[2024-01-24 13:17:42,401] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:42,403] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:42,403] [INFO] DQC Reference Directory: /var/lib/cwl/stg43c8d5e4-e0af-4f67-8bda-0353ef2931d5/dqc_reference
[2024-01-24 13:17:43,634] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:43,635] [INFO] Task started: Prodigal
[2024-01-24 13:17:43,636] [INFO] Running command: gunzip -c /var/lib/cwl/stgc91063f6-5ec3-47fc-9ae1-63bc05f0dcba/GCF_001404515.1_L.albaCECT5095_Spades_Prokka_genomic.fna.gz | prodigal -d GCF_001404515.1_L.albaCECT5095_Spades_Prokka_genomic.fna/cds.fna -a GCF_001404515.1_L.albaCECT5095_Spades_Prokka_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:05,920] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:05,920] [INFO] Task started: HMMsearch
[2024-01-24 13:18:05,920] [INFO] Running command: hmmsearch --tblout GCF_001404515.1_L.albaCECT5095_Spades_Prokka_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43c8d5e4-e0af-4f67-8bda-0353ef2931d5/dqc_reference/reference_markers.hmm GCF_001404515.1_L.albaCECT5095_Spades_Prokka_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:06,372] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:06,374] [INFO] Found 6/6 markers.
[2024-01-24 13:18:06,443] [INFO] Query marker FASTA was written to GCF_001404515.1_L.albaCECT5095_Spades_Prokka_genomic.fna/markers.fasta
[2024-01-24 13:18:06,444] [INFO] Task started: Blastn
[2024-01-24 13:18:06,444] [INFO] Running command: blastn -query GCF_001404515.1_L.albaCECT5095_Spades_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg43c8d5e4-e0af-4f67-8bda-0353ef2931d5/dqc_reference/reference_markers.fasta -out GCF_001404515.1_L.albaCECT5095_Spades_Prokka_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:07,308] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:07,312] [INFO] Selected 23 target genomes.
[2024-01-24 13:18:07,312] [INFO] Target genome list was writen to GCF_001404515.1_L.albaCECT5095_Spades_Prokka_genomic.fna/target_genomes.txt
[2024-01-24 13:18:07,350] [INFO] Task started: fastANI
[2024-01-24 13:18:07,351] [INFO] Running command: fastANI --query /var/lib/cwl/stgc91063f6-5ec3-47fc-9ae1-63bc05f0dcba/GCF_001404515.1_L.albaCECT5095_Spades_Prokka_genomic.fna.gz --refList GCF_001404515.1_L.albaCECT5095_Spades_Prokka_genomic.fna/target_genomes.txt --output GCF_001404515.1_L.albaCECT5095_Spades_Prokka_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:27,523] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:27,524] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43c8d5e4-e0af-4f67-8bda-0353ef2931d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:27,524] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43c8d5e4-e0af-4f67-8bda-0353ef2931d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:27,541] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:27,541] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:27,541] [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
Roseibium album	strain=CECT 5095	GCA_001404515.1	311410	311410	type	True	100.0	2284	2286	95	conclusive
Roseibium aggregatum	strain=IAM 12614	GCA_000168975.1	187304	187304	suspected-type	True	78.8598	680	2286	95	below_threshold
Roseibium marinum	strain=DSM 17023	GCA_002906165.1	281252	281252	type	True	78.56	630	2286	95	below_threshold
Roseibium denhamense	strain=JCM 10543	GCA_009711415.1	76305	76305	type	True	77.9719	418	2286	95	below_threshold
Roseibium alexandrii	strain=DFL-11	GCA_000158095.2	388408	388408	type	True	77.9492	426	2286	95	below_threshold
Roseibium polysiphoniae	strain=KACC 19711	GCA_014842925.1	2571221	2571221	type	True	77.6797	283	2286	95	below_threshold
Roseibium suaedae	strain=DSM 22153	GCA_900142725.1	735517	735517	type	True	77.6098	303	2286	95	below_threshold
Roseibium aestuarii	strain=SYSU M00256-3	GCA_008477545.1	2600299	2600299	type	True	77.5298	281	2286	95	below_threshold
Roseibium hamelinense	strain=NBRC 16783	GCA_009711505.1	150831	150831	type	True	77.4603	238	2286	95	below_threshold
Roseibium hamelinense	strain=ATCC BAA-252	GCA_007830545.1	150831	150831	type	True	77.3553	247	2286	95	below_threshold
Roseibium limicola	strain=CAU 1637	GCA_017313085.1	2816037	2816037	type	True	77.2129	245	2286	95	below_threshold
Pannonibacter indicus	strain=DSM 23407	GCA_001418225.1	466044	466044	type	True	76.9233	234	2286	95	below_threshold
Pannonibacter indicus	strain=DSM 23407	GCA_001517385.1	466044	466044	type	True	76.9233	234	2286	95	below_threshold
Stappia taiwanensis	strain=CCM 7757	GCA_014635285.1	992267	992267	type	True	76.8746	195	2286	95	below_threshold
Stappia taiwanensis	strain=DSM 23284	GCA_013868145.1	992267	992267	type	True	76.8729	202	2286	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	76.4213	88	2286	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	76.3493	104	2286	95	below_threshold
Zhengella mangrovi	strain=X9-2-2	GCA_002727065.1	1982044	1982044	type	True	76.3116	119	2286	95	below_threshold
