[2024-01-24 11:51:24,746] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:24,748] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:24,748] [INFO] DQC Reference Directory: /var/lib/cwl/stgcafdfdd1-a086-4e67-8050-8330fcfa8206/dqc_reference
[2024-01-24 11:51:26,188] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:26,189] [INFO] Task started: Prodigal
[2024-01-24 11:51:26,189] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a28f802-2072-4abf-b57d-0f3efcac5ba1/GCF_002899945.2_ASM289994v2_genomic.fna.gz | prodigal -d GCF_002899945.2_ASM289994v2_genomic.fna/cds.fna -a GCF_002899945.2_ASM289994v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:46,778] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:46,779] [INFO] Task started: HMMsearch
[2024-01-24 11:51:46,779] [INFO] Running command: hmmsearch --tblout GCF_002899945.2_ASM289994v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcafdfdd1-a086-4e67-8050-8330fcfa8206/dqc_reference/reference_markers.hmm GCF_002899945.2_ASM289994v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:47,087] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:47,089] [INFO] Found 6/6 markers.
[2024-01-24 11:51:47,135] [INFO] Query marker FASTA was written to GCF_002899945.2_ASM289994v2_genomic.fna/markers.fasta
[2024-01-24 11:51:47,135] [INFO] Task started: Blastn
[2024-01-24 11:51:47,135] [INFO] Running command: blastn -query GCF_002899945.2_ASM289994v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgcafdfdd1-a086-4e67-8050-8330fcfa8206/dqc_reference/reference_markers.fasta -out GCF_002899945.2_ASM289994v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:47,788] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:47,793] [INFO] Selected 17 target genomes.
[2024-01-24 11:51:47,794] [INFO] Target genome list was writen to GCF_002899945.2_ASM289994v2_genomic.fna/target_genomes.txt
[2024-01-24 11:51:47,800] [INFO] Task started: fastANI
[2024-01-24 11:51:47,800] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a28f802-2072-4abf-b57d-0f3efcac5ba1/GCF_002899945.2_ASM289994v2_genomic.fna.gz --refList GCF_002899945.2_ASM289994v2_genomic.fna/target_genomes.txt --output GCF_002899945.2_ASM289994v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:07,197] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:07,197] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcafdfdd1-a086-4e67-8050-8330fcfa8206/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:07,198] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcafdfdd1-a086-4e67-8050-8330fcfa8206/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:07,213] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:52:07,213] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:07,213] [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
Chryseobacterium viscerum	strain=687B-08	GCA_002899945.2	1037377	1037377	type	True	100.0	1877	1879	95	conclusive
Chryseobacterium sediminis	strain=IMT-174	GCA_008386505.1	1679494	1679494	type	True	87.2934	1329	1879	95	below_threshold
Chryseobacterium panacisoli	strain=Gsoil 183	GCA_008274625.1	1807141	1807141	type	True	87.1933	1340	1879	95	below_threshold
Chryseobacterium rhizoplanae	strain=DSM 29371	GCA_900182655.1	1609531	1609531	type	True	87.0369	1327	1879	95	below_threshold
Chryseobacterium candidae	strain=JC507	GCA_004916905.1	1978493	1978493	type	True	86.4119	1203	1879	95	below_threshold
Chryseobacterium cucumeris	strain=GSE06	GCA_001593385.1	1813611	1813611	type	True	86.2855	1340	1879	95	below_threshold
Chryseobacterium aureum	strain=17S1E7	GCA_003971235.1	2497456	2497456	type	True	85.8001	1325	1879	95	below_threshold
Chryseobacterium culicis	strain=DSM 23031	GCA_900108365.1	680127	680127	type	True	85.5962	1296	1879	95	below_threshold
Chryseobacterium gleum	strain=ATCC 35910	GCA_000143785.1	250	250	type	True	85.5603	1294	1879	95	below_threshold
Chryseobacterium gleum	strain=FDAARGOS_1103	GCA_016766875.1	250	250	type	True	85.56	1306	1879	95	below_threshold
Chryseobacterium jejuense	strain=DSM 19299	GCA_900100075.1	445960	445960	type	True	83.3123	1118	1879	95	below_threshold
Chryseobacterium ureilyticum	strain=DSM 18017	GCA_900156735.1	373668	373668	type	True	83.0701	1073	1879	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	80.778	696	1879	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	80.6359	813	1879	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	80.455	798	1879	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:07,216] [INFO] DFAST Taxonomy check result was written to GCF_002899945.2_ASM289994v2_genomic.fna/tc_result.tsv
