[2024-01-24 13:37:25,964] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:25,965] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:25,966] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd9afe28-e153-4315-9329-589d31da3fec/dqc_reference
[2024-01-24 13:37:27,167] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:27,168] [INFO] Task started: Prodigal
[2024-01-24 13:37:27,168] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e4e4697-4857-4050-b279-b9a36b14bd32/GCF_021491915.1_ASM2149191v1_genomic.fna.gz | prodigal -d GCF_021491915.1_ASM2149191v1_genomic.fna/cds.fna -a GCF_021491915.1_ASM2149191v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:35,552] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:35,553] [INFO] Task started: HMMsearch
[2024-01-24 13:37:35,553] [INFO] Running command: hmmsearch --tblout GCF_021491915.1_ASM2149191v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd9afe28-e153-4315-9329-589d31da3fec/dqc_reference/reference_markers.hmm GCF_021491915.1_ASM2149191v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:35,819] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:35,820] [INFO] Found 6/6 markers.
[2024-01-24 13:37:35,847] [INFO] Query marker FASTA was written to GCF_021491915.1_ASM2149191v1_genomic.fna/markers.fasta
[2024-01-24 13:37:35,848] [INFO] Task started: Blastn
[2024-01-24 13:37:35,848] [INFO] Running command: blastn -query GCF_021491915.1_ASM2149191v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd9afe28-e153-4315-9329-589d31da3fec/dqc_reference/reference_markers.fasta -out GCF_021491915.1_ASM2149191v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:36,847] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:36,851] [INFO] Selected 13 target genomes.
[2024-01-24 13:37:36,851] [INFO] Target genome list was writen to GCF_021491915.1_ASM2149191v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:36,855] [INFO] Task started: fastANI
[2024-01-24 13:37:36,855] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e4e4697-4857-4050-b279-b9a36b14bd32/GCF_021491915.1_ASM2149191v1_genomic.fna.gz --refList GCF_021491915.1_ASM2149191v1_genomic.fna/target_genomes.txt --output GCF_021491915.1_ASM2149191v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:47,295] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:47,296] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd9afe28-e153-4315-9329-589d31da3fec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:47,296] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd9afe28-e153-4315-9329-589d31da3fec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:47,305] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:47,305] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:47,305] [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 everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	100.0	983	985	95	conclusive
Paracoccus acridae	strain=CGMCC 1.15419	GCA_014642735.1	1795310	1795310	type	True	87.6532	832	985	95	below_threshold
Paracoccus lichenicola	strain=YIM 132242	GCA_009708075.1	2665644	2665644	type	True	87.4193	772	985	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	87.4062	782	985	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_014656455.1	1915382	1915382	type	True	86.9347	813	985	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_016757275.1	1915382	1915382	type	True	86.8779	809	985	95	below_threshold
Paracoccus fontiphilus	strain=MVW-1	GCA_017356265.1	1815556	1815556	type	True	86.2579	759	985	95	below_threshold
Paracoccus sediminis	strain=CMB17	GCA_004310385.1	1214787	1214787	type	True	85.9156	753	985	95	below_threshold
Paracoccus sediminis	strain=DSM 26170	GCA_900188295.1	1214787	1214787	type	True	85.8348	754	985	95	below_threshold
Paracoccus subflavus	strain=GY0581	GCA_004310345.1	2528244	2528244	type	True	84.7009	692	985	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	81.1212	612	985	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	80.4816	560	985	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	79.0927	456	985	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:47,306] [INFO] DFAST Taxonomy check result was written to GCF_021491915.1_ASM2149191v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:47,307] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:47,307] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:47,307] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd9afe28-e153-4315-9329-589d31da3fec/dqc_reference/checkm_data
[2024-01-24 13:37:47,308] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:47,336] [INFO] Task started: CheckM
[2024-01-24 13:37:47,336] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021491915.1_ASM2149191v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021491915.1_ASM2149191v1_genomic.fna/checkm_input GCF_021491915.1_ASM2149191v1_genomic.fna/checkm_result
[2024-01-24 13:38:21,590] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:21,591] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:21,606] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:21,606] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:21,606] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021491915.1_ASM2149191v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:21,606] [INFO] Task started: Blastn
[2024-01-24 13:38:21,606] [INFO] Running command: blastn -query GCF_021491915.1_ASM2149191v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd9afe28-e153-4315-9329-589d31da3fec/dqc_reference/reference_markers_gtdb.fasta -out GCF_021491915.1_ASM2149191v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:23,385] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:23,387] [INFO] Selected 8 target genomes.
[2024-01-24 13:38:23,387] [INFO] Target genome list was writen to GCF_021491915.1_ASM2149191v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:23,397] [INFO] Task started: fastANI
[2024-01-24 13:38:23,397] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e4e4697-4857-4050-b279-b9a36b14bd32/GCF_021491915.1_ASM2149191v1_genomic.fna.gz --refList GCF_021491915.1_ASM2149191v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021491915.1_ASM2149191v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:30,055] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:30,061] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:38:30,061] [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_014642735.1	s__Paracoccus acridae	87.6401	833	985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.80	97.80	0.86	0.86	2	-
GCF_009708075.1	s__Paracoccus lichenicola	87.439	771	985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017315735.1	s__Paracoccus sp017315735	87.4062	782	985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900631945.1	s__Paracoccus haematequi	87.2118	795	985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656455.1	s__Paracoccus aerius	86.94	813	985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.01	98.03	0.91	0.84	3	-
GCF_017356265.1	s__Paracoccus fontiphilus	86.2579	759	985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188295.1	s__Paracoccus sediminis	85.8324	754	985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004310345.1	s__Paracoccus subflavus	84.6799	693	985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:30,063] [INFO] GTDB search result was written to GCF_021491915.1_ASM2149191v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:30,063] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:30,066] [INFO] DFAST_QC result json was written to GCF_021491915.1_ASM2149191v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:30,066] [INFO] DFAST_QC completed!
[2024-01-24 13:38:30,066] [INFO] Total running time: 0h1m4s