[2024-01-25 18:57:20,563] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:57:20,565] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:57:20,565] [INFO] DQC Reference Directory: /var/lib/cwl/stg06b407be-9af4-428f-b17a-1d9eb59bb32d/dqc_reference
[2024-01-25 18:57:21,674] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:57:21,675] [INFO] Task started: Prodigal
[2024-01-25 18:57:21,675] [INFO] Running command: gunzip -c /var/lib/cwl/stgfcb93007-c26e-440f-b5e3-0dad2e032b45/GCF_018729455.1_ASM1872945v1_genomic.fna.gz | prodigal -d GCF_018729455.1_ASM1872945v1_genomic.fna/cds.fna -a GCF_018729455.1_ASM1872945v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:57:36,972] [INFO] Task succeeded: Prodigal
[2024-01-25 18:57:36,972] [INFO] Task started: HMMsearch
[2024-01-25 18:57:36,972] [INFO] Running command: hmmsearch --tblout GCF_018729455.1_ASM1872945v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06b407be-9af4-428f-b17a-1d9eb59bb32d/dqc_reference/reference_markers.hmm GCF_018729455.1_ASM1872945v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:57:37,285] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:57:37,286] [INFO] Found 6/6 markers.
[2024-01-25 18:57:37,338] [INFO] Query marker FASTA was written to GCF_018729455.1_ASM1872945v1_genomic.fna/markers.fasta
[2024-01-25 18:57:37,338] [INFO] Task started: Blastn
[2024-01-25 18:57:37,338] [INFO] Running command: blastn -query GCF_018729455.1_ASM1872945v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06b407be-9af4-428f-b17a-1d9eb59bb32d/dqc_reference/reference_markers.fasta -out GCF_018729455.1_ASM1872945v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:57:38,424] [INFO] Task succeeded: Blastn
[2024-01-25 18:57:38,428] [INFO] Selected 29 target genomes.
[2024-01-25 18:57:38,428] [INFO] Target genome list was writen to GCF_018729455.1_ASM1872945v1_genomic.fna/target_genomes.txt
[2024-01-25 18:57:38,439] [INFO] Task started: fastANI
[2024-01-25 18:57:38,439] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcb93007-c26e-440f-b5e3-0dad2e032b45/GCF_018729455.1_ASM1872945v1_genomic.fna.gz --refList GCF_018729455.1_ASM1872945v1_genomic.fna/target_genomes.txt --output GCF_018729455.1_ASM1872945v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:58:06,628] [INFO] Task succeeded: fastANI
[2024-01-25 18:58:06,629] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06b407be-9af4-428f-b17a-1d9eb59bb32d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:58:06,630] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06b407be-9af4-428f-b17a-1d9eb59bb32d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:58:06,647] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:58:06,647] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:58:06,647] [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
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	78.4038	631	2042	95	below_threshold
Methylobrevis pamukkalensis	strain=PK2	GCA_001720135.1	1439726	1439726	type	True	78.2884	563	2042	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	78.2086	721	2042	95	below_threshold
Phreatobacter cathodiphilus	strain=S-12	GCA_003008515.1	1868589	1868589	type	True	77.9888	543	2042	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	77.9668	469	2042	95	below_threshold
Kaistia granuli	strain=Ko04	GCA_000380505.1	363259	363259	type	True	77.9667	484	2042	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	77.9171	551	2042	95	below_threshold
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	77.9161	534	2042	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	77.882	505	2042	95	below_threshold
Pleomorphomonas koreensis	strain=DSM 23070	GCA_000425185.1	257440	257440	type	True	77.7376	513	2042	95	below_threshold
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	77.7016	495	2042	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	77.6957	552	2042	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	77.6503	522	2042	95	below_threshold
Mesorhizobium composti	strain=CC-YTH430	GCA_004801285.1	2675109	2675109	type	True	77.639	475	2042	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	77.5238	550	2042	95	below_threshold
Pannonibacter carbonis	strain=Q4.6	GCA_003012935.1	2067569	2067569	type	True	77.4953	367	2042	95	below_threshold
Rhodopseudomonas pentothenatexigens	strain=JA575	GCA_003385925.1	999699	999699	type	True	77.4808	475	2042	95	below_threshold
Rhodopseudomonas pentothenatexigens	strain=JA575	GCA_900218015.1	999699	999699	type	True	77.4443	480	2042	95	below_threshold
Ancylobacter aquaticus	strain=DSM 101	GCA_004339465.1	100	100	type	True	77.4312	440	2042	95	below_threshold
Azorhizobium caulinodans	strain=ORS 571	GCA_000010525.1	7	7	type	True	77.4076	445	2042	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	77.2656	661	2042	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	77.2571	295	2042	95	below_threshold
Sinorhizobium fredii	strain=USDA205	GCA_009601405.1	380	380	type	True	77.23	400	2042	95	below_threshold
Sinorhizobium fredii	strain=NBRC 14780	GCA_006539605.1	380	380	type	True	77.2268	398	2042	95	below_threshold
Sinorhizobium fredii	strain=USDA 205	GCA_001461695.1	380	380	type	True	77.1809	396	2042	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	77.1512	498	2042	95	below_threshold
