[2024-01-25 19:34:50,842] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:34:50,844] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:34:50,844] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0691a84-3815-448b-9b02-8ec384a32310/dqc_reference
[2024-01-25 19:34:51,961] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:34:51,962] [INFO] Task started: Prodigal
[2024-01-25 19:34:51,962] [INFO] Running command: gunzip -c /var/lib/cwl/stgf88a980d-d3c3-4ea5-8b51-f8b7d72f78c6/GCF_003403015.1_ASM340301v1_genomic.fna.gz | prodigal -d GCF_003403015.1_ASM340301v1_genomic.fna/cds.fna -a GCF_003403015.1_ASM340301v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:35:02,353] [INFO] Task succeeded: Prodigal
[2024-01-25 19:35:02,353] [INFO] Task started: HMMsearch
[2024-01-25 19:35:02,353] [INFO] Running command: hmmsearch --tblout GCF_003403015.1_ASM340301v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0691a84-3815-448b-9b02-8ec384a32310/dqc_reference/reference_markers.hmm GCF_003403015.1_ASM340301v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:35:02,573] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:35:02,574] [INFO] Found 6/6 markers.
[2024-01-25 19:35:02,609] [INFO] Query marker FASTA was written to GCF_003403015.1_ASM340301v1_genomic.fna/markers.fasta
[2024-01-25 19:35:02,609] [INFO] Task started: Blastn
[2024-01-25 19:35:02,609] [INFO] Running command: blastn -query GCF_003403015.1_ASM340301v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0691a84-3815-448b-9b02-8ec384a32310/dqc_reference/reference_markers.fasta -out GCF_003403015.1_ASM340301v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:35:03,538] [INFO] Task succeeded: Blastn
[2024-01-25 19:35:03,542] [INFO] Selected 18 target genomes.
[2024-01-25 19:35:03,542] [INFO] Target genome list was writen to GCF_003403015.1_ASM340301v1_genomic.fna/target_genomes.txt
[2024-01-25 19:35:03,550] [INFO] Task started: fastANI
[2024-01-25 19:35:03,550] [INFO] Running command: fastANI --query /var/lib/cwl/stgf88a980d-d3c3-4ea5-8b51-f8b7d72f78c6/GCF_003403015.1_ASM340301v1_genomic.fna.gz --refList GCF_003403015.1_ASM340301v1_genomic.fna/target_genomes.txt --output GCF_003403015.1_ASM340301v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:35:19,018] [INFO] Task succeeded: fastANI
[2024-01-25 19:35:19,018] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0691a84-3815-448b-9b02-8ec384a32310/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:35:19,018] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0691a84-3815-448b-9b02-8ec384a32310/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:35:19,029] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:35:19,029] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:35:19,029] [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
Fulvimarina endophytica	strain=85	GCA_003403015.1	2293836	2293836	type	True	100.0	1440	1442	95	conclusive
Fulvimarina pelagi	strain=HTCC2506	GCA_000153705.1	217511	217511	type	True	79.8184	617	1442	95	below_threshold
Fulvimarina pelagi	strain=DSM 15513	GCA_001463845.1	217511	217511	type	True	79.7625	618	1442	95	below_threshold
Jiella endophytica	strain=CBS5Q-3	GCA_004519335.1	2558362	2558362	type	True	79.4783	615	1442	95	below_threshold
Aurantimonas manganoxydans	strain=SI85-9A1	GCA_000153465.1	651183	651183	type	True	79.429	575	1442	95	below_threshold
Aurantimonas manganoxydans	strain=DSM 21871	GCA_001463865.1	651183	651183	type	True	79.3909	574	1442	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	79.245	559	1442	95	below_threshold
Aurantimonas aggregata	strain=KCTC 52919	GCA_010500835.1	2047720	2047720	type	True	79.236	556	1442	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	79.2209	635	1442	95	below_threshold
Aurantimonas endophytica	strain=DSM 103570	GCA_014196845.1	1522175	1522175	type	True	79.2207	563	1442	95	below_threshold
Jiella pacifica	strain=40Bstr34	GCA_010500815.1	2696469	2696469	type	True	79.1565	601	1442	95	below_threshold
Aurantimonas marina	strain=SW136	GCA_017183135.1	2780508	2780508	type	True	78.4043	439	1442	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	77.9214	377	1442	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	77.3664	303	1442	95	below_threshold
Pelagovum pacificum	strain=SM1903	GCA_006363825.1	2588711	2588711	type	True	76.5079	129	1442	95	below_threshold
Sinirhodobacter ferrireducens	strain=CCTCC AB2012026	GCA_004022265.1	1215032	1215032	type	True	76.4476	169	1442	95	below_threshold
Sinirhodobacter hankyongi	strain=BO-81	GCA_003664585.1	2294033	2294033	type	True	76.4463	171	1442	95	below_threshold
