[2023-06-19 09:52:27,110] [INFO] DFAST_QC pipeline started.
[2023-06-19 09:52:27,113] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 09:52:27,113] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0cafc5d-e816-4c80-afd4-7ceefde94cf2/dqc_reference
[2023-06-19 09:52:28,446] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 09:52:28,447] [INFO] Task started: Prodigal
[2023-06-19 09:52:28,447] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d22c4ee-c897-45fd-90f0-f23b5c47a5e4/GCA_937895565.1_SRR1561996_bin.107_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937895565.1_SRR1561996_bin.107_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937895565.1_SRR1561996_bin.107_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 09:52:47,809] [INFO] Task succeeded: Prodigal
[2023-06-19 09:52:47,809] [INFO] Task started: HMMsearch
[2023-06-19 09:52:47,809] [INFO] Running command: hmmsearch --tblout GCA_937895565.1_SRR1561996_bin.107_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0cafc5d-e816-4c80-afd4-7ceefde94cf2/dqc_reference/reference_markers.hmm GCA_937895565.1_SRR1561996_bin.107_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-19 09:52:48,136] [INFO] Task succeeded: HMMsearch
[2023-06-19 09:52:48,138] [INFO] Found 6/6 markers.
[2023-06-19 09:52:48,190] [INFO] Query marker FASTA was written to GCA_937895565.1_SRR1561996_bin.107_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-19 09:52:48,191] [INFO] Task started: Blastn
[2023-06-19 09:52:48,191] [INFO] Running command: blastn -query GCA_937895565.1_SRR1561996_bin.107_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0cafc5d-e816-4c80-afd4-7ceefde94cf2/dqc_reference/reference_markers.fasta -out GCA_937895565.1_SRR1561996_bin.107_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 09:52:48,912] [INFO] Task succeeded: Blastn
[2023-06-19 09:52:48,918] [INFO] Selected 15 target genomes.
[2023-06-19 09:52:48,919] [INFO] Target genome list was writen to GCA_937895565.1_SRR1561996_bin.107_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-19 09:52:48,922] [INFO] Task started: fastANI
[2023-06-19 09:52:48,922] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d22c4ee-c897-45fd-90f0-f23b5c47a5e4/GCA_937895565.1_SRR1561996_bin.107_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937895565.1_SRR1561996_bin.107_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937895565.1_SRR1561996_bin.107_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 09:53:07,813] [INFO] Task succeeded: fastANI
[2023-06-19 09:53:07,814] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0cafc5d-e816-4c80-afd4-7ceefde94cf2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 09:53:07,815] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0cafc5d-e816-4c80-afd4-7ceefde94cf2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 09:53:07,832] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 09:53:07,832] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 09:53:07,833] [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 tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	88.5799	1384	1907	95	below_threshold
Flavobacterium nitrogenifigens	strain=NXU-44	GCA_003254565.1	1617283	1617283	type	True	88.431	1351	1907	95	below_threshold
Flavobacterium nitrogenifigens	strain=DSM 29982	GCA_900182675.1	1617283	1617283	type	True	88.4244	1354	1907	95	below_threshold
Flavobacterium sharifuzzamanii	strain=A7.6	GCA_003254585.1	2211133	2211133	type	True	88.2991	1360	1907	95	below_threshold
Flavobacterium tistrianum	strain=GB 56.1	GCA_003254545.1	1685414	1685414	type	True	87.8957	1349	1907	95	below_threshold
Flavobacterium ginsenosidimutans	strain=THG 01	GCA_003254625.1	687844	687844	type	True	87.6461	1356	1907	95	below_threshold
Flavobacterium anhuiense	strain=CGMCC 1.6859	GCA_900101855.1	459526	459526	suspected-type	True	87.4255	1340	1907	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	85.9673	1285	1907	95	below_threshold
Flavobacterium phragmitis	strain=CGMCC 1.10370	GCA_900112575.1	739143	739143	type	True	85.1314	1283	1907	95	below_threshold
Flavobacterium quisquiliarum	strain=EA-12	GCA_019308285.1	1834436	1834436	type	True	85.0758	1296	1907	95	below_threshold
Flavobacterium crocinum	strain=HYN0056	GCA_003122385.1	2183896	2183896	type	True	85.0605	1292	1907	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	83.8349	1192	1907	95	below_threshold
