[2024-01-25 20:00:20,821] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:00:20,823] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:00:20,823] [INFO] DQC Reference Directory: /var/lib/cwl/stg63516494-7071-47a8-8ab3-04ac299b295f/dqc_reference
[2024-01-25 20:00:22,011] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:00:22,011] [INFO] Task started: Prodigal
[2024-01-25 20:00:22,012] [INFO] Running command: gunzip -c /var/lib/cwl/stg739cbd43-de8d-4c4f-8c91-30d59b7f4554/GCF_002196965.1_ASM219696v1_genomic.fna.gz | prodigal -d GCF_002196965.1_ASM219696v1_genomic.fna/cds.fna -a GCF_002196965.1_ASM219696v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:00:32,737] [INFO] Task succeeded: Prodigal
[2024-01-25 20:00:32,738] [INFO] Task started: HMMsearch
[2024-01-25 20:00:32,738] [INFO] Running command: hmmsearch --tblout GCF_002196965.1_ASM219696v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63516494-7071-47a8-8ab3-04ac299b295f/dqc_reference/reference_markers.hmm GCF_002196965.1_ASM219696v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:00:32,973] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:00:32,974] [INFO] Found 6/6 markers.
[2024-01-25 20:00:33,012] [INFO] Query marker FASTA was written to GCF_002196965.1_ASM219696v1_genomic.fna/markers.fasta
[2024-01-25 20:00:33,012] [INFO] Task started: Blastn
[2024-01-25 20:00:33,013] [INFO] Running command: blastn -query GCF_002196965.1_ASM219696v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63516494-7071-47a8-8ab3-04ac299b295f/dqc_reference/reference_markers.fasta -out GCF_002196965.1_ASM219696v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:34,012] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:34,014] [INFO] Selected 15 target genomes.
[2024-01-25 20:00:34,014] [INFO] Target genome list was writen to GCF_002196965.1_ASM219696v1_genomic.fna/target_genomes.txt
[2024-01-25 20:00:34,017] [INFO] Task started: fastANI
[2024-01-25 20:00:34,017] [INFO] Running command: fastANI --query /var/lib/cwl/stg739cbd43-de8d-4c4f-8c91-30d59b7f4554/GCF_002196965.1_ASM219696v1_genomic.fna.gz --refList GCF_002196965.1_ASM219696v1_genomic.fna/target_genomes.txt --output GCF_002196965.1_ASM219696v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:00:47,859] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:47,859] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63516494-7071-47a8-8ab3-04ac299b295f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:00:47,859] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63516494-7071-47a8-8ab3-04ac299b295f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:00:47,869] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 20:00:47,869] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 20:00:47,870] [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
Paracoccus yeei	strain=G1212	GCA_002196965.1	147645	147645	type	True	100.0	1375	1384	95	inconclusive
Paracoccus yeei	strain=ATCC BAA-599	GCA_000622145.1	147645	147645	type	True	99.9885	1361	1384	95	inconclusive
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	95.8623	1029	1384	95	inconclusive
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	85.1533	810	1384	95	below_threshold
Paracoccus aminovorans	strain=DSM 8537	GCA_900113565.1	34004	34004	type	True	85.0435	817	1384	95	below_threshold
Paracoccus aminovorans		GCA_900005615.1	34004	34004	type	True	85.016	824	1384	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_003633525.1	82367	82367	type	True	84.8424	814	1384	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_008824185.1	82367	82367	type	True	84.7731	821	1384	95	below_threshold
Paracoccus limosus	strain=JCM 17370	GCA_009711185.1	913252	913252	type	True	84.7592	837	1384	95	below_threshold
Paracoccus denitrificans	strain=NBRC 102528	GCA_007989485.1	266	266	type	True	84.6085	837	1384	95	below_threshold
Paracoccus lutimaris	strain=CECT 8525	GCA_003337565.1	1490030	1490030	type	True	83.6467	764	1384	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	81.5611	696	1384	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	80.4329	564	1384	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	80.0042	497	1384	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	78.4445	497	1384	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:00:47,871] [INFO] DFAST Taxonomy check result was written to GCF_002196965.1_ASM219696v1_genomic.fna/tc_result.tsv
