[2024-01-25 18:08:20,596] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:08:20,598] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:08:20,598] [INFO] DQC Reference Directory: /var/lib/cwl/stgcfd3de7d-0cd7-4802-82cc-4ddf2dd772c7/dqc_reference
[2024-01-25 18:08:21,785] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:08:21,785] [INFO] Task started: Prodigal
[2024-01-25 18:08:21,786] [INFO] Running command: gunzip -c /var/lib/cwl/stga85faf1c-418e-4496-9510-98fb6b40949b/GCF_003149455.1_ASM314945v1_genomic.fna.gz | prodigal -d GCF_003149455.1_ASM314945v1_genomic.fna/cds.fna -a GCF_003149455.1_ASM314945v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:08:50,201] [INFO] Task succeeded: Prodigal
[2024-01-25 18:08:50,202] [INFO] Task started: HMMsearch
[2024-01-25 18:08:50,202] [INFO] Running command: hmmsearch --tblout GCF_003149455.1_ASM314945v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcfd3de7d-0cd7-4802-82cc-4ddf2dd772c7/dqc_reference/reference_markers.hmm GCF_003149455.1_ASM314945v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:08:50,493] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:08:50,494] [INFO] Found 6/6 markers.
[2024-01-25 18:08:50,544] [INFO] Query marker FASTA was written to GCF_003149455.1_ASM314945v1_genomic.fna/markers.fasta
[2024-01-25 18:08:50,545] [INFO] Task started: Blastn
[2024-01-25 18:08:50,545] [INFO] Running command: blastn -query GCF_003149455.1_ASM314945v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfd3de7d-0cd7-4802-82cc-4ddf2dd772c7/dqc_reference/reference_markers.fasta -out GCF_003149455.1_ASM314945v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:08:51,098] [INFO] Task succeeded: Blastn
[2024-01-25 18:08:51,101] [INFO] Selected 13 target genomes.
[2024-01-25 18:08:51,101] [INFO] Target genome list was writen to GCF_003149455.1_ASM314945v1_genomic.fna/target_genomes.txt
[2024-01-25 18:08:51,113] [INFO] Task started: fastANI
[2024-01-25 18:08:51,113] [INFO] Running command: fastANI --query /var/lib/cwl/stga85faf1c-418e-4496-9510-98fb6b40949b/GCF_003149455.1_ASM314945v1_genomic.fna.gz --refList GCF_003149455.1_ASM314945v1_genomic.fna/target_genomes.txt --output GCF_003149455.1_ASM314945v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:09:05,826] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:05,827] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcfd3de7d-0cd7-4802-82cc-4ddf2dd772c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:09:05,827] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcfd3de7d-0cd7-4802-82cc-4ddf2dd772c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:09:05,836] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:09:05,836] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:09:05,836] [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 deserti	strain=XJ-2	GCA_003149455.1	2164099	2164099	type	True	100.0	2095	2097	95	conclusive
Chitinophaga rhizosphaerae	strain=T16R-86	GCA_003958645.1	1864947	1864947	type	True	81.9131	1271	2097	95	below_threshold
Chitinophaga chungangae	strain=MAH-28	GCA_017742215.1	2821488	2821488	type	True	78.9237	673	2097	95	below_threshold
Chitinophaga barathri	strain=YLT18	GCA_003807585.1	1647451	1647451	type	True	78.9137	685	2097	95	below_threshold
Chitinophaga barathri	strain=YLT18	GCA_003614855.1	1647451	1647451	type	True	78.884	694	2097	95	below_threshold
Chitinophaga lutea	strain=ZY74	GCA_003813775.1	2488634	2488634	type	True	78.7801	670	2097	95	below_threshold
Chitinophaga alhagiae	strain=T22	GCA_003568665.1	2203219	2203219	suspected-type	True	78.3264	580	2097	95	below_threshold
Chitinophaga alhagiae	strain=T22	GCA_003177275.1	2203219	2203219	suspected-type	True	78.3168	322	2097	95	below_threshold
Chitinophaga silvisoli	strain=K20C18050901	GCA_003412465.1	2291814	2291814	type	True	77.1519	168	2097	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:09:05,838] [INFO] DFAST Taxonomy check result was written to GCF_003149455.1_ASM314945v1_genomic.fna/tc_result.tsv
[2024-01-25 18:09:05,838] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:09:05,839] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:09:05,839] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcfd3de7d-0cd7-4802-82cc-4ddf2dd772c7/dqc_reference/checkm_data
[2024-01-25 18:09:05,840] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:09:05,905] [INFO] Task started: CheckM
[2024-01-25 18:09:05,905] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003149455.1_ASM314945v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003149455.1_ASM314945v1_genomic.fna/checkm_input GCF_003149455.1_ASM314945v1_genomic.fna/checkm_result
[2024-01-25 18:10:19,897] [INFO] Task succeeded: CheckM
[2024-01-25 18:10:19,898] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:10:19,918] [INFO] ===== Completeness check finished =====
[2024-01-25 18:10:19,918] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:10:19,920] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003149455.1_ASM314945v1_genomic.fna/markers.fasta)
[2024-01-25 18:10:19,921] [INFO] Task started: Blastn
[2024-01-25 18:10:19,921] [INFO] Running command: blastn -query GCF_003149455.1_ASM314945v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfd3de7d-0cd7-4802-82cc-4ddf2dd772c7/dqc_reference/reference_markers_gtdb.fasta -out GCF_003149455.1_ASM314945v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:20,731] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:20,736] [INFO] Selected 9 target genomes.
[2024-01-25 18:10:20,736] [INFO] Target genome list was writen to GCF_003149455.1_ASM314945v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:10:20,751] [INFO] Task started: fastANI
[2024-01-25 18:10:20,751] [INFO] Running command: fastANI --query /var/lib/cwl/stga85faf1c-418e-4496-9510-98fb6b40949b/GCF_003149455.1_ASM314945v1_genomic.fna.gz --refList GCF_003149455.1_ASM314945v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003149455.1_ASM314945v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:10:32,595] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:32,602] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:10:32,602] [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_003149455.1	s__Chitinophaga deserti	100.0	2095	2097	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_902167325.1	s__Chitinophaga pinensis_A	90.9153	1882	2097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	99.49	99.49	0.97	0.97	3	-
GCF_003958645.1	s__Chitinophaga rhizosphaerae	81.917	1270	2097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017742215.1	s__Chitinophaga sp017742215	78.9165	674	2097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003807585.1	s__Chitinophaga barathri	78.9074	686	2097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003813775.1	s__Chitinophaga lutea	78.7801	670	2097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003568665.1	s__Chitinophaga alhagiae	78.3332	579	2097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007992715.1	s__Chitinophaga cymbidii	78.3257	565	2097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003412465.1	s__Chitinophaga silvisoli	77.1519	168	2097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:10:32,604] [INFO] GTDB search result was written to GCF_003149455.1_ASM314945v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:10:32,604] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:10:32,607] [INFO] DFAST_QC result json was written to GCF_003149455.1_ASM314945v1_genomic.fna/dqc_result.json
[2024-01-25 18:10:32,608] [INFO] DFAST_QC completed!
[2024-01-25 18:10:32,608] [INFO] Total running time: 0h2m12s