[2024-01-25 18:00:35,468] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:00:35,469] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:00:35,469] [INFO] DQC Reference Directory: /var/lib/cwl/stg1433f02e-2422-4341-adf2-c7d67c86e7a7/dqc_reference
[2024-01-25 18:00:36,608] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:00:36,608] [INFO] Task started: Prodigal
[2024-01-25 18:00:36,608] [INFO] Running command: gunzip -c /var/lib/cwl/stg279b3f32-e231-4a37-a926-17ea3cdbed6d/GCF_003412455.1_ASM341245v1_genomic.fna.gz | prodigal -d GCF_003412455.1_ASM341245v1_genomic.fna/cds.fna -a GCF_003412455.1_ASM341245v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:01:03,284] [INFO] Task succeeded: Prodigal
[2024-01-25 18:01:03,284] [INFO] Task started: HMMsearch
[2024-01-25 18:01:03,284] [INFO] Running command: hmmsearch --tblout GCF_003412455.1_ASM341245v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1433f02e-2422-4341-adf2-c7d67c86e7a7/dqc_reference/reference_markers.hmm GCF_003412455.1_ASM341245v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:01:03,594] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:01:03,595] [INFO] Found 6/6 markers.
[2024-01-25 18:01:03,638] [INFO] Query marker FASTA was written to GCF_003412455.1_ASM341245v1_genomic.fna/markers.fasta
[2024-01-25 18:01:03,639] [INFO] Task started: Blastn
[2024-01-25 18:01:03,639] [INFO] Running command: blastn -query GCF_003412455.1_ASM341245v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1433f02e-2422-4341-adf2-c7d67c86e7a7/dqc_reference/reference_markers.fasta -out GCF_003412455.1_ASM341245v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:01:04,214] [INFO] Task succeeded: Blastn
[2024-01-25 18:01:04,217] [INFO] Selected 22 target genomes.
[2024-01-25 18:01:04,217] [INFO] Target genome list was writen to GCF_003412455.1_ASM341245v1_genomic.fna/target_genomes.txt
[2024-01-25 18:01:04,224] [INFO] Task started: fastANI
[2024-01-25 18:01:04,224] [INFO] Running command: fastANI --query /var/lib/cwl/stg279b3f32-e231-4a37-a926-17ea3cdbed6d/GCF_003412455.1_ASM341245v1_genomic.fna.gz --refList GCF_003412455.1_ASM341245v1_genomic.fna/target_genomes.txt --output GCF_003412455.1_ASM341245v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:01:24,136] [INFO] Task succeeded: fastANI
[2024-01-25 18:01:24,136] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1433f02e-2422-4341-adf2-c7d67c86e7a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:01:24,136] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1433f02e-2422-4341-adf2-c7d67c86e7a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:01:24,146] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:01:24,146] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:01:24,147] [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
Deminuibacter soli	strain=K23C18032701	GCA_003412455.1	2291815	2291815	type	True	100.0	1932	1933	95	conclusive
Filimonas lacunae	strain=NBRC 104114	GCA_002355595.1	477680	477680	type	True	77.229	302	1933	95	below_threshold
Filimonas lacunae	strain=DSM 21054	GCA_900156765.1	477680	477680	type	True	77.1808	298	1933	95	below_threshold
Filimonas effusa	strain=TTM-71	GCA_004118675.1	2508721	2508721	type	True	77.1066	201	1933	95	below_threshold
Filimonas zeae	strain=CGMCC 1.15290	GCA_014641615.1	1737353	1737353	type	True	77.0205	315	1933	95	below_threshold
Sediminibacterium ginsengisoli	strain=DSM 22335	GCA_900167075.1	413434	413434	type	True	76.7469	159	1933	95	below_threshold
Panacibacter ginsenosidivorans	strain=Gsoil1550	GCA_007971225.1	1813871	1813871	type	True	76.4907	108	1933	95	below_threshold
Sediminibacterium goheungense	strain=DSM 28323	GCA_004361915.1	1086393	1086393	type	True	76.4308	133	1933	95	below_threshold
Lacibacter cauensis	strain=CGMCC 1.7271	GCA_007830055.1	510947	510947	type	True	76.3254	108	1933	95	below_threshold
Hydrotalea flava	strain=CCUG 51397	GCA_001623405.1	714549	714549	suspected-type	True	76.0855	77	1933	95	below_threshold
Flavihumibacter cheonanensis	strain=WS16	GCA_022352215.1	1442385	1442385	type	True	76.0706	70	1933	95	below_threshold
Paraflavitalea devenefica	strain=X16	GCA_011759375.1	2716334	2716334	type	True	76.0635	139	1933	95	below_threshold
Paraflavitalea soli	strain=5GH32-13	GCA_003555545.1	2315862	2315862	type	True	76.0595	138	1933	95	below_threshold
Limnovirga soli	strain=KCS-6	GCA_013106755.1	2656915	2656915	type	True	75.9295	117	1933	95	below_threshold
Parafilimonas terrae	strain=DSM 28286	GCA_900115755.1	1465490	1465490	type	True	75.8479	118	1933	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:01:24,148] [INFO] DFAST Taxonomy check result was written to GCF_003412455.1_ASM341245v1_genomic.fna/tc_result.tsv