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	76.0691	124	1442	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:35:19,033] [INFO] DFAST Taxonomy check result was written to GCF_003403015.1_ASM340301v1_genomic.fna/tc_result.tsv
[2024-01-25 19:35:19,033] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:35:19,033] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:35:19,033] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0691a84-3815-448b-9b02-8ec384a32310/dqc_reference/checkm_data
[2024-01-25 19:35:19,034] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:35:19,081] [INFO] Task started: CheckM
[2024-01-25 19:35:19,081] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003403015.1_ASM340301v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003403015.1_ASM340301v1_genomic.fna/checkm_input GCF_003403015.1_ASM340301v1_genomic.fna/checkm_result
[2024-01-25 19:35:53,955] [INFO] Task succeeded: CheckM
[2024-01-25 19:35:53,956] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:35:53,979] [INFO] ===== Completeness check finished =====
[2024-01-25 19:35:53,979] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:35:53,980] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003403015.1_ASM340301v1_genomic.fna/markers.fasta)
[2024-01-25 19:35:53,980] [INFO] Task started: Blastn
[2024-01-25 19:35:53,980] [INFO] Running command: blastn -query GCF_003403015.1_ASM340301v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0691a84-3815-448b-9b02-8ec384a32310/dqc_reference/reference_markers_gtdb.fasta -out GCF_003403015.1_ASM340301v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:35:55,978] [INFO] Task succeeded: Blastn
[2024-01-25 19:35:55,981] [INFO] Selected 13 target genomes.
[2024-01-25 19:35:55,982] [INFO] Target genome list was writen to GCF_003403015.1_ASM340301v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:35:55,990] [INFO] Task started: fastANI
[2024-01-25 19:35:55,990] [INFO] Running command: fastANI --query /var/lib/cwl/stgf88a980d-d3c3-4ea5-8b51-f8b7d72f78c6/GCF_003403015.1_ASM340301v1_genomic.fna.gz --refList GCF_003403015.1_ASM340301v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003403015.1_ASM340301v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:36:08,058] [INFO] Task succeeded: fastANI
[2024-01-25 19:36:08,067] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:36:08,067] [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_003403015.1	s__Fulvimarina endophytica	100.0	1440	1442	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Fulvimarina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000153705.1	s__Fulvimarina pelagi	79.8184	617	1442	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Fulvimarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900176465.1	s__Fulvimarina manganoxydans	79.5905	631	1442	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Fulvimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004519335.1	s__Jiella endophytica	79.4629	618	1442	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002088275.1	s__Jiella sp002088275	79.4565	639	1442	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153465.1	s__Aurantimonas manganoxydans	79.4218	576	1442	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.4342	99.99	99.99	1.00	1.00	2	-
GCA_002700095.1	s__Jiella sp002700095	79.3157	601	1442	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017353515.1	s__Jiella sp017353515	79.2475	631	1442	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196845.1	s__Aurantimonas endophytica	79.2244	565	1442	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500835.1	s__Aurantimonas aggregata	79.2109	559	1442	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500815.1	s__Jiella pacifica	79.1584	599	1442	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008271655.1	s__Gemmobacter caeruleus	76.0563	125	1442	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002452815.1	s__UBA6796 sp002452815	75.8026	89	1442	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA6796	95.0	97.98	97.98	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:36:08,069] [INFO] GTDB search result was written to GCF_003403015.1_ASM340301v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:36:08,069] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:36:08,072] [INFO] DFAST_QC result json was written to GCF_003403015.1_ASM340301v1_genomic.fna/dqc_result.json
[2024-01-25 19:36:08,073] [INFO] DFAST_QC completed!
[2024-01-25 19:36:08,073] [INFO] Total running time: 0h1m17s