[2024-01-24 14:05:33,110] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:33,115] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:33,115] [INFO] DQC Reference Directory: /var/lib/cwl/stgb61235be-daf8-47eb-80ac-097c0742f459/dqc_reference
[2024-01-24 14:05:34,414] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:34,415] [INFO] Task started: Prodigal
[2024-01-24 14:05:34,415] [INFO] Running command: gunzip -c /var/lib/cwl/stg656dcaa5-a150-47c0-85c1-1c61b38af40b/GCF_016801025.1_ASM1680102v1_genomic.fna.gz | prodigal -d GCF_016801025.1_ASM1680102v1_genomic.fna/cds.fna -a GCF_016801025.1_ASM1680102v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:49,536] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:49,536] [INFO] Task started: HMMsearch
[2024-01-24 14:05:49,537] [INFO] Running command: hmmsearch --tblout GCF_016801025.1_ASM1680102v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb61235be-daf8-47eb-80ac-097c0742f459/dqc_reference/reference_markers.hmm GCF_016801025.1_ASM1680102v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:49,827] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:49,830] [INFO] Found 6/6 markers.
[2024-01-24 14:05:49,880] [INFO] Query marker FASTA was written to GCF_016801025.1_ASM1680102v1_genomic.fna/markers.fasta
[2024-01-24 14:05:49,881] [INFO] Task started: Blastn
[2024-01-24 14:05:49,881] [INFO] Running command: blastn -query GCF_016801025.1_ASM1680102v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb61235be-daf8-47eb-80ac-097c0742f459/dqc_reference/reference_markers.fasta -out GCF_016801025.1_ASM1680102v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:50,915] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:50,918] [INFO] Selected 19 target genomes.
[2024-01-24 14:05:50,918] [INFO] Target genome list was writen to GCF_016801025.1_ASM1680102v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:50,940] [INFO] Task started: fastANI
[2024-01-24 14:05:50,941] [INFO] Running command: fastANI --query /var/lib/cwl/stg656dcaa5-a150-47c0-85c1-1c61b38af40b/GCF_016801025.1_ASM1680102v1_genomic.fna.gz --refList GCF_016801025.1_ASM1680102v1_genomic.fna/target_genomes.txt --output GCF_016801025.1_ASM1680102v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:07,340] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:07,341] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb61235be-daf8-47eb-80ac-097c0742f459/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:07,341] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb61235be-daf8-47eb-80ac-097c0742f459/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:07,359] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:06:07,359] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:06:07,360] [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
Youhaiella tibetensis	strain=CGMCC 1.12719	GCA_014638565.1	1447062	1447062	type	True	85.3689	1079	1543	95	below_threshold
Youhaiella tibetensis	strain=fig4	GCA_008000755.1	1447062	1447062	type	True	85.3198	1073	1543	95	below_threshold
Devosia elaeis	strain=S37	GCA_001650025.1	1770058	1770058	type	True	79.4244	479	1543	95	below_threshold
Devosia geojensis	strain=BD-c194	GCA_000969415.1	443610	443610	type	True	79.3028	562	1543	95	below_threshold
Devosia ginsengisoli	strain=Gsoil 520	GCA_007859655.1	400770	400770	type	True	79.121	594	1543	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	79.0714	486	1543	95	below_threshold
Devosia insulae	strain=DS-56	GCA_000970465.2	408174	408174	type	True	79.0262	570	1543	95	below_threshold
Devosia salina	strain=SCS-3	GCA_019504385.1	2860336	2860336	type	True	79.0157	488	1543	95	below_threshold
Devosia limi	strain=DSM 17137	GCA_000970435.1	288995	288995	type	True	79.0007	523	1543	95	below_threshold
Devosia limi	strain=DSM 17137	GCA_900128975.1	288995	288995	type	True	78.9691	534	1543	95	below_threshold
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	78.8027	516	1543	95	below_threshold
Devosia chinhatensis	strain=IPL18	GCA_000969445.1	429727	429727	type	True	78.6904	414	1543	95	below_threshold
Devosia epidermidihirudinis	strain=E84	GCA_000971295.1	1293439	1293439	type	True	78.4681	404	1543	95	below_threshold
Devosia rhizoryzae	strain=LEGU1	GCA_016698665.1	2774137	2774137	type	True	78.4501	432	1543	95	below_threshold
Devosia indica	strain=IO390501	GCA_003056405.1	2079253	2079253	type	True	78.4413	421	1543	95	below_threshold
Arsenicitalea aurantiaca	strain=42-50	GCA_003994485.1	1783274	1783274	type	True	78.2471	432	1543	95	below_threshold
Pelagibacterium sediminicola	strain=IMCC34151	GCA_003390885.1	2248761	2248761	type	True	78.2048	307	1543	95	below_threshold
Devosia crocina	strain=IPL20	GCA_900116545.1	429728	429728	type	True	78.1874	360	1543	95	below_threshold
