[2024-01-24 13:18:25,650] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:25,651] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:25,651] [INFO] DQC Reference Directory: /var/lib/cwl/stgc08071a0-cffe-4a9e-8ea0-7b8e1f5957ca/dqc_reference
[2024-01-24 13:18:27,058] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:27,059] [INFO] Task started: Prodigal
[2024-01-24 13:18:27,059] [INFO] Running command: gunzip -c /var/lib/cwl/stg8aa02daf-52e0-4e46-afc9-3a5fff2f8c1d/GCF_012516375.2_ASM1251637v2_genomic.fna.gz | prodigal -d GCF_012516375.2_ASM1251637v2_genomic.fna/cds.fna -a GCF_012516375.2_ASM1251637v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:39,003] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:39,003] [INFO] Task started: HMMsearch
[2024-01-24 13:19:39,003] [INFO] Running command: hmmsearch --tblout GCF_012516375.2_ASM1251637v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc08071a0-cffe-4a9e-8ea0-7b8e1f5957ca/dqc_reference/reference_markers.hmm GCF_012516375.2_ASM1251637v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:39,421] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:39,422] [INFO] Found 6/6 markers.
[2024-01-24 13:19:39,497] [INFO] Query marker FASTA was written to GCF_012516375.2_ASM1251637v2_genomic.fna/markers.fasta
[2024-01-24 13:19:39,498] [INFO] Task started: Blastn
[2024-01-24 13:19:39,498] [INFO] Running command: blastn -query GCF_012516375.2_ASM1251637v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgc08071a0-cffe-4a9e-8ea0-7b8e1f5957ca/dqc_reference/reference_markers.fasta -out GCF_012516375.2_ASM1251637v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:40,151] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:40,155] [INFO] Selected 8 target genomes.
[2024-01-24 13:19:40,155] [INFO] Target genome list was writen to GCF_012516375.2_ASM1251637v2_genomic.fna/target_genomes.txt
[2024-01-24 13:19:40,159] [INFO] Task started: fastANI
[2024-01-24 13:19:40,160] [INFO] Running command: fastANI --query /var/lib/cwl/stg8aa02daf-52e0-4e46-afc9-3a5fff2f8c1d/GCF_012516375.2_ASM1251637v2_genomic.fna.gz --refList GCF_012516375.2_ASM1251637v2_genomic.fna/target_genomes.txt --output GCF_012516375.2_ASM1251637v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:55,048] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:55,049] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc08071a0-cffe-4a9e-8ea0-7b8e1f5957ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:55,049] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc08071a0-cffe-4a9e-8ea0-7b8e1f5957ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:55,057] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:55,057] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:55,057] [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 oryzae	strain=1303	GCA_012516375.2	2725414	2725414	type	True	100.0	2787	2787	95	conclusive
Chitinophaga eiseniae	strain=DSM 22224	GCA_900167135.1	634771	634771	type	True	90.7397	2419	2787	95	below_threshold
Chitinophaga fulva	strain=G-6-1-13	GCA_012927205.1	2728842	2728842	type	True	85.8946	2026	2787	95	below_threshold
Chitinophaga varians	strain=KACC 19415	GCA_014529945.1	2202339	2202339	type	True	85.593	2059	2787	95	below_threshold
Chitinophaga qingshengii	strain=JCM 30026	GCA_014529935.1	1569794	1569794	type	True	83.9373	1857	2787	95	below_threshold
Chitinophaga hostae	strain=2R12	GCA_018224885.1	2831022	2831022	type	True	79.1685	862	2787	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:55,058] [INFO] DFAST Taxonomy check result was written to GCF_012516375.2_ASM1251637v2_genomic.fna/tc_result.tsv
[2024-01-24 13:19:55,059] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:55,059] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:55,059] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc08071a0-cffe-4a9e-8ea0-7b8e1f5957ca/dqc_reference/checkm_data
[2024-01-24 13:19:55,060] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:55,141] [INFO] Task started: CheckM
[2024-01-24 13:19:55,141] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012516375.2_ASM1251637v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012516375.2_ASM1251637v2_genomic.fna/checkm_input GCF_012516375.2_ASM1251637v2_genomic.fna/checkm_result
[2024-01-24 13:22:57,032] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:57,033] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:57,054] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:57,054] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:57,055] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012516375.2_ASM1251637v2_genomic.fna/markers.fasta)
[2024-01-24 13:22:57,055] [INFO] Task started: Blastn
[2024-01-24 13:22:57,055] [INFO] Running command: blastn -query GCF_012516375.2_ASM1251637v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgc08071a0-cffe-4a9e-8ea0-7b8e1f5957ca/dqc_reference/reference_markers_gtdb.fasta -out GCF_012516375.2_ASM1251637v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:57,882] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:57,891] [INFO] Selected 6 target genomes.
[2024-01-24 13:22:57,891] [INFO] Target genome list was writen to GCF_012516375.2_ASM1251637v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:57,898] [INFO] Task started: fastANI
[2024-01-24 13:22:57,898] [INFO] Running command: fastANI --query /var/lib/cwl/stg8aa02daf-52e0-4e46-afc9-3a5fff2f8c1d/GCF_012516375.2_ASM1251637v2_genomic.fna.gz --refList GCF_012516375.2_ASM1251637v2_genomic.fna/target_genomes_gtdb.txt --output GCF_012516375.2_ASM1251637v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:10,971] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:10,978] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:10,978] [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_012516355.1	s__Chitinophaga sp012516355	99.4864	2715	2787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	99.48	99.48	0.97	0.97	2	conclusive
GCF_900167135.1	s__Chitinophaga eiseniae	90.7397	2419	2787	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	85.8958	2026	2787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012641275.1	s__Chitinophaga varians_A	85.7366	2107	2787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014529945.1	s__Chitinophaga varians	85.6045	2056	2787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014529935.1	s__Chitinophaga qingshengii	83.9411	1856	2787	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 13:23:10,979] [INFO] GTDB search result was written to GCF_012516375.2_ASM1251637v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:10,980] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:10,983] [INFO] DFAST_QC result json was written to GCF_012516375.2_ASM1251637v2_genomic.fna/dqc_result.json
[2024-01-24 13:23:10,983] [INFO] DFAST_QC completed!
[2024-01-24 13:23:10,983] [INFO] Total running time: 0h4m45s