True	92.7785	540	683	95	below_threshold
Bartonella mastomydis	strain=008	GCA_900185775.1	1820002	1820002	type	True	92.192	523	683	95	below_threshold
Bartonella elizabethae	strain=ATCC 49927	GCA_000518165.1	807	807	type	True	92.1013	489	683	95	below_threshold
Bartonella elizabethae	strain=ATCC 49927	GCA_902825135.1	807	807	type	True	91.9996	494	683	95	below_threshold
Bartonella elizabethae	strain=F9251	GCA_000278315.1	807	807	type	True	91.9827	504	683	95	below_threshold
Bartonella kosoyi	strain=Tel Aviv	GCA_003606325.3	2133959	2133959	type	True	90.6254	525	683	95	below_threshold
Bartonella gabonensis	strain=669	GCA_903679515.1	2699889	2699889	type	True	89.9411	464	683	95	below_threshold
Bartonella tribocorum	strain=type strain:506 = CIP 105476	GCA_000196435.1	85701	85701	suspected-type	True	89.1872	524	683	95	below_threshold
Bartonella florencae	strain=R4	GCA_000312525.1	928210	928210	type	True	83.7902	461	683	95	below_threshold
Bartonella birtlesii	strain=IBS 325	GCA_000273375.1	111504	111504	type	True	83.1676	424	683	95	below_threshold
Bartonella phoceensis	strain=CIP107707	GCA_902825145.1	270249	270249	type	True	82.911	414	683	95	below_threshold
Bartonella vinsonii subsp. arupensis	strain=ATCC 700727	GCA_902825115.1	110578	33047	type	True	82.6883	396	683	95	below_threshold
Bartonella vinsonii subsp. arupensis	strain=OK-94-513	GCA_000278235.1	110578	33047	type	True	82.5632	407	683	95	below_threshold
Bartonella alsatica	strain=CIP 105477	GCA_013388295.1	52764	52764	type	True	82.4813	389	683	95	below_threshold
Bartonella alsatica	strain=IBS 382	GCA_000280015.1	52764	52764	type	True	82.4325	389	683	95	below_threshold
Bartonella callosciuri	strain=DSM 28538	GCA_014203215.1	686223	686223	type	True	82.4063	388	683	95	below_threshold
Bartonella henselae	strain=FDAARGOS_1462	GCA_019930925.1	38323	38323	type	True	82.3798	438	683	95	below_threshold
Bartonella henselae	strain=Houston-I	GCA_002735245.1	38323	38323	type	True	82.3759	429	683	95	below_threshold
Bartonella doshiae	strain=ATCC 700133	GCA_000526895.1	33044	33044	type	True	81.7038	402	683	95	below_threshold
Bartonella doshiae	strain=NCTC 12862	GCA_000278155.1	33044	33044	type	True	81.7003	412	683	95	below_threshold
Bartonella doshiae	strain=NCTC12862	GCA_900445535.1	33044	33044	type	True	81.6663	412	683	95	below_threshold
Bartonella rattaustraliani	strain=AUST/NH4	GCA_000312565.2	481139	481139	type	True	81.2286	418	683	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:11,886] [INFO] DFAST Taxonomy check result was written to GCF_902162175.1_PRJEB33358_genomic.fna/tc_result.tsv
[2024-01-24 12:32:11,887] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:11,887] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:11,887] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80b8ebd6-be78-4cd7-bf4b-7f1d26e424d1/dqc_reference/checkm_data
[2024-01-24 12:32:11,889] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:11,914] [INFO] Task started: CheckM
[2024-01-24 12:32:11,914] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902162175.1_PRJEB33358_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902162175.1_PRJEB33358_genomic.fna/checkm_input GCF_902162175.1_PRJEB33358_genomic.fna/checkm_result
[2024-01-24 12:32:33,144] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:33,145] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 12.50%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:33,170] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:33,170] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:33,171] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902162175.1_PRJEB33358_genomic.fna/markers.fasta)
[2024-01-24 12:32:33,171] [INFO] Task started: Blastn
[2024-01-24 12:32:33,171] [INFO] Running command: blastn -query GCF_902162175.1_PRJEB33358_genomic.fna/markers.fasta -db /var/lib/cwl/stg80b8ebd6-be78-4cd7-bf4b-7f1d26e424d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_902162175.1_PRJEB33358_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:33,932] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:33,936] [INFO] Selected 19 target genomes.
[2024-01-24 12:32:33,937] [INFO] Target genome list was writen to GCF_902162175.1_PRJEB33358_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:33,958] [INFO] Task started: fastANI
[2024-01-24 12:32:33,959] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd821d5a-f0ed-4114-9820-f087d9c0a21c/GCF_902162175.1_PRJEB33358_genomic.fna.gz --refList GCF_902162175.1_PRJEB33358_genomic.fna/target_genomes_gtdb.txt --output GCF_902162175.1_PRJEB33358_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:43,121] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:43,140] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:32:43,141] [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_003606345.3	s__Bartonella krasnovii	92.7777	540	683	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518165.1	s__Bartonella elizabethae	92.1013	489	683	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.20	95.98	0.98	0.96	7	-
GCF_003606325.2	s__Bartonella kosoyi	90.6612	523	683	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903679515.1	s__Bartonella gabonensis	89.937	465	683	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000196435.1	s__Bartonella tribocorum	89.1914	522	683	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.92	99.90	0.97	0.95	3	-
GCF_002777915.1	s__Bartonella tribocorum_A	89.1191	496	683	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.97	99.97	0.98	0.98	2	-
GCF_018155095.1	s__Bartonella queenslandensis_B	88.7714	484	683	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002778015.1	s__Bartonella tribocorum_B	88.391	469	683	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.97	99.97	0.98	0.98	2	-
GCF_000312585.1	s__Bartonella queenslandensis_A	88.3725	483	683	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902150025.1	s__Bartonella massiliensis	87.8375	508	683	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000312525.1	s__Bartonella florencae	83.8134	460	683	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000273375.1	s__Bartonella birtlesii	83.1381	426	683	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.71	99.25	0.98	0.95	6	-
GCF_902825145.1	s__Bartonella phoceensis	82.899	415	683	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000278295.1	s__Bartonella taylorii	82.8044	440	683	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	98.74	97.76	0.94	0.92	5	-
GCF_000312545.1	s__Bartonella senegalensis	82.7166	420	683	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000278235.1	s__Bartonella arupensis	82.5734	406	683	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.53	99.17	0.97	0.95	3	-
GCF_013388295.1	s__Bartonella alsatica	82.4654	390	683	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.98	99.96	0.99	0.99	3	-
GCF_014203215.1	s__Bartonella callosciuri	82.4088	388	683	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000278135.1	s__Bartonella washoeensis	81.6503	424	683	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	98.94	98.02	0.92	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:43,142] [INFO] GTDB search result was written to GCF_902162175.1_PRJEB33358_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:43,143] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:43,149] [INFO] DFAST_QC result json was written to GCF_902162175.1_PRJEB33358_genomic.fna/dqc_result.json
[2024-01-24 12:32:43,150] [INFO] DFAST_QC completed!
[2024-01-24 12:32:43,150] [INFO] Total running time: 0h0m52s