[2024-01-24 13:25:58,045] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:58,047] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:58,047] [INFO] DQC Reference Directory: /var/lib/cwl/stgf56c0432-76cf-49cd-a10f-aa0639e772b2/dqc_reference
[2024-01-24 13:26:00,375] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:26:00,377] [INFO] Task started: Prodigal
[2024-01-24 13:26:00,377] [INFO] Running command: gunzip -c /var/lib/cwl/stge743eca3-3412-4813-8826-7b13eb2da398/GCF_024359525.1_ASM2435952v1_genomic.fna.gz | prodigal -d GCF_024359525.1_ASM2435952v1_genomic.fna/cds.fna -a GCF_024359525.1_ASM2435952v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:10,929] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:10,930] [INFO] Task started: HMMsearch
[2024-01-24 13:26:10,930] [INFO] Running command: hmmsearch --tblout GCF_024359525.1_ASM2435952v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf56c0432-76cf-49cd-a10f-aa0639e772b2/dqc_reference/reference_markers.hmm GCF_024359525.1_ASM2435952v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:11,221] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:11,223] [INFO] Found 6/6 markers.
[2024-01-24 13:26:11,260] [INFO] Query marker FASTA was written to GCF_024359525.1_ASM2435952v1_genomic.fna/markers.fasta
[2024-01-24 13:26:11,261] [INFO] Task started: Blastn
[2024-01-24 13:26:11,261] [INFO] Running command: blastn -query GCF_024359525.1_ASM2435952v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf56c0432-76cf-49cd-a10f-aa0639e772b2/dqc_reference/reference_markers.fasta -out GCF_024359525.1_ASM2435952v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:12,127] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:12,131] [INFO] Selected 25 target genomes.
[2024-01-24 13:26:12,132] [INFO] Target genome list was writen to GCF_024359525.1_ASM2435952v1_genomic.fna/target_genomes.txt
[2024-01-24 13:26:12,161] [INFO] Task started: fastANI
[2024-01-24 13:26:12,161] [INFO] Running command: fastANI --query /var/lib/cwl/stge743eca3-3412-4813-8826-7b13eb2da398/GCF_024359525.1_ASM2435952v1_genomic.fna.gz --refList GCF_024359525.1_ASM2435952v1_genomic.fna/target_genomes.txt --output GCF_024359525.1_ASM2435952v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:31,198] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:31,198] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf56c0432-76cf-49cd-a10f-aa0639e772b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:31,199] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf56c0432-76cf-49cd-a10f-aa0639e772b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:31,222] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:26:31,222] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:26:31,223] [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 siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	80.1598	594	1212	95	below_threshold
Paracoccus zhejiangensis	strain=J6	GCA_002847445.1	1077935	1077935	type	True	80.1508	624	1212	95	below_threshold
Paracoccus siganidrum	strain=DSM 26381	GCA_003594835.1	1276757	1276757	type	True	80.118	563	1212	95	below_threshold
Paracoccus zeaxanthinifaciens	strain=ATCC 21588	GCA_000420145.1	187400	187400	type	True	80.068	487	1212	95	below_threshold
Paracoccus liaowanqingii	strain=2251	GCA_004683865.2	2560053	2560053	type	True	79.9666	539	1212	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_014656455.1	1915382	1915382	type	True	79.9279	503	1212	95	below_threshold
Paracoccus lichenicola	strain=YIM 132242	GCA_009708075.1	2665644	2665644	type	True	79.9236	515	1212	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_016757275.1	1915382	1915382	type	True	79.9036	499	1212	95	below_threshold
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	79.8672	529	1212	95	below_threshold
Paracoccus tibetensis	strain=CGMCC 1.8925	GCA_900102505.1	336292	336292	type	True	79.855	532	1212	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	79.8388	502	1212	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	79.77	520	1212	95	below_threshold
Paracoccus acridae	strain=CGMCC 1.15419	GCA_014642735.1	1795310	1795310	type	True	79.7287	508	1212	95	below_threshold
Paracoccus hibiscisoli	strain=CCTCC AB2016182	GCA_005048265.1	2023261	2023261	type	True	79.6514	516	1212	95	below_threshold
Paracoccus sediminis	strain=CMB17	GCA_004310385.1	1214787	1214787	type	True	79.5385	497	1212	95	below_threshold
Paracoccus yeei	strain=ATCC BAA-599	GCA_000622145.1	147645	147645	type	True	79.5234	476	1212	95	below_threshold
Paracoccus sediminis	strain=DSM 26170	GCA_900188295.1	1214787	1214787	type	True	79.4889	495	1212	95	below_threshold
Paracoccus alcaliphilus	strain=DSM 8512	GCA_900110285.1	34002	34002	type	True	79.4371	517	1212	95	below_threshold
Paracoccus indicus	strain=IO390502	GCA_003056335.1	2079229	2079229	type	True	79.4266	498	1212	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	79.4142	438	1212	95	below_threshold
Paracoccus salipaludis	strain=WN007	GCA_002287065.1	2032623	2032623	type	True	79.3964	452	1212	95	below_threshold
Paracoccus isoporae	strain=DSM 22220	GCA_900101865.1	591205	591205	type	True	79.1938	433	1212	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	79.1728	504	1212	95	below_threshold
