[2024-01-24 14:55:26,958] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:26,962] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:26,962] [INFO] DQC Reference Directory: /var/lib/cwl/stgf91ebdbf-65e9-4a5a-985a-40637da04df1/dqc_reference
[2024-01-24 14:55:28,270] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:28,271] [INFO] Task started: Prodigal
[2024-01-24 14:55:28,271] [INFO] Running command: gunzip -c /var/lib/cwl/stg9e23d5a2-e977-46f3-8745-3cc06d46fe57/GCF_010093065.1_ASM1009306v1_genomic.fna.gz | prodigal -d GCF_010093065.1_ASM1009306v1_genomic.fna/cds.fna -a GCF_010093065.1_ASM1009306v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:56:07,192] [INFO] Task succeeded: Prodigal
[2024-01-24 14:56:07,192] [INFO] Task started: HMMsearch
[2024-01-24 14:56:07,192] [INFO] Running command: hmmsearch --tblout GCF_010093065.1_ASM1009306v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf91ebdbf-65e9-4a5a-985a-40637da04df1/dqc_reference/reference_markers.hmm GCF_010093065.1_ASM1009306v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:56:07,513] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:56:07,514] [INFO] Found 6/6 markers.
[2024-01-24 14:56:07,572] [INFO] Query marker FASTA was written to GCF_010093065.1_ASM1009306v1_genomic.fna/markers.fasta
[2024-01-24 14:56:07,573] [INFO] Task started: Blastn
[2024-01-24 14:56:07,573] [INFO] Running command: blastn -query GCF_010093065.1_ASM1009306v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf91ebdbf-65e9-4a5a-985a-40637da04df1/dqc_reference/reference_markers.fasta -out GCF_010093065.1_ASM1009306v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:08,153] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:08,157] [INFO] Selected 11 target genomes.
[2024-01-24 14:56:08,158] [INFO] Target genome list was writen to GCF_010093065.1_ASM1009306v1_genomic.fna/target_genomes.txt
[2024-01-24 14:56:08,164] [INFO] Task started: fastANI
[2024-01-24 14:56:08,165] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e23d5a2-e977-46f3-8745-3cc06d46fe57/GCF_010093065.1_ASM1009306v1_genomic.fna.gz --refList GCF_010093065.1_ASM1009306v1_genomic.fna/target_genomes.txt --output GCF_010093065.1_ASM1009306v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:23,927] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:23,928] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf91ebdbf-65e9-4a5a-985a-40637da04df1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:23,928] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf91ebdbf-65e9-4a5a-985a-40637da04df1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:23,954] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:56:23,954] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:56:23,954] [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 agri	strain=H33E-04	GCA_010093065.1	2703787	2703787	type	True	100.0	2656	2656	95	conclusive
Chitinophaga pinensis	strain=DSM 2588	GCA_000024005.1	79329	79329	type	True	82.6105	1709	2656	95	below_threshold
Chitinophaga rhizophila	strain=B61	GCA_019492185.1	2866212	2866212	type	True	81.7792	1449	2656	95	below_threshold
Chitinophaga ginsengisoli	strain=DSM 18107	GCA_003014595.1	363837	363837	type	True	80.9105	1221	2656	95	below_threshold
Chitinophaga filiformis	strain=DSM 527	GCA_900102545.1	104663	104663	type	True	80.7558	1257	2656	95	below_threshold
Chitinophaga oryzae	strain=1303	GCA_012516375.2	2725414	2725414	type	True	77.6628	311	2656	95	below_threshold
Chitinophaga varians	strain=KACC 19415	GCA_014529945.1	2202339	2202339	type	True	77.3083	320	2656	95	below_threshold
Chitinophaga japonensis	strain=DSM 13484	GCA_007830125.1	104662	104662	type	True	76.6931	293	2656	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:23,956] [INFO] DFAST Taxonomy check result was written to GCF_010093065.1_ASM1009306v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:23,956] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:23,957] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:23,957] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf91ebdbf-65e9-4a5a-985a-40637da04df1/dqc_reference/checkm_data
[2024-01-24 14:56:23,958] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:24,058] [INFO] Task started: CheckM
[2024-01-24 14:56:24,058] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010093065.1_ASM1009306v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010093065.1_ASM1009306v1_genomic.fna/checkm_input GCF_010093065.1_ASM1009306v1_genomic.fna/checkm_result
[2024-01-24 14:58:05,314] [INFO] Task succeeded: CheckM
[2024-01-24 14:58:05,316] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:58:05,339] [INFO] ===== Completeness check finished =====
[2024-01-24 14:58:05,339] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:58:05,339] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010093065.1_ASM1009306v1_genomic.fna/markers.fasta)
[2024-01-24 14:58:05,340] [INFO] Task started: Blastn
[2024-01-24 14:58:05,340] [INFO] Running command: blastn -query GCF_010093065.1_ASM1009306v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf91ebdbf-65e9-4a5a-985a-40637da04df1/dqc_reference/reference_markers_gtdb.fasta -out GCF_010093065.1_ASM1009306v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:58:06,123] [INFO] Task succeeded: Blastn
[2024-01-24 14:58:06,126] [INFO] Selected 11 target genomes.
[2024-01-24 14:58:06,126] [INFO] Target genome list was writen to GCF_010093065.1_ASM1009306v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:58:06,135] [INFO] Task started: fastANI
[2024-01-24 14:58:06,135] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e23d5a2-e977-46f3-8745-3cc06d46fe57/GCF_010093065.1_ASM1009306v1_genomic.fna.gz --refList GCF_010093065.1_ASM1009306v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010093065.1_ASM1009306v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:58:26,903] [INFO] Task succeeded: fastANI
[2024-01-24 14:58:26,914] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:58:26,914] [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_010093065.1	s__Chitinophaga agri	100.0	2655	2656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007896845.1	s__Chitinophaga pinensis_C	82.8566	1607	2656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114995.1	s__Chitinophaga sp900114995	82.6664	1742	2656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024005.1	s__Chitinophaga pinensis	82.5957	1712	2656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014595.1	s__Chitinophaga ginsengisoli	80.9109	1222	2656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182155.1	s__Chitinophaga sp003182155	80.8229	1252	2656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016467415.1	s__Chitinophaga sp016467415	80.8088	1201	2656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142925.1	s__Chitinophaga sp900142925	80.706	1272	2656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902168105.1	s__Chitinophaga sp902168105	80.5568	1219	2656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012516355.1	s__Chitinophaga sp012516355	77.6521	310	2656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	99.48	99.48	0.97	0.97	2	-
GCF_014529945.1	s__Chitinophaga varians	77.3204	319	2656	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 14:58:26,916] [INFO] GTDB search result was written to GCF_010093065.1_ASM1009306v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:58:26,917] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:58:26,920] [INFO] DFAST_QC result json was written to GCF_010093065.1_ASM1009306v1_genomic.fna/dqc_result.json
[2024-01-24 14:58:26,920] [INFO] DFAST_QC completed!
[2024-01-24 14:58:26,920] [INFO] Total running time: 0h2m60s