[2024-01-24 14:55:07,758] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:07,760] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:07,760] [INFO] DQC Reference Directory: /var/lib/cwl/stg74e0cd2e-1921-4f52-8190-a09357938f2b/dqc_reference
[2024-01-24 14:55:09,468] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:09,471] [INFO] Task started: Prodigal
[2024-01-24 14:55:09,472] [INFO] Running command: gunzip -c /var/lib/cwl/stg24f84e38-e8d2-4b6d-9d21-308edc2e4bd0/GCF_003568665.1_ASM356866v1_genomic.fna.gz | prodigal -d GCF_003568665.1_ASM356866v1_genomic.fna/cds.fna -a GCF_003568665.1_ASM356866v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:46,433] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:46,434] [INFO] Task started: HMMsearch
[2024-01-24 14:55:46,434] [INFO] Running command: hmmsearch --tblout GCF_003568665.1_ASM356866v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74e0cd2e-1921-4f52-8190-a09357938f2b/dqc_reference/reference_markers.hmm GCF_003568665.1_ASM356866v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:46,774] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:46,776] [INFO] Found 6/6 markers.
[2024-01-24 14:55:46,831] [INFO] Query marker FASTA was written to GCF_003568665.1_ASM356866v1_genomic.fna/markers.fasta
[2024-01-24 14:55:46,832] [INFO] Task started: Blastn
[2024-01-24 14:55:46,832] [INFO] Running command: blastn -query GCF_003568665.1_ASM356866v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74e0cd2e-1921-4f52-8190-a09357938f2b/dqc_reference/reference_markers.fasta -out GCF_003568665.1_ASM356866v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:47,433] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:47,436] [INFO] Selected 10 target genomes.
[2024-01-24 14:55:47,436] [INFO] Target genome list was writen to GCF_003568665.1_ASM356866v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:47,449] [INFO] Task started: fastANI
[2024-01-24 14:55:47,449] [INFO] Running command: fastANI --query /var/lib/cwl/stg24f84e38-e8d2-4b6d-9d21-308edc2e4bd0/GCF_003568665.1_ASM356866v1_genomic.fna.gz --refList GCF_003568665.1_ASM356866v1_genomic.fna/target_genomes.txt --output GCF_003568665.1_ASM356866v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:59,475] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:59,476] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74e0cd2e-1921-4f52-8190-a09357938f2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:59,476] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74e0cd2e-1921-4f52-8190-a09357938f2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:59,491] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:55:59,491] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:59,491] [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 alhagiae	strain=T22	GCA_003568665.1	2203219	2203219	suspected-type	True	100.0	2037	2038	95	conclusive
Chitinophaga alhagiae	strain=T22	GCA_003177275.1	2203219	2203219	suspected-type	True	99.9712	889	2038	95	conclusive
Chitinophaga lutea	strain=ZY74	GCA_003813775.1	2488634	2488634	type	True	82.2218	1250	2038	95	below_threshold
Chitinophaga barathri	strain=YLT18	GCA_003614855.1	1647451	1647451	type	True	79.8049	875	2038	95	below_threshold
Chitinophaga chungangae	strain=MAH-28	GCA_017742215.1	2821488	2821488	type	True	79.787	966	2038	95	below_threshold
Chitinophaga barathri	strain=YLT18	GCA_003807585.1	1647451	1647451	type	True	79.7732	867	2038	95	below_threshold
Chitinophaga rhizosphaerae	strain=T16R-86	GCA_003958645.1	1864947	1864947	type	True	78.6703	665	2038	95	below_threshold
Chitinophaga japonensis	strain=DSM 13484	GCA_007830125.1	104662	104662	type	True	77.7324	539	2038	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	75.1006	59	2038	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:59,493] [INFO] DFAST Taxonomy check result was written to GCF_003568665.1_ASM356866v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:59,493] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:59,494] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:59,494] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74e0cd2e-1921-4f52-8190-a09357938f2b/dqc_reference/checkm_data
[2024-01-24 14:55:59,495] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:59,551] [INFO] Task started: CheckM
[2024-01-24 14:55:59,551] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003568665.1_ASM356866v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003568665.1_ASM356866v1_genomic.fna/checkm_input GCF_003568665.1_ASM356866v1_genomic.fna/checkm_result
[2024-01-24 14:57:31,559] [INFO] Task succeeded: CheckM
[2024-01-24 14:57:31,561] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:57:31,580] [INFO] ===== Completeness check finished =====
[2024-01-24 14:57:31,580] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:57:31,581] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003568665.1_ASM356866v1_genomic.fna/markers.fasta)
[2024-01-24 14:57:31,581] [INFO] Task started: Blastn
[2024-01-24 14:57:31,581] [INFO] Running command: blastn -query GCF_003568665.1_ASM356866v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74e0cd2e-1921-4f52-8190-a09357938f2b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003568665.1_ASM356866v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:57:32,408] [INFO] Task succeeded: Blastn
[2024-01-24 14:57:32,412] [INFO] Selected 8 target genomes.
[2024-01-24 14:57:32,412] [INFO] Target genome list was writen to GCF_003568665.1_ASM356866v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:57:32,419] [INFO] Task started: fastANI
[2024-01-24 14:57:32,420] [INFO] Running command: fastANI --query /var/lib/cwl/stg24f84e38-e8d2-4b6d-9d21-308edc2e4bd0/GCF_003568665.1_ASM356866v1_genomic.fna.gz --refList GCF_003568665.1_ASM356866v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003568665.1_ASM356866v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:42,892] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:42,907] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:42,908] [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_003568665.1	s__Chitinophaga alhagiae	100.0	2037	2038	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003813775.1	s__Chitinophaga lutea	82.2156	1251	2038	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992715.1	s__Chitinophaga cymbidii	79.91	907	2038	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	79.7817	967	2038	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	79.7668	870	2038	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008086345.1	s__Chitinophaga sp008086345	79.4195	744	2038	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017849435.1	s__Chitinophaga niabensis_A	79.1641	645	2038	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830125.1	s__Chitinophaga japonensis	77.7317	539	2038	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 14:57:42,910] [INFO] GTDB search result was written to GCF_003568665.1_ASM356866v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:42,910] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:42,916] [INFO] DFAST_QC result json was written to GCF_003568665.1_ASM356866v1_genomic.fna/dqc_result.json
[2024-01-24 14:57:42,916] [INFO] DFAST_QC completed!
[2024-01-24 14:57:42,916] [INFO] Total running time: 0h2m35s