[2024-01-24 13:57:40,759] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:40,761] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:40,761] [INFO] DQC Reference Directory: /var/lib/cwl/stg31054477-ddcc-487c-859b-2bce8d5a4351/dqc_reference
[2024-01-24 13:57:42,070] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:42,071] [INFO] Task started: Prodigal
[2024-01-24 13:57:42,071] [INFO] Running command: gunzip -c /var/lib/cwl/stg5636aaa6-0a4f-42a3-8331-e04ca9e7d15f/GCF_007644105.1_ASM764410v1_genomic.fna.gz | prodigal -d GCF_007644105.1_ASM764410v1_genomic.fna/cds.fna -a GCF_007644105.1_ASM764410v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:55,303] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:55,303] [INFO] Task started: HMMsearch
[2024-01-24 13:57:55,303] [INFO] Running command: hmmsearch --tblout GCF_007644105.1_ASM764410v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31054477-ddcc-487c-859b-2bce8d5a4351/dqc_reference/reference_markers.hmm GCF_007644105.1_ASM764410v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:55,625] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:55,627] [INFO] Found 6/6 markers.
[2024-01-24 13:57:55,668] [INFO] Query marker FASTA was written to GCF_007644105.1_ASM764410v1_genomic.fna/markers.fasta
[2024-01-24 13:57:55,669] [INFO] Task started: Blastn
[2024-01-24 13:57:55,669] [INFO] Running command: blastn -query GCF_007644105.1_ASM764410v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31054477-ddcc-487c-859b-2bce8d5a4351/dqc_reference/reference_markers.fasta -out GCF_007644105.1_ASM764410v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:56,662] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:56,665] [INFO] Selected 17 target genomes.
[2024-01-24 13:57:56,666] [INFO] Target genome list was writen to GCF_007644105.1_ASM764410v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:56,672] [INFO] Task started: fastANI
[2024-01-24 13:57:56,673] [INFO] Running command: fastANI --query /var/lib/cwl/stg5636aaa6-0a4f-42a3-8331-e04ca9e7d15f/GCF_007644105.1_ASM764410v1_genomic.fna.gz --refList GCF_007644105.1_ASM764410v1_genomic.fna/target_genomes.txt --output GCF_007644105.1_ASM764410v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:12,917] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:12,918] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31054477-ddcc-487c-859b-2bce8d5a4351/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:12,918] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31054477-ddcc-487c-859b-2bce8d5a4351/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:12,938] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:12,938] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:12,938] [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
Elioraea rosea	strain=PF-30	GCA_007644105.1	2492390	2492390	type	True	100.0	1446	1448	95	conclusive
Elioraea tepida	strain=MS-P2	GCA_019203965.1	2843330	2843330	type	True	81.5345	804	1448	95	below_threshold
Elioraea thermophila	strain=YIM 72297	GCA_003336755.1	2185104	2185104	type	True	79.0047	520	1448	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	78.0655	564	1448	95	below_threshold
Roseomonas oryzicola	strain=KCTC 22478	GCA_012163135.1	535904	535904	type	True	77.8168	535	1448	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	77.6846	423	1448	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	77.6802	427	1448	95	below_threshold
Roseomonas coralli	strain=M0104	GCA_009829925.1	2545983	2545983	type	True	77.6574	426	1448	95	below_threshold
Acidisphaera rubrifaciens	strain=HS-AP3	GCA_000964365.1	50715	50715	type	True	77.5071	236	1448	95	below_threshold
Belnapia arida	strain=T18	GCA_016773205.1	2804533	2804533	type	True	77.4467	441	1448	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	77.3997	384	1448	95	below_threshold
Roseomonas rosea	strain=DSM 14916	GCA_900141905.1	198092	198092	type	True	77.2528	364	1448	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	77.1922	396	1448	95	below_threshold
Roseomonas oryzae	strain=KCTC 42542	GCA_008386565.1	1608942	1608942	type	True	77.1742	339	1448	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	77.0892	384	1448	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	76.3175	227	1448	95	below_threshold
Devosia geojensis	strain=BD-c194	GCA_000969415.1	443610	443610	type	True	76.1444	178	1448	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:12,940] [INFO] DFAST Taxonomy check result was written to GCF_007644105.1_ASM764410v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:12,941] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:12,941] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:12,941] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31054477-ddcc-487c-859b-2bce8d5a4351/dqc_reference/checkm_data
[2024-01-24 13:58:12,942] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:12,985] [INFO] Task started: CheckM
[2024-01-24 13:58:12,985] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007644105.1_ASM764410v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007644105.1_ASM764410v1_genomic.fna/checkm_input GCF_007644105.1_ASM764410v1_genomic.fna/checkm_result
[2024-01-24 13:58:56,829] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:56,831] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:56,846] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:56,846] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:56,847] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007644105.1_ASM764410v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:56,847] [INFO] Task started: Blastn
[2024-01-24 13:58:56,847] [INFO] Running command: blastn -query GCF_007644105.1_ASM764410v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31054477-ddcc-487c-859b-2bce8d5a4351/dqc_reference/reference_markers_gtdb.fasta -out GCF_007644105.1_ASM764410v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:58,662] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:58,666] [INFO] Selected 12 target genomes.
[2024-01-24 13:58:58,666] [INFO] Target genome list was writen to GCF_007644105.1_ASM764410v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:58,679] [INFO] Task started: fastANI
[2024-01-24 13:58:58,680] [INFO] Running command: fastANI --query /var/lib/cwl/stg5636aaa6-0a4f-42a3-8331-e04ca9e7d15f/GCF_007644105.1_ASM764410v1_genomic.fna.gz --refList GCF_007644105.1_ASM764410v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007644105.1_ASM764410v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:09,729] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:09,746] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:09,746] [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_007644105.1	s__Elioraea_A rosea	100.0	1446	1448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Elioraea_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_019203965.1	s__Elioraea_A sp019203965	81.5518	803	1448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Elioraea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006704265.1	s__Elioraea sp006704265	80.3922	681	1448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Elioraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378465.1	s__Elioraea tepidiphila	80.2332	749	1448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Elioraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003336755.1	s__Elioraea thermophila	78.9868	522	1448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Elioraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116135.1	s__Roseomonas aestuarii	77.9133	471	1448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173615.1	s__Roseomonas_A sp003173615	77.7738	554	1448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000164635.1	s__Roseomonas cervicalis	77.7008	421	1448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240635.1	s__JAFEFJ01 sp018240635	77.6583	344	1448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFEFJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009829925.1	s__Roseomonas coralli	77.6372	428	1448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258945.1	s__Paracraurococcus frigidaeris	77.5846	509	1448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903944925.1	s__Rhodopila sp903944925	76.6978	224	1448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodopila	95.0	99.96	99.95	0.97	0.97	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:09,748] [INFO] GTDB search result was written to GCF_007644105.1_ASM764410v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:09,749] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:09,752] [INFO] DFAST_QC result json was written to GCF_007644105.1_ASM764410v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:09,752] [INFO] DFAST_QC completed!
[2024-01-24 13:59:09,753] [INFO] Total running time: 0h1m29s