[2024-01-24 10:58:06,469] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:58:06,473] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:58:06,473] [INFO] DQC Reference Directory: /var/lib/cwl/stgdbbe1295-7119-4ad2-a86b-2b6fbfa38efe/dqc_reference
[2024-01-24 10:58:09,634] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:58:09,635] [INFO] Task started: Prodigal
[2024-01-24 10:58:09,635] [INFO] Running command: gunzip -c /var/lib/cwl/stg21bb2919-71a7-4a7b-9aac-e3174b4bd98d/GCF_017742215.1_ASM1774221v1_genomic.fna.gz | prodigal -d GCF_017742215.1_ASM1774221v1_genomic.fna/cds.fna -a GCF_017742215.1_ASM1774221v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:45,224] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:45,224] [INFO] Task started: HMMsearch
[2024-01-24 10:58:45,224] [INFO] Running command: hmmsearch --tblout GCF_017742215.1_ASM1774221v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdbbe1295-7119-4ad2-a86b-2b6fbfa38efe/dqc_reference/reference_markers.hmm GCF_017742215.1_ASM1774221v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:45,614] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:45,616] [INFO] Found 6/6 markers.
[2024-01-24 10:58:45,664] [INFO] Query marker FASTA was written to GCF_017742215.1_ASM1774221v1_genomic.fna/markers.fasta
[2024-01-24 10:58:45,664] [INFO] Task started: Blastn
[2024-01-24 10:58:45,664] [INFO] Running command: blastn -query GCF_017742215.1_ASM1774221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbbe1295-7119-4ad2-a86b-2b6fbfa38efe/dqc_reference/reference_markers.fasta -out GCF_017742215.1_ASM1774221v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:46,299] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:46,303] [INFO] Selected 12 target genomes.
[2024-01-24 10:58:46,303] [INFO] Target genome list was writen to GCF_017742215.1_ASM1774221v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:46,309] [INFO] Task started: fastANI
[2024-01-24 10:58:46,310] [INFO] Running command: fastANI --query /var/lib/cwl/stg21bb2919-71a7-4a7b-9aac-e3174b4bd98d/GCF_017742215.1_ASM1774221v1_genomic.fna.gz --refList GCF_017742215.1_ASM1774221v1_genomic.fna/target_genomes.txt --output GCF_017742215.1_ASM1774221v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:59,757] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:59,758] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdbbe1295-7119-4ad2-a86b-2b6fbfa38efe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:59,758] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdbbe1295-7119-4ad2-a86b-2b6fbfa38efe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:59,774] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:59,774] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:59,775] [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 chungangae	strain=MAH-28	GCA_017742215.1	2821488	2821488	type	True	100.0	2006	2007	95	conclusive
Chitinophaga barathri	strain=YLT18	GCA_003807585.1	1647451	1647451	type	True	84.7732	1500	2007	95	below_threshold
Chitinophaga barathri	strain=YLT18	GCA_003614855.1	1647451	1647451	type	True	84.7536	1511	2007	95	below_threshold
Chitinophaga lutea	strain=ZY74	GCA_003813775.1	2488634	2488634	type	True	80.466	1015	2007	95	below_threshold
Chitinophaga alhagiae	strain=T22	GCA_003177275.1	2203219	2203219	suspected-type	True	80.0065	474	2007	95	below_threshold
Chitinophaga alhagiae	strain=T22	GCA_003568665.1	2203219	2203219	suspected-type	True	79.848	937	2007	95	below_threshold
Chitinophaga rhizosphaerae	strain=T16R-86	GCA_003958645.1	1864947	1864947	type	True	79.71	873	2007	95	below_threshold
Chitinophaga hostae	strain=2R12	GCA_018224885.1	2831022	2831022	type	True	76.6425	235	2007	95	below_threshold
Hymenobacter terricola	strain=3F2	GCA_017921975.2	2819236	2819236	type	True	75.1453	64	2007	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:59,777] [INFO] DFAST Taxonomy check result was written to GCF_017742215.1_ASM1774221v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:59,777] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:59,778] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:59,778] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdbbe1295-7119-4ad2-a86b-2b6fbfa38efe/dqc_reference/checkm_data
[2024-01-24 10:58:59,779] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:59,843] [INFO] Task started: CheckM
[2024-01-24 10:58:59,844] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017742215.1_ASM1774221v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017742215.1_ASM1774221v1_genomic.fna/checkm_input GCF_017742215.1_ASM1774221v1_genomic.fna/checkm_result
[2024-01-24 11:00:30,898] [INFO] Task succeeded: CheckM
[2024-01-24 11:00:30,899] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:00:30,920] [INFO] ===== Completeness check finished =====
[2024-01-24 11:00:30,920] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:00:30,921] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017742215.1_ASM1774221v1_genomic.fna/markers.fasta)
[2024-01-24 11:00:30,921] [INFO] Task started: Blastn
[2024-01-24 11:00:30,922] [INFO] Running command: blastn -query GCF_017742215.1_ASM1774221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbbe1295-7119-4ad2-a86b-2b6fbfa38efe/dqc_reference/reference_markers_gtdb.fasta -out GCF_017742215.1_ASM1774221v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:00:31,740] [INFO] Task succeeded: Blastn
[2024-01-24 11:00:31,744] [INFO] Selected 7 target genomes.
[2024-01-24 11:00:31,744] [INFO] Target genome list was writen to GCF_017742215.1_ASM1774221v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:00:31,751] [INFO] Task started: fastANI
[2024-01-24 11:00:31,752] [INFO] Running command: fastANI --query /var/lib/cwl/stg21bb2919-71a7-4a7b-9aac-e3174b4bd98d/GCF_017742215.1_ASM1774221v1_genomic.fna.gz --refList GCF_017742215.1_ASM1774221v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017742215.1_ASM1774221v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:00:41,943] [INFO] Task succeeded: fastANI
[2024-01-24 11:00:41,955] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:00:41,955] [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_017742215.1	s__Chitinophaga sp017742215	100.0	2006	2007	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_003807585.1	s__Chitinophaga barathri	84.7611	1502	2007	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	80.4894	1011	2007	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	80.2535	952	2007	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	79.8542	937	2007	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003958645.1	s__Chitinophaga rhizosphaerae	79.7068	874	2007	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008086345.1	s__Chitinophaga sp008086345	79.3366	752	2007	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 11:00:41,957] [INFO] GTDB search result was written to GCF_017742215.1_ASM1774221v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:00:41,958] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:00:41,962] [INFO] DFAST_QC result json was written to GCF_017742215.1_ASM1774221v1_genomic.fna/dqc_result.json
[2024-01-24 11:00:41,962] [INFO] DFAST_QC completed!
[2024-01-24 11:00:41,962] [INFO] Total running time: 0h2m35s