Paracoccus lutimaris	strain=CECT 8525	GCA_003337565.1	1490030	1490030	type	True	79.1153	474	1212	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	78.9253	481	1212	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:31,399] [INFO] DFAST Taxonomy check result was written to GCF_024359525.1_ASM2435952v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:31,406] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:31,407] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:31,407] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf56c0432-76cf-49cd-a10f-aa0639e772b2/dqc_reference/checkm_data
[2024-01-24 13:26:31,410] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:31,464] [INFO] Task started: CheckM
[2024-01-24 13:26:31,464] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024359525.1_ASM2435952v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024359525.1_ASM2435952v1_genomic.fna/checkm_input GCF_024359525.1_ASM2435952v1_genomic.fna/checkm_result
[2024-01-24 13:27:08,377] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:08,379] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:08,404] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:08,404] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:08,404] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024359525.1_ASM2435952v1_genomic.fna/markers.fasta)
[2024-01-24 13:27:08,405] [INFO] Task started: Blastn
[2024-01-24 13:27:08,405] [INFO] Running command: blastn -query GCF_024359525.1_ASM2435952v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf56c0432-76cf-49cd-a10f-aa0639e772b2/dqc_reference/reference_markers_gtdb.fasta -out GCF_024359525.1_ASM2435952v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:09,710] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:09,714] [INFO] Selected 24 target genomes.
[2024-01-24 13:27:09,715] [INFO] Target genome list was writen to GCF_024359525.1_ASM2435952v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:09,736] [INFO] Task started: fastANI
[2024-01-24 13:27:09,736] [INFO] Running command: fastANI --query /var/lib/cwl/stge743eca3-3412-4813-8826-7b13eb2da398/GCF_024359525.1_ASM2435952v1_genomic.fna.gz --refList GCF_024359525.1_ASM2435952v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024359525.1_ASM2435952v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:27,340] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:27,366] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:27:27,366] [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_018860165.1	s__Paracoccus sp018860165	80.2103	572	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002847445.1	s__Paracoccus zhejiangensis	80.1651	621	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003709565.1	s__Paracoccus siganidrum	80.1464	595	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.98	0.98	2	-
GCF_017356265.1	s__Paracoccus fontiphilus	80.1445	500	1212	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	80.1274	525	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420145.1	s__Paracoccus zeaxanthinifaciens	80.0451	489	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009708075.1	s__Paracoccus lichenicola	79.9544	512	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004683865.2	s__Paracoccus liaowanqingii	79.9522	542	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	96.54	96.54	0.86	0.86	2	-
GCF_014656455.1	s__Paracoccus aerius	79.9279	503	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.01	98.03	0.91	0.84	3	-
GCF_018860625.1	s__Paracoccus sp018860625	79.9227	476	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016446475.1	s__Paracoccus binzhouensis	79.8853	525	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006151785.1	s__Paracoccus marcusii	79.8842	497	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.50	96.78	0.86	0.75	9	-
GCF_017744015.1	s__Paracoccus sp002732665	79.8508	550	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.29	98.58	0.98	0.95	3	-
GCF_900102505.1	s__Paracoccus tibetensis	79.8449	533	1212	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	79.789	518	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014642735.1	s__Paracoccus acridae	79.7363	507	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.80	97.80	0.86	0.86	2	-
GCF_005048265.1	s__Paracoccus hibiscisoli	79.6306	518	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	96.40	96.40	0.91	0.91	2	-
GCF_900188295.1	s__Paracoccus sediminis	79.4993	494	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900110285.1	s__Paracoccus alcaliphilus	79.4375	517	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003255745.1	s__Paracoccus saliphilus_A	79.3953	463	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101865.1	s__Paracoccus isoporae	79.1834	434	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013868135.1	s__Paracoccus sp013868135	79.1342	463	1212	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	79.1151	474	1212	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	78.847	297	1212	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 13:27:27,368] [INFO] GTDB search result was written to GCF_024359525.1_ASM2435952v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:27,368] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:27,374] [INFO] DFAST_QC result json was written to GCF_024359525.1_ASM2435952v1_genomic.fna/dqc_result.json
[2024-01-24 13:27:27,374] [INFO] DFAST_QC completed!
[2024-01-24 13:27:27,374] [INFO] Total running time: 0h1m29s