[2024-01-24 15:27:20,829] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:20,830] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:20,831] [INFO] DQC Reference Directory: /var/lib/cwl/stg6fe8b554-0aee-4867-8dac-9a8a178f5e1a/dqc_reference
[2024-01-24 15:27:23,291] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:23,293] [INFO] Task started: Prodigal
[2024-01-24 15:27:23,293] [INFO] Running command: gunzip -c /var/lib/cwl/stg281fccab-0068-4e5b-8f8d-423faff25758/GCF_003254565.1_ASM325456v1_genomic.fna.gz | prodigal -d GCF_003254565.1_ASM325456v1_genomic.fna/cds.fna -a GCF_003254565.1_ASM325456v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:41,750] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:41,750] [INFO] Task started: HMMsearch
[2024-01-24 15:27:41,750] [INFO] Running command: hmmsearch --tblout GCF_003254565.1_ASM325456v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6fe8b554-0aee-4867-8dac-9a8a178f5e1a/dqc_reference/reference_markers.hmm GCF_003254565.1_ASM325456v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:42,045] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:42,046] [INFO] Found 6/6 markers.
[2024-01-24 15:27:42,100] [INFO] Query marker FASTA was written to GCF_003254565.1_ASM325456v1_genomic.fna/markers.fasta
[2024-01-24 15:27:42,101] [INFO] Task started: Blastn
[2024-01-24 15:27:42,101] [INFO] Running command: blastn -query GCF_003254565.1_ASM325456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fe8b554-0aee-4867-8dac-9a8a178f5e1a/dqc_reference/reference_markers.fasta -out GCF_003254565.1_ASM325456v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:42,784] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:42,788] [INFO] Selected 16 target genomes.
[2024-01-24 15:27:42,789] [INFO] Target genome list was writen to GCF_003254565.1_ASM325456v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:42,822] [INFO] Task started: fastANI
[2024-01-24 15:27:42,822] [INFO] Running command: fastANI --query /var/lib/cwl/stg281fccab-0068-4e5b-8f8d-423faff25758/GCF_003254565.1_ASM325456v1_genomic.fna.gz --refList GCF_003254565.1_ASM325456v1_genomic.fna/target_genomes.txt --output GCF_003254565.1_ASM325456v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:28:07,030] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:07,030] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6fe8b554-0aee-4867-8dac-9a8a178f5e1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:28:07,031] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6fe8b554-0aee-4867-8dac-9a8a178f5e1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:28:07,045] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:28:07,045] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:28:07,046] [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 nitrogenifigens	strain=NXU-44	GCA_003254565.1	1617283	1617283	type	True	100.0	1766	1769	95	conclusive
Flavobacterium nitrogenifigens	strain=DSM 29982	GCA_900182675.1	1617283	1617283	type	True	99.9991	1769	1769	95	conclusive
Flavobacterium sharifuzzamanii	strain=A7.6	GCA_003254585.1	2211133	2211133	type	True	92.0952	1413	1769	95	below_threshold
Flavobacterium tistrianum	strain=GB 56.1	GCA_003254545.1	1685414	1685414	type	True	90.727	1390	1769	95	below_threshold
Flavobacterium anhuiense	strain=CGMCC 1.6859	GCA_900101855.1	459526	459526	suspected-type	True	89.3961	1397	1769	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	88.4758	1347	1769	95	below_threshold
Flavobacterium phragmitis	strain=CGMCC 1.10370	GCA_900112575.1	739143	739143	type	True	85.5975	1258	1769	95	below_threshold
Flavobacterium crocinum	strain=HYN0056	GCA_003122385.1	2183896	2183896	type	True	85.4751	1232	1769	95	below_threshold
Flavobacterium quisquiliarum	strain=EA-12	GCA_019308285.1	1834436	1834436	type	True	85.3997	1216	1769	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	85.3987	1241	1769	95	below_threshold
Flavobacterium johnsoniae	strain=ATCC 17061	GCA_002221975.1	986	986	type	True	84.2948	1180	1769	95	below_threshold
Flavobacterium zhairuonense	strain=A5.7	GCA_004352915.1	2493631	2493631	type	True	84.1156	1095	1769	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	83.7446	1149	1769	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	83.6304	1082	1769	95	below_threshold
