[2024-01-24 13:40:33,901] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:33,904] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:33,904] [INFO] DQC Reference Directory: /var/lib/cwl/stgede84267-28ec-4da4-9cce-fcf16f8395c4/dqc_reference
[2024-01-24 13:40:35,217] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:35,218] [INFO] Task started: Prodigal
[2024-01-24 13:40:35,218] [INFO] Running command: gunzip -c /var/lib/cwl/stg3455832b-1d2f-4b48-b94f-d8c44de8c7a3/GCF_025989125.1_ASM2598912v1_genomic.fna.gz | prodigal -d GCF_025989125.1_ASM2598912v1_genomic.fna/cds.fna -a GCF_025989125.1_ASM2598912v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:43:15,255] [INFO] Task succeeded: Prodigal
[2024-01-24 13:43:15,256] [INFO] Task started: HMMsearch
[2024-01-24 13:43:15,256] [INFO] Running command: hmmsearch --tblout GCF_025989125.1_ASM2598912v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgede84267-28ec-4da4-9cce-fcf16f8395c4/dqc_reference/reference_markers.hmm GCF_025989125.1_ASM2598912v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:43:15,647] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:43:15,648] [INFO] Found 6/6 markers.
[2024-01-24 13:43:15,712] [INFO] Query marker FASTA was written to GCF_025989125.1_ASM2598912v1_genomic.fna/markers.fasta
[2024-01-24 13:43:15,712] [INFO] Task started: Blastn
[2024-01-24 13:43:15,712] [INFO] Running command: blastn -query GCF_025989125.1_ASM2598912v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgede84267-28ec-4da4-9cce-fcf16f8395c4/dqc_reference/reference_markers.fasta -out GCF_025989125.1_ASM2598912v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:16,299] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:16,303] [INFO] Selected 9 target genomes.
[2024-01-24 13:43:16,304] [INFO] Target genome list was writen to GCF_025989125.1_ASM2598912v1_genomic.fna/target_genomes.txt
[2024-01-24 13:43:16,340] [INFO] Task started: fastANI
[2024-01-24 13:43:16,340] [INFO] Running command: fastANI --query /var/lib/cwl/stg3455832b-1d2f-4b48-b94f-d8c44de8c7a3/GCF_025989125.1_ASM2598912v1_genomic.fna.gz --refList GCF_025989125.1_ASM2598912v1_genomic.fna/target_genomes.txt --output GCF_025989125.1_ASM2598912v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:43:28,241] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:28,242] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgede84267-28ec-4da4-9cce-fcf16f8395c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:43:28,242] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgede84267-28ec-4da4-9cce-fcf16f8395c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:43:28,257] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:43:28,257] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:43:28,257] [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
Chitinophaga niastensis	strain=DSM 24859	GCA_003014755.1	536980	536980	type	True	80.4952	938	2856	95	below_threshold
Chitinophaga arvensicola	strain=DSM 3695	GCA_900110835.1	29529	29529	type	True	80.4328	868	2856	95	below_threshold
Chitinophaga hostae	strain=2R12	GCA_018224885.1	2831022	2831022	type	True	80.1575	878	2856	95	below_threshold
Chitinophaga ginsengisegetis	strain=DSM 18108	GCA_900168065.1	393003	393003	type	True	80.139	904	2856	95	below_threshold
Chitinophaga solisilvae	strain=O9	GCA_009928525.1	1233460	1233460	type	True	79.6333	948	2856	95	below_threshold
Chitinophaga fulva	strain=G-6-1-13	GCA_012927205.1	2728842	2728842	type	True	79.4397	834	2856	95	below_threshold
Chitinophaga qingshengii	strain=JCM 30026	GCA_014529935.1	1569794	1569794	type	True	79.4335	872	2856	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:43:28,259] [INFO] DFAST Taxonomy check result was written to GCF_025989125.1_ASM2598912v1_genomic.fna/tc_result.tsv
[2024-01-24 13:43:28,260] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:43:28,260] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:43:28,260] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgede84267-28ec-4da4-9cce-fcf16f8395c4/dqc_reference/checkm_data
[2024-01-24 13:43:28,261] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:43:28,340] [INFO] Task started: CheckM
[2024-01-24 13:43:28,340] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025989125.1_ASM2598912v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025989125.1_ASM2598912v1_genomic.fna/checkm_input GCF_025989125.1_ASM2598912v1_genomic.fna/checkm_result
[2024-01-24 13:49:52,082] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:52,084] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:52,105] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:52,105] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:52,107] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025989125.1_ASM2598912v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:52,107] [INFO] Task started: Blastn
[2024-01-24 13:49:52,108] [INFO] Running command: blastn -query GCF_025989125.1_ASM2598912v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgede84267-28ec-4da4-9cce-fcf16f8395c4/dqc_reference/reference_markers_gtdb.fasta -out GCF_025989125.1_ASM2598912v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:52,993] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:52,997] [INFO] Selected 13 target genomes.
[2024-01-24 13:49:52,997] [INFO] Target genome list was writen to GCF_025989125.1_ASM2598912v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:53,008] [INFO] Task started: fastANI
[2024-01-24 13:49:53,009] [INFO] Running command: fastANI --query /var/lib/cwl/stg3455832b-1d2f-4b48-b94f-d8c44de8c7a3/GCF_025989125.1_ASM2598912v1_genomic.fna.gz --refList GCF_025989125.1_ASM2598912v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025989125.1_ASM2598912v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:13,865] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:13,876] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:50:13,877] [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_003014755.1	s__Chitinophaga niastensis	80.4907	939	2856	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110835.1	s__Chitinophaga arvensicola	80.4328	868	2856	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018224885.1	s__Chitinophaga sp018224885	80.1629	878	2856	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168065.1	s__Chitinophaga ginsengisegetis	80.1464	904	2856	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	98.27	98.27	0.94	0.94	3	-
GCA_017745275.1	s__Chitinophaga sp017745275	80.0816	847	2856	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363865.1	s__Chitinophaga sp004363865	80.0504	931	2856	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902150045.1	s__Chitinophaga polysaccharea_A	79.9557	810	2856	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	96.96	96.96	0.91	0.91	2	-
GCF_007829335.1	s__Chitinophaga polysaccharea_B	79.9231	818	2856	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012726295.1	s__Chitinophaga sp012726295	79.9069	814	2856	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	99.43	99.43	0.94	0.94	2	-
GCF_012641265.1	s__Chitinophaga eiseniae_A	79.8774	843	2856	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003994345.2	s__Chitinophaga extrema	79.5651	952	2856	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	98.60	98.60	0.96	0.96	2	-
GCF_014529935.1	s__Chitinophaga qingshengii	79.4337	873	2856	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927205.1	s__Chitinophaga fulva	79.4211	837	2856	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:13,878] [INFO] GTDB search result was written to GCF_025989125.1_ASM2598912v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:13,879] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:13,883] [INFO] DFAST_QC result json was written to GCF_025989125.1_ASM2598912v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:13,884] [INFO] DFAST_QC completed!
[2024-01-24 13:50:13,884] [INFO] Total running time: 0h9m40s