[2024-01-24 11:52:07,216] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:07,217] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:07,217] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcafdfdd1-a086-4e67-8050-8330fcfa8206/dqc_reference/checkm_data
[2024-01-24 11:52:07,218] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:07,296] [INFO] Task started: CheckM
[2024-01-24 11:52:07,297] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002899945.2_ASM289994v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002899945.2_ASM289994v2_genomic.fna/checkm_input GCF_002899945.2_ASM289994v2_genomic.fna/checkm_result
[2024-01-24 11:53:08,578] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:08,579] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:08,605] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:08,605] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:08,605] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002899945.2_ASM289994v2_genomic.fna/markers.fasta)
[2024-01-24 11:53:08,606] [INFO] Task started: Blastn
[2024-01-24 11:53:08,606] [INFO] Running command: blastn -query GCF_002899945.2_ASM289994v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgcafdfdd1-a086-4e67-8050-8330fcfa8206/dqc_reference/reference_markers_gtdb.fasta -out GCF_002899945.2_ASM289994v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:09,459] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:09,466] [INFO] Selected 17 target genomes.
[2024-01-24 11:53:09,466] [INFO] Target genome list was writen to GCF_002899945.2_ASM289994v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:09,478] [INFO] Task started: fastANI
[2024-01-24 11:53:09,479] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a28f802-2072-4abf-b57d-0f3efcac5ba1/GCF_002899945.2_ASM289994v2_genomic.fna.gz --refList GCF_002899945.2_ASM289994v2_genomic.fna/target_genomes_gtdb.txt --output GCF_002899945.2_ASM289994v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:30,055] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:30,075] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:30,075] [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_002899945.2	s__Chryseobacterium viscerum	100.0	1877	1879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.88	95.74	0.91	0.87	3	conclusive
GCF_903969135.1	s__Chryseobacterium sp900156935	87.4732	1382	1879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.11	99.11	0.93	0.93	2	-
GCF_000799235.1	s__Chryseobacterium sp000799235	87.4364	1348	1879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799335.1	s__Chryseobacterium sp000799335	87.3991	1369	1879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386505.1	s__Chryseobacterium sediminis	87.2934	1329	1879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.62	96.62	0.92	0.92	2	-
GCF_002979455.1	s__Chryseobacterium sp002979455	87.2595	1358	1879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008274625.1	s__Chryseobacterium sp008274625	87.1996	1339	1879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004119445.1	s__Chryseobacterium sp004119445	87.1521	1315	1879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002979755.1	s__Chryseobacterium culicis_A	87.0631	1369	1879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.05	96.10	0.96	0.92	3	-
GCF_900182655.1	s__Chryseobacterium rhizoplanae	87.0369	1327	1879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	95.47	95.07	0.88	0.87	3	-
GCF_000745535.1	s__Chryseobacterium sp000745535	86.8673	1395	1879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002025665.1	s__Chryseobacterium indologenes_F	86.7282	1364	1879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799375.1	s__Chryseobacterium aquifrigidense	86.5228	1308	1879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.62	98.62	0.95	0.95	2	-
GCF_003971235.1	s__Chryseobacterium aureum	85.8001	1325	1879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006829085.1	s__Chryseobacterium sp006829085	85.4355	1340	1879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.29	97.29	0.93	0.93	2	-
GCF_900100075.1	s__Chryseobacterium jejuense	83.3124	1118	1879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_900156735.1	s__Chryseobacterium ureilyticum	83.0782	1072	1879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:30,077] [INFO] GTDB search result was written to GCF_002899945.2_ASM289994v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:30,077] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:30,081] [INFO] DFAST_QC result json was written to GCF_002899945.2_ASM289994v2_genomic.fna/dqc_result.json
[2024-01-24 11:53:30,082] [INFO] DFAST_QC completed!
[2024-01-24 11:53:30,082] [INFO] Total running time: 0h2m5s