[2024-01-25 18:01:24,149] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:01:24,149] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:01:24,149] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1433f02e-2422-4341-adf2-c7d67c86e7a7/dqc_reference/checkm_data
[2024-01-25 18:01:24,150] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:01:24,208] [INFO] Task started: CheckM
[2024-01-25 18:01:24,208] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003412455.1_ASM341245v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003412455.1_ASM341245v1_genomic.fna/checkm_input GCF_003412455.1_ASM341245v1_genomic.fna/checkm_result
[2024-01-25 18:02:33,374] [INFO] Task succeeded: CheckM
[2024-01-25 18:02:33,375] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:02:33,396] [INFO] ===== Completeness check finished =====
[2024-01-25 18:02:33,396] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:02:33,397] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003412455.1_ASM341245v1_genomic.fna/markers.fasta)
[2024-01-25 18:02:33,397] [INFO] Task started: Blastn
[2024-01-25 18:02:33,397] [INFO] Running command: blastn -query GCF_003412455.1_ASM341245v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1433f02e-2422-4341-adf2-c7d67c86e7a7/dqc_reference/reference_markers_gtdb.fasta -out GCF_003412455.1_ASM341245v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:02:34,287] [INFO] Task succeeded: Blastn
[2024-01-25 18:02:34,290] [INFO] Selected 20 target genomes.
[2024-01-25 18:02:34,290] [INFO] Target genome list was writen to GCF_003412455.1_ASM341245v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:02:34,315] [INFO] Task started: fastANI
[2024-01-25 18:02:34,316] [INFO] Running command: fastANI --query /var/lib/cwl/stg279b3f32-e231-4a37-a926-17ea3cdbed6d/GCF_003412455.1_ASM341245v1_genomic.fna.gz --refList GCF_003412455.1_ASM341245v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003412455.1_ASM341245v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:02:52,739] [INFO] Task succeeded: fastANI
[2024-01-25 18:02:52,748] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:02:52,748] [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_003412455.1	s__Deminuibacter soli	100.0	1932	1933	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Deminuibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007994055.1	s__Filimonas endophytica	77.3379	275	1933	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Filimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003097095.1	s__Filimonas sp003097095	77.2787	279	1933	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Filimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355595.1	s__Filimonas lacunae	77.2148	301	1933	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Filimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004118675.1	s__Filimonas effusa	77.1066	201	1933	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Filimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641615.1	s__Filimonas zeae	77.0256	316	1933	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Filimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017306865.1	s__JAFKHH01 sp017306865	76.8296	203	1933	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JAFKHH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001302245.1	s__PMP191F sp001302245	76.7114	169	1933	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__PMP191F	95.0	99.37	99.37	0.95	0.95	2	-
GCA_016183765.1	s__Sediminibacterium sp016183765	76.4344	150	1933	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873345.1	s__Flavitalea sp014873345	76.3186	60	1933	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016741945.1	s__Sediminibacterium sp016741945	76.0848	53	1933	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002478885.1	s__Panacibacter sp002478885	76.0711	99	1933	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Panacibacter	95.0	99.95	99.95	0.95	0.95	2	-
GCF_003555545.1	s__Paraflavitalea soli	76.0595	138	1933	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Paraflavitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016710935.1	s__Ferruginibacter sp016710935	75.8132	72	1933	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:02:52,762] [INFO] GTDB search result was written to GCF_003412455.1_ASM341245v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:02:52,763] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:02:52,769] [INFO] DFAST_QC result json was written to GCF_003412455.1_ASM341245v1_genomic.fna/dqc_result.json
[2024-01-25 18:02:52,769] [INFO] DFAST_QC completed!
[2024-01-25 18:02:52,769] [INFO] Total running time: 0h2m17s