[2024-01-24 13:22:02,196] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:02,198] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:02,198] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d05bccb-f282-4906-91d9-03fa2a06d21e/dqc_reference
[2024-01-24 13:22:03,522] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:03,523] [INFO] Task started: Prodigal
[2024-01-24 13:22:03,523] [INFO] Running command: gunzip -c /var/lib/cwl/stge8f698c6-27e1-407a-b4a6-3872f180469b/GCF_019160155.1_ASM1916015v1_genomic.fna.gz | prodigal -d GCF_019160155.1_ASM1916015v1_genomic.fna/cds.fna -a GCF_019160155.1_ASM1916015v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:16,950] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:16,950] [INFO] Task started: HMMsearch
[2024-01-24 13:22:16,951] [INFO] Running command: hmmsearch --tblout GCF_019160155.1_ASM1916015v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d05bccb-f282-4906-91d9-03fa2a06d21e/dqc_reference/reference_markers.hmm GCF_019160155.1_ASM1916015v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:17,245] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:17,247] [INFO] Found 6/6 markers.
[2024-01-24 13:22:17,294] [INFO] Query marker FASTA was written to GCF_019160155.1_ASM1916015v1_genomic.fna/markers.fasta
[2024-01-24 13:22:17,295] [INFO] Task started: Blastn
[2024-01-24 13:22:17,295] [INFO] Running command: blastn -query GCF_019160155.1_ASM1916015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d05bccb-f282-4906-91d9-03fa2a06d21e/dqc_reference/reference_markers.fasta -out GCF_019160155.1_ASM1916015v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:18,442] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:18,445] [INFO] Selected 27 target genomes.
[2024-01-24 13:22:18,446] [INFO] Target genome list was writen to GCF_019160155.1_ASM1916015v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:18,502] [INFO] Task started: fastANI
[2024-01-24 13:22:18,503] [INFO] Running command: fastANI --query /var/lib/cwl/stge8f698c6-27e1-407a-b4a6-3872f180469b/GCF_019160155.1_ASM1916015v1_genomic.fna.gz --refList GCF_019160155.1_ASM1916015v1_genomic.fna/target_genomes.txt --output GCF_019160155.1_ASM1916015v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:45,592] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:45,593] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d05bccb-f282-4906-91d9-03fa2a06d21e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:45,593] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d05bccb-f282-4906-91d9-03fa2a06d21e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:45,614] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:22:45,614] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:22:45,615] [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
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	78.5478	558	1608	95	below_threshold
Methylobrevis pamukkalensis	strain=PK2	GCA_001720135.1	1439726	1439726	type	True	78.4325	477	1608	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	78.2676	674	1608	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	78.1477	556	1608	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	78.0058	456	1608	95	below_threshold
Phreatobacter cathodiphilus	strain=S-12	GCA_003008515.1	1868589	1868589	type	True	77.7928	505	1608	95	below_threshold
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	77.7603	463	1608	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	77.7567	461	1608	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_003258835.1	34017	34017	type	True	77.7336	487	1608	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	77.7335	430	1608	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	77.6298	352	1608	95	below_threshold
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	77.5473	447	1608	95	below_threshold
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	77.472	410	1608	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	77.4617	479	1608	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	77.4604	438	1608	95	below_threshold
Pannonibacter phragmitetus	strain=NCTC13350	GCA_900454465.1	121719	121719	suspected-type	True	77.4195	276	1608	95	below_threshold
Azorhizobium caulinodans	strain=ORS 571	GCA_000010525.1	7	7	type	True	77.3234	386	1608	95	below_threshold
Pannonibacter phragmitetus	strain=DSM 14782	GCA_000382365.1	121719	121719	suspected-type	True	77.304	276	1608	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	77.2064	407	1608	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	77.1941	582	1608	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	77.1691	573	1608	95	below_threshold
Shinella zoogloeoides	strain=DSM 287	GCA_009826855.1	352475	352475	type	True	77.1151	350	1608	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	77.1082	574	1608	95	below_threshold
Ancylobacter aquaticus	strain=DSM 101	GCA_004339465.1	100	100	type	True	77.0892	385	1608	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	76.9937	415	1608	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	76.9545	502	1608	95	below_threshold
Lichenibacterium minor	strain=RmlP026	GCA_004137685.1	2316528	2316528	type	True	76.6595	410	1608	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:45,616] [INFO] DFAST Taxonomy check result was written to GCF_019160155.1_ASM1916015v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:45,617] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:45,617] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:45,617] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d05bccb-f282-4906-91d9-03fa2a06d21e/dqc_reference/checkm_data
[2024-01-24 13:22:45,618] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:45,675] [INFO] Task started: CheckM
[2024-01-24 13:22:45,675] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019160155.1_ASM1916015v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019160155.1_ASM1916015v1_genomic.fna/checkm_input GCF_019160155.1_ASM1916015v1_genomic.fna/checkm_result
[2024-01-24 13:23:54,950] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:54,957] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:54,981] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:54,981] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:54,981] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019160155.1_ASM1916015v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:54,982] [INFO] Task started: Blastn
[2024-01-24 13:23:54,982] [INFO] Running command: blastn -query GCF_019160155.1_ASM1916015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d05bccb-f282-4906-91d9-03fa2a06d21e/dqc_reference/reference_markers_gtdb.fasta -out GCF_019160155.1_ASM1916015v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:57,139] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:57,143] [INFO] Selected 7 target genomes.
[2024-01-24 13:23:57,143] [INFO] Target genome list was writen to GCF_019160155.1_ASM1916015v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:57,159] [INFO] Task started: fastANI
[2024-01-24 13:23:57,160] [INFO] Running command: fastANI --query /var/lib/cwl/stge8f698c6-27e1-407a-b4a6-3872f180469b/GCF_019160155.1_ASM1916015v1_genomic.fna.gz --refList GCF_019160155.1_ASM1916015v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019160155.1_ASM1916015v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:06,347] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:06,354] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:06,355] [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_019160155.1	s__Pinisolibacter aquiterrae	100.0	1608	1608	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Pinisolibacter	95.0	96.46	96.46	0.88	0.88	2	conclusive
GCA_012517025.1	s__Pinisolibacter sp012517025	85.5065	794	1608	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Pinisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002298965.1	s__Pinisolibacter sp002298965	85.0942	769	1608	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Pinisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004328075.1	s__Siculibacillus lacustris	82.0769	901	1608	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Siculibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018729455.1	s__Prosthecomicrobium_A sp018729455	79.0436	709	1608	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Prosthecomicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001305515.1	s__Prosthecomicrobium_A hirschii	79.0204	737	1608	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Prosthecomicrobium_A	95.0	97.89	97.89	0.95	0.95	2	-
GCF_014199915.1	s__Prosthecomicrobium pneumaticum	77.6327	532	1608	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Prosthecomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:06,357] [INFO] GTDB search result was written to GCF_019160155.1_ASM1916015v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:06,357] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:06,363] [INFO] DFAST_QC result json was written to GCF_019160155.1_ASM1916015v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:06,363] [INFO] DFAST_QC completed!
[2024-01-24 13:24:06,363] [INFO] Total running time: 0h2m4s