Pelagibacterium xiamenense	strain=HS1C4-1	GCA_021166475.1	2901140	2901140	type	True	77.697	300	1543	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:07,362] [INFO] DFAST Taxonomy check result was written to GCF_016801025.1_ASM1680102v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:07,363] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:07,363] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:07,364] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb61235be-daf8-47eb-80ac-097c0742f459/dqc_reference/checkm_data
[2024-01-24 14:06:07,365] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:07,411] [INFO] Task started: CheckM
[2024-01-24 14:06:07,412] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016801025.1_ASM1680102v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016801025.1_ASM1680102v1_genomic.fna/checkm_input GCF_016801025.1_ASM1680102v1_genomic.fna/checkm_result
[2024-01-24 14:06:52,019] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:52,020] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:52,040] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:52,041] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:52,041] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016801025.1_ASM1680102v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:52,041] [INFO] Task started: Blastn
[2024-01-24 14:06:52,041] [INFO] Running command: blastn -query GCF_016801025.1_ASM1680102v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb61235be-daf8-47eb-80ac-097c0742f459/dqc_reference/reference_markers_gtdb.fasta -out GCF_016801025.1_ASM1680102v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:53,900] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:53,904] [INFO] Selected 20 target genomes.
[2024-01-24 14:06:53,904] [INFO] Target genome list was writen to GCF_016801025.1_ASM1680102v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:53,943] [INFO] Task started: fastANI
[2024-01-24 14:06:53,943] [INFO] Running command: fastANI --query /var/lib/cwl/stg656dcaa5-a150-47c0-85c1-1c61b38af40b/GCF_016801025.1_ASM1680102v1_genomic.fna.gz --refList GCF_016801025.1_ASM1680102v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016801025.1_ASM1680102v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:13,415] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:13,431] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:13,431] [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_016801025.1	s__Paradevosia shaoguanensis	100.0	1543	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Paradevosia	95.0	97.16	97.13	0.92	0.92	4	conclusive
GCF_008000755.1	s__Youhaiella tibetensis	85.322	1073	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Youhaiella	95.0	99.26	98.52	0.98	0.97	3	-
GCF_001650025.1	s__Devosia elaeis	79.3956	482	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000969415.1	s__Devosia geojensis	79.3068	562	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307495.1	s__Devosia_A sp017307495	79.2802	547	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	98.70	98.70	0.95	0.95	2	-
GCA_018828145.1	s__Devosia sp018828145	79.2566	543	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	99.99	99.98	0.99	0.98	4	-
GCA_014860165.1	s__Devosia sp014860165	79.22	532	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873135.1	s__Devosia_A sp014873135	79.215	543	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426345.1	s__Devosia sp001426345	79.1691	558	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899085.1	s__Devosia_A sp001899085	79.1225	626	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	99.98	99.97	0.99	0.99	3	-
GCF_007859655.1	s__Devosia ginsengisoli	79.106	595	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016698645.1	s__Devosia sp016698645	79.0606	488	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001402915.1	s__Devosia_A sp001402915	78.9784	601	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128975.1	s__Devosia limi	78.9687	535	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	99.98	99.98	0.97	0.97	2	-
GCA_001899065.1	s__Devosia_A sp001899065	78.902	525	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	98.96	98.00	0.93	0.88	3	-
GCF_001425235.1	s__Devosia_A sp001425235	78.8608	618	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	97.96	97.96	0.95	0.95	2	-
GCA_903842455.1	s__Devosia_A sp903842455	78.6774	479	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000969445.1	s__Devosia chinhatensis	78.6446	414	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056355.1	s__Devosia naphthalenivorans	78.5098	447	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056405.1	s__Devosia indica	78.495	416	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:13,433] [INFO] GTDB search result was written to GCF_016801025.1_ASM1680102v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:13,433] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:13,437] [INFO] DFAST_QC result json was written to GCF_016801025.1_ASM1680102v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:13,438] [INFO] DFAST_QC completed!
[2024-01-24 14:07:13,438] [INFO] Total running time: 0h1m40s