Flavobacterium foetidum	strain=JCM 32085	GCA_004634245.1	2026681	2026681	type	True	83.5967	1046	1769	95	below_threshold
Flavobacterium davisii	strain=90-106	GCA_019565505.1	2906077	2906077	type	True	76.7192	143	1769	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:28:07,047] [INFO] DFAST Taxonomy check result was written to GCF_003254565.1_ASM325456v1_genomic.fna/tc_result.tsv
[2024-01-24 15:28:07,048] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:28:07,048] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:28:07,049] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6fe8b554-0aee-4867-8dac-9a8a178f5e1a/dqc_reference/checkm_data
[2024-01-24 15:28:07,050] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:28:07,113] [INFO] Task started: CheckM
[2024-01-24 15:28:07,113] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003254565.1_ASM325456v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003254565.1_ASM325456v1_genomic.fna/checkm_input GCF_003254565.1_ASM325456v1_genomic.fna/checkm_result
[2024-01-24 15:29:02,378] [INFO] Task succeeded: CheckM
[2024-01-24 15:29:02,380] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:29:02,400] [INFO] ===== Completeness check finished =====
[2024-01-24 15:29:02,400] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:29:02,401] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003254565.1_ASM325456v1_genomic.fna/markers.fasta)
[2024-01-24 15:29:02,401] [INFO] Task started: Blastn
[2024-01-24 15:29:02,401] [INFO] Running command: blastn -query GCF_003254565.1_ASM325456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fe8b554-0aee-4867-8dac-9a8a178f5e1a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003254565.1_ASM325456v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:29:03,372] [INFO] Task succeeded: Blastn
[2024-01-24 15:29:03,378] [INFO] Selected 14 target genomes.
[2024-01-24 15:29:03,378] [INFO] Target genome list was writen to GCF_003254565.1_ASM325456v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:29:03,389] [INFO] Task started: fastANI
[2024-01-24 15:29:03,390] [INFO] Running command: fastANI --query /var/lib/cwl/stg281fccab-0068-4e5b-8f8d-423faff25758/GCF_003254565.1_ASM325456v1_genomic.fna.gz --refList GCF_003254565.1_ASM325456v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003254565.1_ASM325456v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:29:21,696] [INFO] Task succeeded: fastANI
[2024-01-24 15:29:21,728] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:29:21,729] [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_003254565.1	s__Flavobacterium nitrogenifigens	100.0	1766	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_003254585.1	s__Flavobacterium sharifuzzamanii	92.0923	1414	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254545.1	s__Flavobacterium tistrianum	90.7153	1391	1769	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	90.603	1382	1769	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	90.0149	987	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004151235.1	s__Flavobacterium anhuiense_A	89.9545	1406	1769	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	89.4068	1396	1769	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	89.3339	1397	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002303885.1	s__Flavobacterium sp002303885	88.5732	1335	1769	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	88.482	1352	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.61	96.61	0.90	0.90	2	-
GCF_003254625.1	s__Flavobacterium ginsenosidimutans	87.6982	1312	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112575.1	s__Flavobacterium phragmitis	85.597	1258	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016645.1	s__Flavobacterium johnsoniae	84.4109	1185	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.23	96.72	0.94	0.86	7	-
GCF_004352915.1	s__Flavobacterium zhairuonense	84.1245	1094	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:29:21,733] [INFO] GTDB search result was written to GCF_003254565.1_ASM325456v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:29:21,734] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:29:21,740] [INFO] DFAST_QC result json was written to GCF_003254565.1_ASM325456v1_genomic.fna/dqc_result.json
[2024-01-24 15:29:21,741] [INFO] DFAST_QC completed!
[2024-01-24 15:29:21,741] [INFO] Total running time: 0h2m1s