Rhizobium pseudoryzae	strain=DSM 19479	GCA_011046245.1	379684	379684	type	True	76.2633	118	2286	95	below_threshold
Aurantimonas marina	strain=SW136	GCA_017183135.1	2780508	2780508	type	True	76.2108	79	2286	95	below_threshold
Rhodopseudomonas faecalis	strain=JCM 11668	GCA_003217325.1	99655	99655	type	True	75.7775	65	2286	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:27,543] [INFO] DFAST Taxonomy check result was written to GCF_001404515.1_L.albaCECT5095_Spades_Prokka_genomic.fna/tc_result.tsv
[2024-01-24 13:18:27,544] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:27,544] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:27,544] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43c8d5e4-e0af-4f67-8bda-0353ef2931d5/dqc_reference/checkm_data
[2024-01-24 13:18:27,545] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:27,613] [INFO] Task started: CheckM
[2024-01-24 13:18:27,613] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001404515.1_L.albaCECT5095_Spades_Prokka_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001404515.1_L.albaCECT5095_Spades_Prokka_genomic.fna/checkm_input GCF_001404515.1_L.albaCECT5095_Spades_Prokka_genomic.fna/checkm_result
[2024-01-24 13:19:33,087] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:33,088] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:33,109] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:33,110] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:33,110] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001404515.1_L.albaCECT5095_Spades_Prokka_genomic.fna/markers.fasta)
[2024-01-24 13:19:33,111] [INFO] Task started: Blastn
[2024-01-24 13:19:33,111] [INFO] Running command: blastn -query GCF_001404515.1_L.albaCECT5095_Spades_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg43c8d5e4-e0af-4f67-8bda-0353ef2931d5/dqc_reference/reference_markers_gtdb.fasta -out GCF_001404515.1_L.albaCECT5095_Spades_Prokka_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:34,601] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:34,604] [INFO] Selected 14 target genomes.
[2024-01-24 13:19:34,604] [INFO] Target genome list was writen to GCF_001404515.1_L.albaCECT5095_Spades_Prokka_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:34,617] [INFO] Task started: fastANI
[2024-01-24 13:19:34,617] [INFO] Running command: fastANI --query /var/lib/cwl/stgc91063f6-5ec3-47fc-9ae1-63bc05f0dcba/GCF_001404515.1_L.albaCECT5095_Spades_Prokka_genomic.fna.gz --refList GCF_001404515.1_L.albaCECT5095_Spades_Prokka_genomic.fna/target_genomes_gtdb.txt --output GCF_001404515.1_L.albaCECT5095_Spades_Prokka_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:53,565] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:53,578] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:53,579] [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_001404515.1	s__Roseibium album	100.0	2284	2286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	98.84	98.04	0.95	0.92	13	conclusive
GCF_000521215.1	s__Roseibium sp000521215	94.9799	2114	2286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001999245.1	s__Roseibium aggregatum_A	78.8743	718	2286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	97.61	96.85	0.93	0.89	16	-
GCF_000168975.1	s__Roseibium aggregatum	78.8698	679	2286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002237595.1	s__Roseibium sp002237595	78.8242	772	2286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002906165.1	s__Roseibium marinum	78.5791	627	2286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363435.1	s__Roseibium sp009363435	78.5425	582	2286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643925.1	s__Roseibium sp017643925	78.5178	696	2286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	99.99	99.99	0.99	0.99	2	-
GCA_008107755.1	s__Roseibium sp008107755	78.4704	543	2286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075075.1	s__Roseibium sp003075075	78.4624	629	2286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001624695.1	s__Roseibium sp001624695	78.3939	609	2286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017309185.1	s__Roseibium aggregatum_B	78.3641	638	2286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418225.1	s__Pannonibacter indicus	76.9233	234	2286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter	95.0	96.01	95.55	0.94	0.89	12	-
GCF_003610575.1	s__Stappia sp003610575	76.7902	212	2286	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	98.18	98.18	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:53,581] [INFO] GTDB search result was written to GCF_001404515.1_L.albaCECT5095_Spades_Prokka_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:53,582] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:53,586] [INFO] DFAST_QC result json was written to GCF_001404515.1_L.albaCECT5095_Spades_Prokka_genomic.fna/dqc_result.json
[2024-01-24 13:19:53,586] [INFO] DFAST_QC completed!
[2024-01-24 13:19:53,586] [INFO] Total running time: 0h2m11s