[2024-01-25 19:48:50,720] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:48:50,721] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:48:50,721] [INFO] DQC Reference Directory: /var/lib/cwl/stg67c2b833-c443-4910-968e-4e33f24f8606/dqc_reference
[2024-01-25 19:48:51,890] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:48:51,891] [INFO] Task started: Prodigal
[2024-01-25 19:48:51,891] [INFO] Running command: gunzip -c /var/lib/cwl/stged76da3d-2ec4-49ae-8072-dbe7ab281312/GCF_026870175.2_ASM2687017v2_genomic.fna.gz | prodigal -d GCF_026870175.2_ASM2687017v2_genomic.fna/cds.fna -a GCF_026870175.2_ASM2687017v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:49:05,703] [INFO] Task succeeded: Prodigal
[2024-01-25 19:49:05,703] [INFO] Task started: HMMsearch
[2024-01-25 19:49:05,703] [INFO] Running command: hmmsearch --tblout GCF_026870175.2_ASM2687017v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67c2b833-c443-4910-968e-4e33f24f8606/dqc_reference/reference_markers.hmm GCF_026870175.2_ASM2687017v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:49:05,976] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:49:05,977] [INFO] Found 6/6 markers.
[2024-01-25 19:49:06,013] [INFO] Query marker FASTA was written to GCF_026870175.2_ASM2687017v2_genomic.fna/markers.fasta
[2024-01-25 19:49:06,013] [INFO] Task started: Blastn
[2024-01-25 19:49:06,013] [INFO] Running command: blastn -query GCF_026870175.2_ASM2687017v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg67c2b833-c443-4910-968e-4e33f24f8606/dqc_reference/reference_markers.fasta -out GCF_026870175.2_ASM2687017v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:49:06,677] [INFO] Task succeeded: Blastn
[2024-01-25 19:49:06,680] [INFO] Selected 22 target genomes.
[2024-01-25 19:49:06,680] [INFO] Target genome list was writen to GCF_026870175.2_ASM2687017v2_genomic.fna/target_genomes.txt
[2024-01-25 19:49:06,693] [INFO] Task started: fastANI
[2024-01-25 19:49:06,693] [INFO] Running command: fastANI --query /var/lib/cwl/stged76da3d-2ec4-49ae-8072-dbe7ab281312/GCF_026870175.2_ASM2687017v2_genomic.fna.gz --refList GCF_026870175.2_ASM2687017v2_genomic.fna/target_genomes.txt --output GCF_026870175.2_ASM2687017v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:49:23,639] [INFO] Task succeeded: fastANI
[2024-01-25 19:49:23,640] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67c2b833-c443-4910-968e-4e33f24f8606/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:49:23,640] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67c2b833-c443-4910-968e-4e33f24f8606/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:49:23,651] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:49:23,651] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:49:23,651] [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 laiguense	strain=LB2P30	GCA_003097655.1	2169409	2169409	type	True	84.4545	861	1526	95	below_threshold
Flavobacterium aquariorum	strain=IMCC34762	GCA_003254745.1	2217670	2217670	type	True	82.1187	816	1526	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	81.8408	774	1526	95	below_threshold
Flavobacterium gilvum	strain=EM1308	GCA_001761465.1	1492737	1492737	type	True	80.8099	631	1526	95	below_threshold
Flavobacterium gilvum	strain=EM1308	GCA_000735535.1	1492737	1492737	type	True	80.5427	600	1526	95	below_threshold
Flavobacterium aquicola	strain=DSM 100880	GCA_003385115.1	1682742	1682742	type	True	80.4965	663	1526	95	below_threshold
Flavobacterium psychrolimnae	strain=LMG 22018	GCA_003312425.1	249351	249351	type	True	79.1621	424	1526	95	below_threshold
Flavobacterium gawalongense	strain=GSP16	GCA_007097265.1	2594432	2594432	type	True	79.1482	472	1526	95	below_threshold
Flavobacterium sandaracinum	strain=LB-D12	GCA_004349135.1	2541733	2541733	type	True	78.9176	417	1526	95	below_threshold
Flavobacterium muglaense	strain=F-60	GCA_014305155.1	2764716	2764716	type	True	78.8893	361	1526	95	below_threshold
Flavobacterium piscis	strain=CCUG 60099	GCA_002222045.1	1114874	1114874	type	True	78.8821	424	1526	95	below_threshold
Flavobacterium urumqiense	strain=CGMCC 1.9230	GCA_900108015.1	935224	935224	type	True	78.8629	453	1526	95	below_threshold
Flavobacterium piscis	strain=CCUG 60099	GCA_001686925.1	1114874	1114874	type	True	78.8386	433	1526	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	78.7563	411	1526	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	78.6496	415	1526	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	78.5778	407	1526	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	78.4924	425	1526	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:49:23,652] [INFO] DFAST Taxonomy check result was written to GCF_026870175.2_ASM2687017v2_genomic.fna/tc_result.tsv