[2024-01-25 20:00:47,872] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:00:47,872] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:00:47,872] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63516494-7071-47a8-8ab3-04ac299b295f/dqc_reference/checkm_data
[2024-01-25 20:00:47,873] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:00:47,920] [INFO] Task started: CheckM
[2024-01-25 20:00:47,921] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002196965.1_ASM219696v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002196965.1_ASM219696v1_genomic.fna/checkm_input GCF_002196965.1_ASM219696v1_genomic.fna/checkm_result
[2024-01-25 20:01:29,083] [INFO] Task succeeded: CheckM
[2024-01-25 20:01:29,084] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:01:29,099] [INFO] ===== Completeness check finished =====
[2024-01-25 20:01:29,099] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:01:29,099] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002196965.1_ASM219696v1_genomic.fna/markers.fasta)
[2024-01-25 20:01:29,100] [INFO] Task started: Blastn
[2024-01-25 20:01:29,100] [INFO] Running command: blastn -query GCF_002196965.1_ASM219696v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63516494-7071-47a8-8ab3-04ac299b295f/dqc_reference/reference_markers_gtdb.fasta -out GCF_002196965.1_ASM219696v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:01:31,092] [INFO] Task succeeded: Blastn
[2024-01-25 20:01:31,095] [INFO] Selected 13 target genomes.
[2024-01-25 20:01:31,096] [INFO] Target genome list was writen to GCF_002196965.1_ASM219696v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:01:31,101] [INFO] Task started: fastANI
[2024-01-25 20:01:31,101] [INFO] Running command: fastANI --query /var/lib/cwl/stg739cbd43-de8d-4c4f-8c91-30d59b7f4554/GCF_002196965.1_ASM219696v1_genomic.fna.gz --refList GCF_002196965.1_ASM219696v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002196965.1_ASM219696v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:01:44,125] [INFO] Task succeeded: fastANI
[2024-01-25 20:01:44,135] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:01:44,136] [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_000622145.1	s__Paracoccus yeei	99.9885	1361	1384	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	96.0533	98.39	97.89	0.87	0.83	7	conclusive
GCF_003285265.1	s__Paracoccus mutanolyticus	95.836	1030	1384	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	96.0533	N/A	N/A	N/A	N/A	1	-
GCF_001546115.1	s__Paracoccus aminovorans_B	85.6349	864	1384	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	95.35	95.35	0.81	0.81	2	-
GCF_016446475.1	s__Paracoccus binzhouensis	85.1013	814	1384	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900005615.1	s__Paracoccus aminovorans	84.9973	824	1384	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000763885.1	s__Paracoccus versutus	84.9474	846	1384	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	98.67	98.17	0.87	0.76	7	-
GCF_009711185.1	s__Paracoccus limosus	84.8006	834	1384	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008824185.1	s__Paracoccus pantotrophus	84.7973	819	1384	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.22	98.98	0.90	0.84	8	-
GCF_000518925.1	s__Paracoccus sp000518925	84.7764	857	1384	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.13	98.71	0.90	0.89	3	-
GCF_900100045.1	s__Paracoccus denitrificans	84.5449	853	1384	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.78	98.70	0.97	0.88	7	-
GCF_001447385.1	s__Paracoccus sp001447385	84.4424	843	1384	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337565.1	s__Paracoccus lutimaris	83.6064	767	1384	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018056045.1	s__Paracoccus sp018056045	82.4383	478	1384	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:01:44,137] [INFO] GTDB search result was written to GCF_002196965.1_ASM219696v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:01:44,137] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:01:44,140] [INFO] DFAST_QC result json was written to GCF_002196965.1_ASM219696v1_genomic.fna/dqc_result.json
[2024-01-25 20:01:44,141] [INFO] DFAST_QC completed!
[2024-01-25 20:01:44,141] [INFO] Total running time: 0h1m23s