[2024-01-25 18:12:35,681] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:12:35,683] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:12:35,683] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b6e938d-a0ed-4b12-8af2-d4a058f12eb7/dqc_reference
[2024-01-25 18:12:36,829] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:12:36,830] [INFO] Task started: Prodigal
[2024-01-25 18:12:36,830] [INFO] Running command: gunzip -c /var/lib/cwl/stgd565896b-9f0b-4f5f-a607-7f5702bdcea0/GCF_014197255.1_ASM1419725v1_genomic.fna.gz | prodigal -d GCF_014197255.1_ASM1419725v1_genomic.fna/cds.fna -a GCF_014197255.1_ASM1419725v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:12:40,438] [INFO] Task succeeded: Prodigal
[2024-01-25 18:12:40,438] [INFO] Task started: HMMsearch
[2024-01-25 18:12:40,438] [INFO] Running command: hmmsearch --tblout GCF_014197255.1_ASM1419725v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b6e938d-a0ed-4b12-8af2-d4a058f12eb7/dqc_reference/reference_markers.hmm GCF_014197255.1_ASM1419725v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:12:40,661] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:12:40,662] [INFO] Found 6/6 markers.
[2024-01-25 18:12:40,691] [INFO] Query marker FASTA was written to GCF_014197255.1_ASM1419725v1_genomic.fna/markers.fasta
[2024-01-25 18:12:40,692] [INFO] Task started: Blastn
[2024-01-25 18:12:40,692] [INFO] Running command: blastn -query GCF_014197255.1_ASM1419725v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b6e938d-a0ed-4b12-8af2-d4a058f12eb7/dqc_reference/reference_markers.fasta -out GCF_014197255.1_ASM1419725v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:41,310] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:41,314] [INFO] Selected 17 target genomes.
[2024-01-25 18:12:41,315] [INFO] Target genome list was writen to GCF_014197255.1_ASM1419725v1_genomic.fna/target_genomes.txt
[2024-01-25 18:12:41,329] [INFO] Task started: fastANI
[2024-01-25 18:12:41,329] [INFO] Running command: fastANI --query /var/lib/cwl/stgd565896b-9f0b-4f5f-a607-7f5702bdcea0/GCF_014197255.1_ASM1419725v1_genomic.fna.gz --refList GCF_014197255.1_ASM1419725v1_genomic.fna/target_genomes.txt --output GCF_014197255.1_ASM1419725v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:12:49,603] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:49,604] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b6e938d-a0ed-4b12-8af2-d4a058f12eb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:12:49,604] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b6e938d-a0ed-4b12-8af2-d4a058f12eb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:12:49,615] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:12:49,615] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:12:49,616] [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 fuyuanensis	strain=DSM 100694	GCA_014197255.1	1460968	1460968	type	True	100.0	605	607	95	conclusive
Bartonella grahamii	strain=NCTC12860	GCA_900445635.1	33045	33045	type	True	87.9569	547	607	95	below_threshold
Bartonella grahamii	strain=ATCC 700132	GCA_000518085.1	33045	33045	type	True	87.9329	534	607	95	below_threshold
Bartonella rattimassiliensis	strain=15908	GCA_000312605.2	270250	270250	type	True	87.294	504	607	95	below_threshold
Bartonella rattimassiliensis	strain=15908	GCA_000278215.1	270250	270250	type	True	87.0755	537	607	95	below_threshold
Bartonella tribocorum	strain=type strain:506 = CIP 105476	GCA_000196435.1	85701	85701	suspected-type	True	86.9908	550	607	95	below_threshold
Bartonella gabonensis	strain=669	GCA_903679515.1	2699889	2699889	type	True	86.5844	496	607	95	below_threshold
Bartonella kosoyi	strain=Tel Aviv	GCA_003606325.3	2133959	2133959	type	True	86.5458	532	607	95	below_threshold
Bartonella elizabethae	strain=ATCC 49927	GCA_000518165.1	807	807	type	True	86.4744	510	607	95	below_threshold
Bartonella elizabethae	strain=ATCC 49927	GCA_902825135.1	807	807	type	True	86.3882	506	607	95	below_threshold
Bartonella elizabethae	strain=F9251	GCA_000278315.1	807	807	type	True	86.3372	518	607	95	below_threshold
Bartonella krasnovii	strain=OE 1-1	GCA_003606345.3	2267275	2267275	type	True	85.7977	528	607	95	below_threshold
Bartonella saheliensis	strain=077	GCA_902162175.1	1457016	1457016	type	True	85.5879	442	607	95	below_threshold
Bartonella henselae	strain=FDAARGOS_1462	GCA_019930925.1	38323	38323	type	True	81.9847	443	607	95	below_threshold
Bartonella henselae	strain=Houston-I	GCA_002735245.1	38323	38323	type	True	81.9454	447	607	95	below_threshold