[2024-01-25 19:49:23,653] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:49:23,653] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:49:23,653] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67c2b833-c443-4910-968e-4e33f24f8606/dqc_reference/checkm_data
[2024-01-25 19:49:23,654] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:49:23,700] [INFO] Task started: CheckM
[2024-01-25 19:49:23,700] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026870175.2_ASM2687017v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026870175.2_ASM2687017v2_genomic.fna/checkm_input GCF_026870175.2_ASM2687017v2_genomic.fna/checkm_result
[2024-01-25 19:50:06,919] [INFO] Task succeeded: CheckM
[2024-01-25 19:50:06,920] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:50:06,944] [INFO] ===== Completeness check finished =====
[2024-01-25 19:50:06,945] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:50:06,946] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026870175.2_ASM2687017v2_genomic.fna/markers.fasta)
[2024-01-25 19:50:06,946] [INFO] Task started: Blastn
[2024-01-25 19:50:06,946] [INFO] Running command: blastn -query GCF_026870175.2_ASM2687017v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg67c2b833-c443-4910-968e-4e33f24f8606/dqc_reference/reference_markers_gtdb.fasta -out GCF_026870175.2_ASM2687017v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:50:08,014] [INFO] Task succeeded: Blastn
[2024-01-25 19:50:08,017] [INFO] Selected 18 target genomes.
[2024-01-25 19:50:08,017] [INFO] Target genome list was writen to GCF_026870175.2_ASM2687017v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:50:08,043] [INFO] Task started: fastANI
[2024-01-25 19:50:08,043] [INFO] Running command: fastANI --query /var/lib/cwl/stged76da3d-2ec4-49ae-8072-dbe7ab281312/GCF_026870175.2_ASM2687017v2_genomic.fna.gz --refList GCF_026870175.2_ASM2687017v2_genomic.fna/target_genomes_gtdb.txt --output GCF_026870175.2_ASM2687017v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:50:23,705] [INFO] Task succeeded: fastANI
[2024-01-25 19:50:23,715] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:50:23,715] [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_003097655.1	s__Flavobacterium laiguense	84.4544	861	1526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097385.1	s__Flavobacterium sp007097385	83.9923	974	1526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013284035.1	s__Flavobacterium sp003096795	82.3251	823	1526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.66	97.66	0.93	0.93	2	-
GCF_003254745.1	s__Flavobacterium aquariorum	82.1276	815	1526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002001005.1	s__Flavobacterium sp002001005	81.8476	738	1526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797935.1	s__Flavobacterium sp002797935	81.1567	739	1526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813295.1	s__Flavobacterium sp002813295	81.0573	702	1526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001761465.1	s__Flavobacterium gilvum	80.7432	632	1526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003385115.1	s__Flavobacterium aquicola	80.4941	665	1526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015351475.1	s__Flavobacterium sp015351475	80.1505	666	1526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003312425.1	s__Flavobacterium psychrolimnae	79.1678	423	1526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349135.1	s__Flavobacterium sandaracinum	78.9166	417	1526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001027725.1	s__Flavobacterium sp001027725	78.8919	406	1526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009664855.1	s__Flavobacterium sp009664855	78.5917	440	1526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.90	98.90	0.89	0.89	2	-
GCF_004303025.1	s__Flavobacterium sp004303025	77.0686	207	1526	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 19:50:23,717] [INFO] GTDB search result was written to GCF_026870175.2_ASM2687017v2_genomic.fna/result_gtdb.tsv
[2024-01-25 19:50:23,718] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:50:23,721] [INFO] DFAST_QC result json was written to GCF_026870175.2_ASM2687017v2_genomic.fna/dqc_result.json
[2024-01-25 19:50:23,721] [INFO] DFAST_QC completed!
[2024-01-25 19:50:23,722] [INFO] Total running time: 0h1m33s