[2024-01-25 20:24:05,464] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:24:05,465] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:24:05,465] [INFO] DQC Reference Directory: /var/lib/cwl/stgdcf1f410-2e5b-4e6a-8362-cc1337dd3baf/dqc_reference
[2024-01-25 20:24:06,630] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:24:06,632] [INFO] Task started: Prodigal
[2024-01-25 20:24:06,632] [INFO] Running command: gunzip -c /var/lib/cwl/stg5d35e11e-b1bb-48f5-8f5c-57e14b1f586e/GCF_900455865.1_50618_A01_genomic.fna.gz | prodigal -d GCF_900455865.1_50618_A01_genomic.fna/cds.fna -a GCF_900455865.1_50618_A01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:24:17,292] [INFO] Task succeeded: Prodigal
[2024-01-25 20:24:17,293] [INFO] Task started: HMMsearch
[2024-01-25 20:24:17,293] [INFO] Running command: hmmsearch --tblout GCF_900455865.1_50618_A01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdcf1f410-2e5b-4e6a-8362-cc1337dd3baf/dqc_reference/reference_markers.hmm GCF_900455865.1_50618_A01_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:24:17,510] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:24:17,511] [INFO] Found 6/6 markers.
[2024-01-25 20:24:17,544] [INFO] Query marker FASTA was written to GCF_900455865.1_50618_A01_genomic.fna/markers.fasta
[2024-01-25 20:24:17,544] [INFO] Task started: Blastn
[2024-01-25 20:24:17,544] [INFO] Running command: blastn -query GCF_900455865.1_50618_A01_genomic.fna/markers.fasta -db /var/lib/cwl/stgdcf1f410-2e5b-4e6a-8362-cc1337dd3baf/dqc_reference/reference_markers.fasta -out GCF_900455865.1_50618_A01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:24:18,403] [INFO] Task succeeded: Blastn
[2024-01-25 20:24:18,406] [INFO] Selected 17 target genomes.
[2024-01-25 20:24:18,406] [INFO] Target genome list was writen to GCF_900455865.1_50618_A01_genomic.fna/target_genomes.txt
[2024-01-25 20:24:18,441] [INFO] Task started: fastANI
[2024-01-25 20:24:18,441] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d35e11e-b1bb-48f5-8f5c-57e14b1f586e/GCF_900455865.1_50618_A01_genomic.fna.gz --refList GCF_900455865.1_50618_A01_genomic.fna/target_genomes.txt --output GCF_900455865.1_50618_A01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:24:37,246] [INFO] Task succeeded: fastANI
[2024-01-25 20:24:37,246] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdcf1f410-2e5b-4e6a-8362-cc1337dd3baf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:24:37,247] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdcf1f410-2e5b-4e6a-8362-cc1337dd3baf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:24:37,257] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:24:37,257] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:24:37,257] [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
Roseomonas gilardii subsp. rosea	strain=NCTC13290	GCA_900455865.1	243956	257708	type	True	100.0	1372	1374	95	conclusive
Roseomonas gilardii subsp. rosea	strain=ATCC BAA-691	GCA_000518625.1	243956	257708	type	True	99.9797	1336	1374	95	conclusive
Roseomonas mucosa	strain=NCTC13291	GCA_900455935.1	207340	207340	type	True	93.3193	1237	1374	95	below_threshold
Roseomonas mucosa	strain=ATCC BAA-692	GCA_000622225.1	207340	207340	type	True	93.2493	1233	1374	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	80.4114	694	1374	95	below_threshold
Roseomonas coralli	strain=M0104	GCA_009829925.1	2545983	2545983	type	True	80.1336	709	1374	95	below_threshold
Roseomonas wenyumeiae	strain=Z23	GCA_003696345.1	2478470	2478470	type	True	79.9746	729	1374	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	79.9648	644	1374	95	below_threshold
Roseomonas pecuniae	strain=DSM 25622	GCA_014199205.1	693023	693023	type	True	79.8356	690	1374	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	79.5473	680	1374	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	79.409	581	1374	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	78.8739	532	1374	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	78.6846	548	1374	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	78.6099	520	1374	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	78.5145	529	1374	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	78.3173	552	1374	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	77.6789	506	1374	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:24:37,260] [INFO] DFAST Taxonomy check result was written to GCF_900455865.1_50618_A01_genomic.fna/tc_result.tsv
