[2024-01-24 12:43:54,222] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:43:54,225] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:43:54,225] [INFO] DQC Reference Directory: /var/lib/cwl/stgb73c2ff2-d040-4563-8143-ff0945d9bc7a/dqc_reference
[2024-01-24 12:43:59,337] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:43:59,338] [INFO] Task started: Prodigal
[2024-01-24 12:43:59,339] [INFO] Running command: gunzip -c /var/lib/cwl/stg22fe3604-e78f-45ff-b3b4-ba3a81fb6039/GCF_023078375.1_ASM2307837v1_genomic.fna.gz | prodigal -d GCF_023078375.1_ASM2307837v1_genomic.fna/cds.fna -a GCF_023078375.1_ASM2307837v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:12,886] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:12,887] [INFO] Task started: HMMsearch
[2024-01-24 12:44:12,887] [INFO] Running command: hmmsearch --tblout GCF_023078375.1_ASM2307837v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb73c2ff2-d040-4563-8143-ff0945d9bc7a/dqc_reference/reference_markers.hmm GCF_023078375.1_ASM2307837v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:13,171] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:13,173] [INFO] Found 6/6 markers.
[2024-01-24 12:44:13,216] [INFO] Query marker FASTA was written to GCF_023078375.1_ASM2307837v1_genomic.fna/markers.fasta
[2024-01-24 12:44:13,216] [INFO] Task started: Blastn
[2024-01-24 12:44:13,216] [INFO] Running command: blastn -query GCF_023078375.1_ASM2307837v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb73c2ff2-d040-4563-8143-ff0945d9bc7a/dqc_reference/reference_markers.fasta -out GCF_023078375.1_ASM2307837v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:14,083] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:14,087] [INFO] Selected 14 target genomes.
[2024-01-24 12:44:14,088] [INFO] Target genome list was writen to GCF_023078375.1_ASM2307837v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:14,115] [INFO] Task started: fastANI
[2024-01-24 12:44:14,115] [INFO] Running command: fastANI --query /var/lib/cwl/stg22fe3604-e78f-45ff-b3b4-ba3a81fb6039/GCF_023078375.1_ASM2307837v1_genomic.fna.gz --refList GCF_023078375.1_ASM2307837v1_genomic.fna/target_genomes.txt --output GCF_023078375.1_ASM2307837v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:29,524] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:29,525] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb73c2ff2-d040-4563-8143-ff0945d9bc7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:29,525] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb73c2ff2-d040-4563-8143-ff0945d9bc7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:29,538] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:44:29,538] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:44:29,538] [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	92.7892	1236	1541	95	below_threshold
Roseomonas gilardii subsp. rosea	strain=ATCC BAA-691	GCA_000518625.1	243956	257708	type	True	92.5801	1288	1541	95	below_threshold
Roseomonas mucosa	strain=NCTC13291	GCA_900455935.1	207340	207340	type	True	92.0432	1310	1541	95	below_threshold
Roseomonas mucosa	strain=ATCC BAA-692	GCA_000622225.1	207340	207340	type	True	92.0171	1297	1541	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	80.1836	703	1541	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	79.6769	700	1541	95	below_threshold
Roseomonas wenyumeiae	strain=Z23	GCA_003696345.1	2478470	2478470	type	True	79.6667	785	1541	95	below_threshold
Roseomonas pecuniae	strain=DSM 25622	GCA_014199205.1	693023	693023	type	True	79.6388	691	1541	95	below_threshold
Roseomonas oryzae	strain=KCTC 42542	GCA_008386565.1	1608942	1608942	type	True	79.458	676	1541	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	79.3247	697	1541	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	78.9494	577	1541	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	78.5463	479	1541	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	78.4958	541	1541	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	78.2708	551	1541	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:29,540] [INFO] DFAST Taxonomy check result was written to GCF_023078375.1_ASM2307837v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:29,541] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:29,541] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:29,541] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb73c2ff2-d040-4563-8143-ff0945d9bc7a/dqc_reference/checkm_data
[2024-01-24 12:44:29,543] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:29,590] [INFO] Task started: CheckM
[2024-01-24 12:44:29,590] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023078375.1_ASM2307837v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023078375.1_ASM2307837v1_genomic.fna/checkm_input GCF_023078375.1_ASM2307837v1_genomic.fna/checkm_result
[2024-01-24 12:45:46,743] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:46,744] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:46,767] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:46,768] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:46,768] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023078375.1_ASM2307837v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:46,768] [INFO] Task started: Blastn
[2024-01-24 12:45:46,769] [INFO] Running command: blastn -query GCF_023078375.1_ASM2307837v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb73c2ff2-d040-4563-8143-ff0945d9bc7a/dqc_reference/reference_markers_gtdb.fasta -out GCF_023078375.1_ASM2307837v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:48,386] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:48,394] [INFO] Selected 20 target genomes.
[2024-01-24 12:45:48,394] [INFO] Target genome list was writen to GCF_023078375.1_ASM2307837v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:48,413] [INFO] Task started: fastANI
[2024-01-24 12:45:48,413] [INFO] Running command: fastANI --query /var/lib/cwl/stg22fe3604-e78f-45ff-b3b4-ba3a81fb6039/GCF_023078375.1_ASM2307837v1_genomic.fna.gz --refList GCF_023078375.1_ASM2307837v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023078375.1_ASM2307837v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:10,770] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:10,788] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:46:10,788] [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	92.625	1382	1541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	96.77	95.72	0.89	0.83	6	-
GCF_000622225.1	s__Roseomonas mucosa	92.0171	1297	1541	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	80.199	701	1541	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	80.1537	689	1541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014490445.1	s__Roseomonas ludipueritiae	79.9412	676	1541	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	79.7688	743	1541	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	79.7194	778	1541	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	79.6909	684	1541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017654485.1	s__Roseomonas sp017654485	79.6296	707	1541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	99.93	99.93	0.97	0.97	2	-
GCF_902706185.1	s__Roseomonas sp902706185	79.51	754	1541	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	79.5079	645	1541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386565.1	s__Roseomonas oryzae	79.4762	673	1541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001982615.1	s__Roseomonas deserti	79.4242	754	1541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013112485.1	s__Paracraurococcus sp013112485	79.1213	706	1541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006438825.1	s__Roseomonas nepalensis	79.1102	699	1541	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	79.0358	656	1541	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	78.9831	573	1541	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_004761865.1	s__Crenalkalicoccus roseus	78.9338	619	1541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Crenalkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927745.1	s__Roseomonas_B sp012927745	78.5658	562	1541	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_003241695.1	s__Hansschlegelia sp003241695	76.1397	200	1541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:10,790] [INFO] GTDB search result was written to GCF_023078375.1_ASM2307837v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:10,790] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:10,795] [INFO] DFAST_QC result json was written to GCF_023078375.1_ASM2307837v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:10,795] [INFO] DFAST_QC completed!
[2024-01-24 12:46:10,795] [INFO] Total running time: 0h2m17s