Flavobacterium denitrificans	strain=DSM 15936	GCA_000425445.1	281361	281361	type	True	83.7927	1085	1907	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	83.2438	1093	1907	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	77.5606	245	1907	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 09:53:07,835] [INFO] DFAST Taxonomy check result was written to GCA_937895565.1_SRR1561996_bin.107_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-19 09:53:07,835] [INFO] ===== Taxonomy check completed =====
[2023-06-19 09:53:07,835] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 09:53:07,836] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0cafc5d-e816-4c80-afd4-7ceefde94cf2/dqc_reference/checkm_data
[2023-06-19 09:53:07,837] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 09:53:07,897] [INFO] Task started: CheckM
[2023-06-19 09:53:07,897] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937895565.1_SRR1561996_bin.107_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937895565.1_SRR1561996_bin.107_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937895565.1_SRR1561996_bin.107_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-19 09:54:03,689] [INFO] Task succeeded: CheckM
[2023-06-19 09:54:03,690] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 09:54:03,714] [INFO] ===== Completeness check finished =====
[2023-06-19 09:54:03,715] [INFO] ===== Start GTDB Search =====
[2023-06-19 09:54:03,715] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937895565.1_SRR1561996_bin.107_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-19 09:54:03,715] [INFO] Task started: Blastn
[2023-06-19 09:54:03,715] [INFO] Running command: blastn -query GCA_937895565.1_SRR1561996_bin.107_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0cafc5d-e816-4c80-afd4-7ceefde94cf2/dqc_reference/reference_markers_gtdb.fasta -out GCA_937895565.1_SRR1561996_bin.107_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 09:54:04,636] [INFO] Task succeeded: Blastn
[2023-06-19 09:54:04,642] [INFO] Selected 15 target genomes.
[2023-06-19 09:54:04,642] [INFO] Target genome list was writen to GCA_937895565.1_SRR1561996_bin.107_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 09:54:04,653] [INFO] Task started: fastANI
[2023-06-19 09:54:04,654] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d22c4ee-c897-45fd-90f0-f23b5c47a5e4/GCA_937895565.1_SRR1561996_bin.107_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937895565.1_SRR1561996_bin.107_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937895565.1_SRR1561996_bin.107_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 09:54:24,153] [INFO] Task succeeded: fastANI
[2023-06-19 09:54:24,172] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 09:54:24,172] [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_016405855.1	s__Flavobacterium sp002399805	96.5944	1630	1907	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.61	96.61	0.90	0.90	2	conclusive
GCF_013388355.1	s__Flavobacterium sp013388355	89.1405	1016	1907	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	88.6012	1425	1907	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	88.4851	1398	1907	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	88.431	1351	1907	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003254585.1	s__Flavobacterium sharifuzzamanii	88.3296	1357	1907	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	87.9178	1382	1907	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	87.8957	1349	1907	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744675.1	s__Flavobacterium sp017744675	87.6562	1373	1907	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254625.1	s__Flavobacterium ginsenosidimutans	87.646	1356	1907	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	87.4297	1340	1907	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	87.3953	1356	1907	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902167265.1	s__Flavobacterium anhuiense_B	85.9644	1318	1907	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	4	-
GCF_013393195.1	s__Flavobacterium collinsii_A	85.1936	1286	1907	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	85.1232	1284	1907	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 09:54:24,175] [INFO] GTDB search result was written to GCA_937895565.1_SRR1561996_bin.107_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-19 09:54:24,175] [INFO] ===== GTDB Search completed =====
[2023-06-19 09:54:24,180] [INFO] DFAST_QC result json was written to GCA_937895565.1_SRR1561996_bin.107_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-19 09:54:24,180] [INFO] DFAST_QC completed!
[2023-06-19 09:54:24,180] [INFO] Total running time: 0h1m57s