[2024-01-25 18:04:05,569] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:04:05,571] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:04:05,571] [INFO] DQC Reference Directory: /var/lib/cwl/stg448e2092-257d-42f8-9962-b655d812687e/dqc_reference
[2024-01-25 18:04:06,753] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:04:06,754] [INFO] Task started: Prodigal
[2024-01-25 18:04:06,754] [INFO] Running command: gunzip -c /var/lib/cwl/stg137a354d-574f-4ce1-a1cc-965cc8c16b86/GCF_003254545.1_ASM325454v1_genomic.fna.gz | prodigal -d GCF_003254545.1_ASM325454v1_genomic.fna/cds.fna -a GCF_003254545.1_ASM325454v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:04:21,341] [INFO] Task succeeded: Prodigal
[2024-01-25 18:04:21,341] [INFO] Task started: HMMsearch
[2024-01-25 18:04:21,341] [INFO] Running command: hmmsearch --tblout GCF_003254545.1_ASM325454v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg448e2092-257d-42f8-9962-b655d812687e/dqc_reference/reference_markers.hmm GCF_003254545.1_ASM325454v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:04:21,604] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:04:21,605] [INFO] Found 6/6 markers.
[2024-01-25 18:04:21,645] [INFO] Query marker FASTA was written to GCF_003254545.1_ASM325454v1_genomic.fna/markers.fasta
[2024-01-25 18:04:21,645] [INFO] Task started: Blastn
[2024-01-25 18:04:21,645] [INFO] Running command: blastn -query GCF_003254545.1_ASM325454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg448e2092-257d-42f8-9962-b655d812687e/dqc_reference/reference_markers.fasta -out GCF_003254545.1_ASM325454v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:04:22,285] [INFO] Task succeeded: Blastn
[2024-01-25 18:04:22,288] [INFO] Selected 15 target genomes.
[2024-01-25 18:04:22,288] [INFO] Target genome list was writen to GCF_003254545.1_ASM325454v1_genomic.fna/target_genomes.txt
[2024-01-25 18:04:22,294] [INFO] Task started: fastANI
[2024-01-25 18:04:22,294] [INFO] Running command: fastANI --query /var/lib/cwl/stg137a354d-574f-4ce1-a1cc-965cc8c16b86/GCF_003254545.1_ASM325454v1_genomic.fna.gz --refList GCF_003254545.1_ASM325454v1_genomic.fna/target_genomes.txt --output GCF_003254545.1_ASM325454v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:04:40,408] [INFO] Task succeeded: fastANI
[2024-01-25 18:04:40,408] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg448e2092-257d-42f8-9962-b655d812687e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:04:40,408] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg448e2092-257d-42f8-9962-b655d812687e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:04:40,420] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:04:40,420] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:04:40,421] [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
Flavobacterium tistrianum	strain=GB 56.1	GCA_003254545.1	1685414	1685414	type	True	100.0	1664	1665	95	conclusive
Flavobacterium sharifuzzamanii	strain=A7.6	GCA_003254585.1	2211133	2211133	type	True	91.1031	1438	1665	95	below_threshold
Flavobacterium nitrogenifigens	strain=NXU-44	GCA_003254565.1	1617283	1617283	type	True	90.7972	1368	1665	95	below_threshold
Flavobacterium nitrogenifigens	strain=DSM 29982	GCA_900182675.1	1617283	1617283	type	True	90.7743	1385	1665	95	below_threshold
Flavobacterium anhuiense	strain=CGMCC 1.6859	GCA_900101855.1	459526	459526	suspected-type	True	90.2087	1385	1665	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	88.2435	1327	1665	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	85.6494	1172	1665	95	below_threshold
Flavobacterium phragmitis	strain=CGMCC 1.10370	GCA_900112575.1	739143	739143	type	True	85.6419	1236	1665	95	below_threshold
Flavobacterium quisquiliarum	strain=EA-12	GCA_019308285.1	1834436	1834436	type	True	85.4147	1196	1665	95	below_threshold
Flavobacterium crocinum	strain=HYN0056	GCA_003122385.1	2183896	2183896	type	True	85.349	1221	1665	95	below_threshold
Flavobacterium zhairuonense	strain=A5.7	GCA_004352915.1	2493631	2493631	type	True	84.0013	1079	1665	95	below_threshold
Flavobacterium denitrificans	strain=DSM 15936	GCA_000425445.1	281361	281361	type	True	83.6782	1043	1665	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	83.6194	1157	1665	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	83.4741	1064	1665	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	77.2428	175	1665	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:04:40,427] [INFO] DFAST Taxonomy check result was written to GCF_003254545.1_ASM325454v1_genomic.fna/tc_result.tsv
