[2024-01-24 14:28:17,879] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:17,880] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:17,880] [INFO] DQC Reference Directory: /var/lib/cwl/stgae2b6149-0029-44de-bc35-0de74ac9b781/dqc_reference
[2024-01-24 14:28:20,481] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:20,482] [INFO] Task started: Prodigal
[2024-01-24 14:28:20,482] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0fc49b0-75d1-450a-bed8-d5a65fc887a9/GCF_007341385.1_ASM734138v1_genomic.fna.gz | prodigal -d GCF_007341385.1_ASM734138v1_genomic.fna/cds.fna -a GCF_007341385.1_ASM734138v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:38,385] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:38,385] [INFO] Task started: HMMsearch
[2024-01-24 14:28:38,385] [INFO] Running command: hmmsearch --tblout GCF_007341385.1_ASM734138v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgae2b6149-0029-44de-bc35-0de74ac9b781/dqc_reference/reference_markers.hmm GCF_007341385.1_ASM734138v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:38,702] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:38,703] [INFO] Found 6/6 markers.
[2024-01-24 14:28:38,772] [INFO] Query marker FASTA was written to GCF_007341385.1_ASM734138v1_genomic.fna/markers.fasta
[2024-01-24 14:28:38,773] [INFO] Task started: Blastn
[2024-01-24 14:28:38,773] [INFO] Running command: blastn -query GCF_007341385.1_ASM734138v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae2b6149-0029-44de-bc35-0de74ac9b781/dqc_reference/reference_markers.fasta -out GCF_007341385.1_ASM734138v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:39,497] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:39,501] [INFO] Selected 18 target genomes.
[2024-01-24 14:28:39,501] [INFO] Target genome list was writen to GCF_007341385.1_ASM734138v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:39,507] [INFO] Task started: fastANI
[2024-01-24 14:28:39,507] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0fc49b0-75d1-450a-bed8-d5a65fc887a9/GCF_007341385.1_ASM734138v1_genomic.fna.gz --refList GCF_007341385.1_ASM734138v1_genomic.fna/target_genomes.txt --output GCF_007341385.1_ASM734138v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:29:00,648] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:00,649] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgae2b6149-0029-44de-bc35-0de74ac9b781/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:29:00,649] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgae2b6149-0029-44de-bc35-0de74ac9b781/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:29:00,669] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:29:00,670] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:29:00,670] [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 daemonense	strain=JCM 19455	GCA_007341385.1	1393049	1393049	type	True	100.0	1566	1569	95	conclusive
Flavobacterium resistens	strain=DSM 19382	GCA_009674815.1	443612	443612	type	True	86.8632	1260	1569	95	below_threshold
Flavobacterium resistens	strain=DSM 19382	GCA_900182645.1	443612	443612	type	True	86.8547	1256	1569	95	below_threshold
Flavobacterium zhairuonense	strain=A5.7	GCA_004352915.1	2493631	2493631	type	True	86.3452	1239	1569	95	below_threshold
Flavobacterium denitrificans	strain=DSM 15936	GCA_000425445.1	281361	281361	type	True	85.9159	1173	1569	95	below_threshold
Flavobacterium cutihirudinis	strain=DSM 25795	GCA_003385895.1	1265740	1265740	type	True	85.3478	1094	1569	95	below_threshold
Flavobacterium defluvii	strain=DSM 17963	GCA_900129555.1	370979	370979	type	True	83.7622	1018	1569	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	83.6779	1038	1569	95	below_threshold
Flavobacterium ginsenosidimutans	strain=THG 01	GCA_003254625.1	687844	687844	type	True	83.497	1044	1569	95	below_threshold
Flavobacterium sharifuzzamanii	strain=A7.6	GCA_003254585.1	2211133	2211133	type	True	83.4872	1019	1569	95	below_threshold
Flavobacterium plurextorum	strain=CCUG 60112	GCA_002217395.1	1114867	1114867	type	True	83.4778	958	1569	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	83.3	1020	1569	95	below_threshold
Flavobacterium phragmitis	strain=CGMCC 1.10370	GCA_900112575.1	739143	739143	type	True	83.1715	990	1569	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	83.077	990	1569	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	82.9385	1009	1569	95	below_threshold