Bartonella doshiae	strain=NCTC 12862	GCA_000278155.1	33044	33044	type	True	81.3254	425	607	95	below_threshold
Bartonella doshiae	strain=NCTC12862	GCA_900445535.1	33044	33044	type	True	81.2848	436	607	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:12:49,619] [INFO] DFAST Taxonomy check result was written to GCF_014197255.1_ASM1419725v1_genomic.fna/tc_result.tsv
[2024-01-25 18:12:49,620] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:12:49,620] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:12:49,620] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b6e938d-a0ed-4b12-8af2-d4a058f12eb7/dqc_reference/checkm_data
[2024-01-25 18:12:49,621] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:12:49,647] [INFO] Task started: CheckM
[2024-01-25 18:12:49,647] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014197255.1_ASM1419725v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014197255.1_ASM1419725v1_genomic.fna/checkm_input GCF_014197255.1_ASM1419725v1_genomic.fna/checkm_result
[2024-01-25 18:13:06,495] [INFO] Task succeeded: CheckM
[2024-01-25 18:13:06,497] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:13:06,517] [INFO] ===== Completeness check finished =====
[2024-01-25 18:13:06,517] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:13:06,517] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014197255.1_ASM1419725v1_genomic.fna/markers.fasta)
[2024-01-25 18:13:06,518] [INFO] Task started: Blastn
[2024-01-25 18:13:06,518] [INFO] Running command: blastn -query GCF_014197255.1_ASM1419725v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b6e938d-a0ed-4b12-8af2-d4a058f12eb7/dqc_reference/reference_markers_gtdb.fasta -out GCF_014197255.1_ASM1419725v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:07,485] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:07,489] [INFO] Selected 14 target genomes.
[2024-01-25 18:13:07,489] [INFO] Target genome list was writen to GCF_014197255.1_ASM1419725v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:13:07,501] [INFO] Task started: fastANI
[2024-01-25 18:13:07,501] [INFO] Running command: fastANI --query /var/lib/cwl/stgd565896b-9f0b-4f5f-a607-7f5702bdcea0/GCF_014197255.1_ASM1419725v1_genomic.fna.gz --refList GCF_014197255.1_ASM1419725v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014197255.1_ASM1419725v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:13:14,424] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:14,432] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:13:14,433] [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_014197255.1	s__Bartonella fuyuanensis	100.0	605	607	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	conclusive
GCF_000518085.1	s__Bartonella grahamii	87.9329	534	607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.67	99.54	0.97	0.95	5	-
GCF_000278215.1	s__Bartonella rattimassiliensis	87.1179	536	607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.95	99.95	0.99	0.99	2	-
GCF_000196435.1	s__Bartonella tribocorum	86.9655	551	607	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	86.7143	532	607	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	86.6665	521	607	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_018155095.1	s__Bartonella queenslandensis_B	86.6626	524	607	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	86.5855	497	607	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_003606325.2	s__Bartonella kosoyi	86.5643	531	607	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	86.535	508	607	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_000518165.1	s__Bartonella elizabethae	86.451	511	607	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_003606345.3	s__Bartonella krasnovii	85.7747	529	607	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	81.9767	462	607	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_000278155.1	s__Bartonella doshiae	81.3318	425	607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	98.97	97.90	0.96	0.87	9	-
--------------------------------------------------------------------------------
[2024-01-25 18:13:14,434] [INFO] GTDB search result was written to GCF_014197255.1_ASM1419725v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:13:14,435] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:13:14,437] [INFO] DFAST_QC result json was written to GCF_014197255.1_ASM1419725v1_genomic.fna/dqc_result.json
[2024-01-25 18:13:14,438] [INFO] DFAST_QC completed!
[2024-01-25 18:13:14,438] [INFO] Total running time: 0h0m39s