[2024-01-24 13:22:02,263] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:02,265] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:02,265] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c9e475f-1582-4250-8211-13ca611a2ae6/dqc_reference
[2024-01-24 13:22:03,604] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:03,605] [INFO] Task started: Prodigal
[2024-01-24 13:22:03,605] [INFO] Running command: gunzip -c /var/lib/cwl/stgb3adc5b3-6141-4134-9101-9fc173b4896f/GCF_003993775.1_ASM399377v1_genomic.fna.gz | prodigal -d GCF_003993775.1_ASM399377v1_genomic.fna/cds.fna -a GCF_003993775.1_ASM399377v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:15,186] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:15,186] [INFO] Task started: HMMsearch
[2024-01-24 13:22:15,186] [INFO] Running command: hmmsearch --tblout GCF_003993775.1_ASM399377v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c9e475f-1582-4250-8211-13ca611a2ae6/dqc_reference/reference_markers.hmm GCF_003993775.1_ASM399377v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:15,468] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:15,469] [INFO] Found 6/6 markers.
[2024-01-24 13:22:15,506] [INFO] Query marker FASTA was written to GCF_003993775.1_ASM399377v1_genomic.fna/markers.fasta
[2024-01-24 13:22:15,507] [INFO] Task started: Blastn
[2024-01-24 13:22:15,507] [INFO] Running command: blastn -query GCF_003993775.1_ASM399377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c9e475f-1582-4250-8211-13ca611a2ae6/dqc_reference/reference_markers.fasta -out GCF_003993775.1_ASM399377v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:16,510] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:16,513] [INFO] Selected 14 target genomes.
[2024-01-24 13:22:16,514] [INFO] Target genome list was writen to GCF_003993775.1_ASM399377v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:16,519] [INFO] Task started: fastANI
[2024-01-24 13:22:16,519] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3adc5b3-6141-4134-9101-9fc173b4896f/GCF_003993775.1_ASM399377v1_genomic.fna.gz --refList GCF_003993775.1_ASM399377v1_genomic.fna/target_genomes.txt --output GCF_003993775.1_ASM399377v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:29,807] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:29,808] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c9e475f-1582-4250-8211-13ca611a2ae6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:29,808] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c9e475f-1582-4250-8211-13ca611a2ae6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:29,820] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:22:29,820] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:22:29,820] [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
Frigidibacter albus	strain=SP32	GCA_009908165.1	1465486	1465486	type	True	82.3834	784	1333	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_010993795.1	1465486	1465486	type	True	82.3445	790	1333	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009881095.1	1465486	1465486	type	True	82.3245	792	1333	95	below_threshold
Frigidibacter albus	strain=CGMCC 1.13995	GCA_014640395.1	1465486	1465486	type	True	82.2648	797	1333	95	below_threshold
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	82.0885	808	1333	95	below_threshold
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	80.2211	594	1333	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	80.1884	584	1333	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	80.1588	587	1333	95	below_threshold
Phaeovulum vinaykumarii	strain=JA123	GCA_900217755.1	407234	407234	type	True	79.9057	561	1333	95	below_threshold
Phaeovulum vinaykumarii	strain=DSM 18714	GCA_900156695.1	407234	407234	type	True	79.8746	567	1333	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	79.623	546	1333	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	79.3583	543	1333	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	78.8431	550	1333	95	below_threshold
Pseudogemmobacter bohemicus	strain=Cd-10	GCA_003290025.1	2250708	2250708	type	True	78.4294	444	1333	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:29,822] [INFO] DFAST Taxonomy check result was written to GCF_003993775.1_ASM399377v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:29,822] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:29,822] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:29,823] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c9e475f-1582-4250-8211-13ca611a2ae6/dqc_reference/checkm_data
[2024-01-24 13:22:29,824] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:29,865] [INFO] Task started: CheckM
[2024-01-24 13:22:29,865] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003993775.1_ASM399377v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003993775.1_ASM399377v1_genomic.fna/checkm_input GCF_003993775.1_ASM399377v1_genomic.fna/checkm_result
[2024-01-24 13:23:14,042] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:14,044] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:14,064] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:14,064] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:14,065] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003993775.1_ASM399377v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:14,065] [INFO] Task started: Blastn
[2024-01-24 13:23:14,065] [INFO] Running command: blastn -query GCF_003993775.1_ASM399377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c9e475f-1582-4250-8211-13ca611a2ae6/dqc_reference/reference_markers_gtdb.fasta -out GCF_003993775.1_ASM399377v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:15,970] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:15,974] [INFO] Selected 14 target genomes.
[2024-01-24 13:23:15,974] [INFO] Target genome list was writen to GCF_003993775.1_ASM399377v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:16,003] [INFO] Task started: fastANI
[2024-01-24 13:23:16,003] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3adc5b3-6141-4134-9101-9fc173b4896f/GCF_003993775.1_ASM399377v1_genomic.fna.gz --refList GCF_003993775.1_ASM399377v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003993775.1_ASM399377v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:27,768] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:27,788] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:27,788] [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_003993775.1	s__Frigidibacter sp003993775	100.0	1331	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002423245.1	s__Frigidibacter sp002423245	82.5573	656	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	98.55	98.55	0.85	0.85	2	-
GCF_009908165.1	s__Frigidibacter albus	82.3501	788	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	100.00	100.00	1.00	0.99	4	-
GCF_001620265.1	s__Frigidibacter mobilis	82.0957	807	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763725.1	s__JACXUX01 sp014763725	80.7734	495	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JACXUX01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011043545.1	s__JAAKGP01 sp011043545	80.2788	661	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAAKGP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002973535.1	s__Albidovulum denitrificans	80.0884	598	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240425.1	s__TMP-24 sp018240425	79.9276	521	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__TMP-24	95.0	99.95	99.95	0.97	0.97	2	-
GCF_900156695.1	s__Bieblia_A vinaykumarii	79.8845	566	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Bieblia_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018139985.1	s__JAGSOU01 sp018139985	79.793	538	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280515.1	s__Albidovulum sp002280515	79.7228	534	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012905.2	s__Cereibacter_A sphaeroides	79.7049	610	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.1736	98.82	96.57	0.94	0.87	24	-
GCA_008933605.1	s__Albidovulum sp008933605	79.6305	480	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002356635.1	s__QY30 sp002356635	79.4541	536	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__QY30	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:27,790] [INFO] GTDB search result was written to GCF_003993775.1_ASM399377v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:27,790] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:27,794] [INFO] DFAST_QC result json was written to GCF_003993775.1_ASM399377v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:27,794] [INFO] DFAST_QC completed!
[2024-01-24 13:23:27,794] [INFO] Total running time: 0h1m26s