Sinorhizobium meliloti	strain=NBRC 14782	GCA_006539625.1	382	382	type	True	77.0993	343	2042	95	below_threshold
Roseibium aestuarii	strain=SYSU M00256-3	GCA_008477545.1	2600299	2600299	type	True	77.0956	344	2042	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	76.5141	287	2042	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:58:06,648] [INFO] DFAST Taxonomy check result was written to GCF_018729455.1_ASM1872945v1_genomic.fna/tc_result.tsv
[2024-01-25 18:58:06,649] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:58:06,649] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:58:06,649] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06b407be-9af4-428f-b17a-1d9eb59bb32d/dqc_reference/checkm_data
[2024-01-25 18:58:06,650] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:58:06,712] [INFO] Task started: CheckM
[2024-01-25 18:58:06,713] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018729455.1_ASM1872945v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018729455.1_ASM1872945v1_genomic.fna/checkm_input GCF_018729455.1_ASM1872945v1_genomic.fna/checkm_result
[2024-01-25 18:59:03,813] [INFO] Task succeeded: CheckM
[2024-01-25 18:59:03,814] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:59:03,870] [INFO] ===== Completeness check finished =====
[2024-01-25 18:59:03,871] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:59:03,871] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018729455.1_ASM1872945v1_genomic.fna/markers.fasta)
[2024-01-25 18:59:03,871] [INFO] Task started: Blastn
[2024-01-25 18:59:03,871] [INFO] Running command: blastn -query GCF_018729455.1_ASM1872945v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06b407be-9af4-428f-b17a-1d9eb59bb32d/dqc_reference/reference_markers_gtdb.fasta -out GCF_018729455.1_ASM1872945v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:06,252] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:06,255] [INFO] Selected 14 target genomes.
[2024-01-25 18:59:06,255] [INFO] Target genome list was writen to GCF_018729455.1_ASM1872945v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:59:06,264] [INFO] Task started: fastANI
[2024-01-25 18:59:06,264] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcb93007-c26e-440f-b5e3-0dad2e032b45/GCF_018729455.1_ASM1872945v1_genomic.fna.gz --refList GCF_018729455.1_ASM1872945v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018729455.1_ASM1872945v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:59:22,446] [INFO] Task succeeded: fastANI
[2024-01-25 18:59:22,456] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:59:22,456] [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
GCA_018729455.1	s__Prosthecomicrobium_A sp018729455	100.0	2039	2042	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Prosthecomicrobium_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001305515.1	s__Prosthecomicrobium_A hirschii	93.5065	1892	2042	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Prosthecomicrobium_A	95.0	97.89	97.89	0.95	0.95	2	-
GCA_002298965.1	s__Pinisolibacter sp002298965	79.147	541	2042	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Pinisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019160155.1	s__Pinisolibacter aquiterrae	79.0122	707	2042	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Pinisolibacter	95.0	96.46	96.46	0.88	0.88	2	-
GCF_004328075.1	s__Siculibacillus lacustris	78.8119	712	2042	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Siculibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012517025.1	s__Pinisolibacter sp012517025	78.7931	530	2042	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Pinisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793065.1	s__JAEULV01 sp016793065	78.5696	573	2042	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__JAEULV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001927285.1	s__Mongoliimonas terrestris	77.9509	624	2042	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Mongoliimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423225.1	s__Kaistia adipata	77.9341	549	2042	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016629525.1	s__Kaistia sp016629525	77.8523	556	2042	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464235.1	s__Phreatobacter sp001464235	77.7208	487	2042	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526315.1	s__Methylopila sp000526315	77.4778	461	2042	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Methylopila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001461695.1	s__Sinorhizobium fredii	77.1807	396	2042	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	98.55	96.82	0.88	0.82	17	-
GCA_007118805.1	s__SKQW01 sp007118805	76.4855	317	2042	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Tepidamorphaceae;g__SKQW01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:59:22,457] [INFO] GTDB search result was written to GCF_018729455.1_ASM1872945v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:59:22,459] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:59:22,463] [INFO] DFAST_QC result json was written to GCF_018729455.1_ASM1872945v1_genomic.fna/dqc_result.json
[2024-01-25 18:59:22,463] [INFO] DFAST_QC completed!
[2024-01-25 18:59:22,463] [INFO] Total running time: 0h2m2s