Flavobacterium hibernum	strain=ATCC 51468	GCA_002217315.1	37752	37752	type	True	82.5785	960	1569	95	below_threshold
Flavobacterium foetidum	strain=JCM 32085	GCA_004634245.1	2026681	2026681	type	True	82.2984	918	1569	95	below_threshold
Flavobacterium oreochromis	strain=Costa Rica 04-02-TN	GCA_019565455.1	2906078	2906078	type	True	76.7917	163	1569	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:29:00,672] [INFO] DFAST Taxonomy check result was written to GCF_007341385.1_ASM734138v1_genomic.fna/tc_result.tsv
[2024-01-24 14:29:00,672] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:29:00,672] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:29:00,673] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgae2b6149-0029-44de-bc35-0de74ac9b781/dqc_reference/checkm_data
[2024-01-24 14:29:00,674] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:29:00,728] [INFO] Task started: CheckM
[2024-01-24 14:29:00,728] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007341385.1_ASM734138v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007341385.1_ASM734138v1_genomic.fna/checkm_input GCF_007341385.1_ASM734138v1_genomic.fna/checkm_result
[2024-01-24 14:29:53,119] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:53,121] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:53,140] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:53,141] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:53,141] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007341385.1_ASM734138v1_genomic.fna/markers.fasta)
[2024-01-24 14:29:53,141] [INFO] Task started: Blastn
[2024-01-24 14:29:53,142] [INFO] Running command: blastn -query GCF_007341385.1_ASM734138v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae2b6149-0029-44de-bc35-0de74ac9b781/dqc_reference/reference_markers_gtdb.fasta -out GCF_007341385.1_ASM734138v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:54,143] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:54,147] [INFO] Selected 15 target genomes.
[2024-01-24 14:29:54,147] [INFO] Target genome list was writen to GCF_007341385.1_ASM734138v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:54,158] [INFO] Task started: fastANI
[2024-01-24 14:29:54,159] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0fc49b0-75d1-450a-bed8-d5a65fc887a9/GCF_007341385.1_ASM734138v1_genomic.fna.gz --refList GCF_007341385.1_ASM734138v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007341385.1_ASM734138v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:30:12,952] [INFO] Task succeeded: fastANI
[2024-01-24 14:30:12,967] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:30:12,968] [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_007341385.1	s__Flavobacterium daemonense	100.0	1566	1569	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_009711135.1	s__Flavobacterium sp009711135	87.9674	1286	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362055.1	s__Flavobacterium sp004362055	87.4042	1248	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182645.1	s__Flavobacterium resistens	86.8547	1256	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000745775.1	s__Flavobacterium sp000745775	86.8498	1234	1569	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	86.3516	1238	1569	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	85.9159	1173	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385895.1	s__Flavobacterium cutihirudinis	85.3578	1093	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002482975.1	s__Flavobacterium sp002482975	83.9112	1043	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254585.1	s__Flavobacterium sharifuzzamanii	83.5005	1017	1569	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	83.4713	1047	1569	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	83.367	1024	1569	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	83.3331	1037	1569	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	83.3127	1029	1569	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	83.1458	993	1569	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 14:30:12,970] [INFO] GTDB search result was written to GCF_007341385.1_ASM734138v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:30:12,971] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:30:12,975] [INFO] DFAST_QC result json was written to GCF_007341385.1_ASM734138v1_genomic.fna/dqc_result.json
[2024-01-24 14:30:12,976] [INFO] DFAST_QC completed!
[2024-01-24 14:30:12,976] [INFO] Total running time: 0h1m55s