[2024-01-25 18:04:40,428] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:04:40,428] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:04:40,428] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg448e2092-257d-42f8-9962-b655d812687e/dqc_reference/checkm_data
[2024-01-25 18:04:40,429] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:04:40,492] [INFO] Task started: CheckM
[2024-01-25 18:04:40,493] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003254545.1_ASM325454v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003254545.1_ASM325454v1_genomic.fna/checkm_input GCF_003254545.1_ASM325454v1_genomic.fna/checkm_result
[2024-01-25 18:05:23,872] [INFO] Task succeeded: CheckM
[2024-01-25 18:05:23,874] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:05:23,902] [INFO] ===== Completeness check finished =====
[2024-01-25 18:05:23,902] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:05:23,902] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003254545.1_ASM325454v1_genomic.fna/markers.fasta)
[2024-01-25 18:05:23,903] [INFO] Task started: Blastn
[2024-01-25 18:05:23,903] [INFO] Running command: blastn -query GCF_003254545.1_ASM325454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg448e2092-257d-42f8-9962-b655d812687e/dqc_reference/reference_markers_gtdb.fasta -out GCF_003254545.1_ASM325454v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:05:24,845] [INFO] Task succeeded: Blastn
[2024-01-25 18:05:24,848] [INFO] Selected 15 target genomes.
[2024-01-25 18:05:24,849] [INFO] Target genome list was writen to GCF_003254545.1_ASM325454v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:05:24,858] [INFO] Task started: fastANI
[2024-01-25 18:05:24,858] [INFO] Running command: fastANI --query /var/lib/cwl/stg137a354d-574f-4ce1-a1cc-965cc8c16b86/GCF_003254545.1_ASM325454v1_genomic.fna.gz --refList GCF_003254545.1_ASM325454v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003254545.1_ASM325454v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:05:44,550] [INFO] Task succeeded: fastANI
[2024-01-25 18:05:44,559] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:05:44,559] [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_003254545.1	s__Flavobacterium tistrianum	100.0	1664	1665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003254585.1	s__Flavobacterium sharifuzzamanii	91.1052	1438	1665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254565.1	s__Flavobacterium nitrogenifigens	90.809	1367	1665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_004151235.1	s__Flavobacterium anhuiense_A	90.4759	1424	1665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016735615.1	s__Flavobacterium sp016735615	90.3807	1370	1665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101855.1	s__Flavobacterium anhuiense	90.2087	1385	1665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.61	97.43	0.90	0.88	4	-
GCF_009826975.1	s__Flavobacterium sp009826975	90.0991	1369	1665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013388355.1	s__Flavobacterium sp013388355	89.4889	1001	1665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016405855.1	s__Flavobacterium sp002399805	88.0193	1350	1665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.61	96.61	0.90	0.90	2	-
GCA_017744675.1	s__Flavobacterium sp017744675	87.7615	1364	1665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207905.1	s__Flavobacterium notoginsengisoli	85.6994	1217	1665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900112575.1	s__Flavobacterium phragmitis	85.6492	1235	1665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003122385.1	s__Flavobacterium crocinum	85.3473	1221	1665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004352915.1	s__Flavobacterium zhairuonense	84.0102	1078	1665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425445.1	s__Flavobacterium denitrificans	83.6608	1045	1665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:05:44,561] [INFO] GTDB search result was written to GCF_003254545.1_ASM325454v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:05:44,561] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:05:44,565] [INFO] DFAST_QC result json was written to GCF_003254545.1_ASM325454v1_genomic.fna/dqc_result.json
[2024-01-25 18:05:44,565] [INFO] DFAST_QC completed!
[2024-01-25 18:05:44,565] [INFO] Total running time: 0h1m39s