[2024-01-25 20:24:37,260] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:24:37,260] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:24:37,260] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdcf1f410-2e5b-4e6a-8362-cc1337dd3baf/dqc_reference/checkm_data
[2024-01-25 20:24:37,261] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:24:37,304] [INFO] Task started: CheckM
[2024-01-25 20:24:37,304] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900455865.1_50618_A01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900455865.1_50618_A01_genomic.fna/checkm_input GCF_900455865.1_50618_A01_genomic.fna/checkm_result
[2024-01-25 20:25:37,917] [INFO] Task succeeded: CheckM
[2024-01-25 20:25:37,918] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:25:37,941] [INFO] ===== Completeness check finished =====
[2024-01-25 20:25:37,942] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:25:37,942] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900455865.1_50618_A01_genomic.fna/markers.fasta)
[2024-01-25 20:25:37,943] [INFO] Task started: Blastn
[2024-01-25 20:25:37,943] [INFO] Running command: blastn -query GCF_900455865.1_50618_A01_genomic.fna/markers.fasta -db /var/lib/cwl/stgdcf1f410-2e5b-4e6a-8362-cc1337dd3baf/dqc_reference/reference_markers_gtdb.fasta -out GCF_900455865.1_50618_A01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:25:39,637] [INFO] Task succeeded: Blastn
[2024-01-25 20:25:39,640] [INFO] Selected 19 target genomes.
[2024-01-25 20:25:39,640] [INFO] Target genome list was writen to GCF_900455865.1_50618_A01_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:25:39,701] [INFO] Task started: fastANI
[2024-01-25 20:25:39,702] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d35e11e-b1bb-48f5-8f5c-57e14b1f586e/GCF_900455865.1_50618_A01_genomic.fna.gz --refList GCF_900455865.1_50618_A01_genomic.fna/target_genomes_gtdb.txt --output GCF_900455865.1_50618_A01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:26:00,784] [INFO] Task succeeded: fastANI
[2024-01-25 20:26:00,796] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:26:00,796] [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_001941945.1	s__Roseomonas gilardii	96.4817	1274	1374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	96.77	95.72	0.89	0.83	6	conclusive
GCF_000622225.1	s__Roseomonas mucosa	93.2427	1234	1374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	99.41	98.67	0.95	0.89	8	-
GCF_002631185.1	s__Roseomonas rhizosphaerae	80.637	725	1374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000164635.1	s__Roseomonas cervicalis	80.3764	699	1374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016107285.1	s__Roseomonas sp016107285	80.2127	689	1374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009829925.1	s__Roseomonas coralli	80.1164	712	1374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003696345.1	s__Roseomonas sp003696345	79.9635	730	1374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014199205.1	s__Roseomonas pecuniae	79.8428	689	1374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017813395.1	s__Roseomonas sp017813395	79.7599	632	1374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141905.1	s__Roseomonas rosea	79.7586	681	1374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902706185.1	s__Roseomonas sp902706185	79.5207	731	1374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199195.1	s__Roseomonas_B alkaliterrae	79.4434	577	1374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	99.89	99.89	0.97	0.97	2	-
GCF_006438825.1	s__Roseomonas nepalensis	79.2793	676	1374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016107305.1	s__Roseomonas sp016107305	79.1484	625	1374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711725.1	s__Roseomonas aerilata	79.1421	641	1374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016106005.1	s__Roseomonas_B sp016106005	78.895	485	1374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015223225.1	s__Roseomonas sp015223225	78.6784	574	1374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007129145.1	s__Roseococcus sp007129145	78.6128	268	1374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241695.1	s__Hansschlegelia sp003241695	76.2827	208	1374	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:26:00,798] [INFO] GTDB search result was written to GCF_900455865.1_50618_A01_genomic.fna/result_gtdb.tsv
[2024-01-25 20:26:00,798] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:26:00,801] [INFO] DFAST_QC result json was written to GCF_900455865.1_50618_A01_genomic.fna/dqc_result.json
[2024-01-25 20:26:00,801] [INFO] DFAST_QC completed!
[2024-01-25 20:26:00,802] [INFO] Total running time: 0h1m55s