[2024-01-24 11:59:12,761] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:12,764] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:12,765] [INFO] DQC Reference Directory: /var/lib/cwl/stgbbcf6a40-aa47-48e5-b11b-e6b6abf77666/dqc_reference
[2024-01-24 11:59:14,131] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:14,132] [INFO] Task started: Prodigal
[2024-01-24 11:59:14,132] [INFO] Running command: gunzip -c /var/lib/cwl/stgfda13189-972a-40b6-bdf6-7175c5c400d3/GCF_016765795.1_ASM1676579v1_genomic.fna.gz | prodigal -d GCF_016765795.1_ASM1676579v1_genomic.fna/cds.fna -a GCF_016765795.1_ASM1676579v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:26,906] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:26,906] [INFO] Task started: HMMsearch
[2024-01-24 11:59:26,906] [INFO] Running command: hmmsearch --tblout GCF_016765795.1_ASM1676579v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbbcf6a40-aa47-48e5-b11b-e6b6abf77666/dqc_reference/reference_markers.hmm GCF_016765795.1_ASM1676579v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:27,229] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:27,231] [INFO] Found 6/6 markers.
[2024-01-24 11:59:27,282] [INFO] Query marker FASTA was written to GCF_016765795.1_ASM1676579v1_genomic.fna/markers.fasta
[2024-01-24 11:59:27,283] [INFO] Task started: Blastn
[2024-01-24 11:59:27,283] [INFO] Running command: blastn -query GCF_016765795.1_ASM1676579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbcf6a40-aa47-48e5-b11b-e6b6abf77666/dqc_reference/reference_markers.fasta -out GCF_016765795.1_ASM1676579v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:28,325] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:28,329] [INFO] Selected 16 target genomes.
[2024-01-24 11:59:28,329] [INFO] Target genome list was writen to GCF_016765795.1_ASM1676579v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:28,335] [INFO] Task started: fastANI
[2024-01-24 11:59:28,335] [INFO] Running command: fastANI --query /var/lib/cwl/stgfda13189-972a-40b6-bdf6-7175c5c400d3/GCF_016765795.1_ASM1676579v1_genomic.fna.gz --refList GCF_016765795.1_ASM1676579v1_genomic.fna/target_genomes.txt --output GCF_016765795.1_ASM1676579v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:41,839] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:41,839] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbbcf6a40-aa47-48e5-b11b-e6b6abf77666/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:41,839] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbbcf6a40-aa47-48e5-b11b-e6b6abf77666/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:41,852] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:59:41,853] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:59:41,853] [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
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	79.658	626	1259	95	below_threshold
Gemmobacter aquatilis	strain=DSM 3857	GCA_900110025.1	933059	933059	type	True	79.5354	662	1259	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	79.4899	615	1259	95	below_threshold
Gemmobacter lutimaris	strain=YJ-T1-11	GCA_003570715.1	2306023	2306023	type	True	79.2595	582	1259	95	below_threshold
Gemmobacter caeni	strain=CGMCC 1.7745	GCA_007830625.1	589035	589035	type	True	79.216	586	1259	95	below_threshold
Gemmobacter caeni	strain=DSM 21823	GCA_003054195.1	589035	589035	type	True	79.1884	586	1259	95	below_threshold
Gemmobacter straminiformis	strain=CAM-8	GCA_014243445.1	2045119	2045119	type	True	79.0464	591	1259	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	79.0185	538	1259	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	78.9823	586	1259	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	78.9098	526	1259	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	78.8872	576	1259	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	78.8864	587	1259	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	78.8691	576	1259	95	below_threshold
Gemmobacter nectariphilus	strain=DSM 15620	GCA_000429765.1	220343	220343	type	True	78.7166	475	1259	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	78.6254	517	1259	95	below_threshold
Rhodobacter tardus	strain=CYK-10	GCA_009925085.1	2699202	2699202	type	True	78.4928	468	1259	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:41,855] [INFO] DFAST Taxonomy check result was written to GCF_016765795.1_ASM1676579v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:41,855] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:41,855] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:41,855] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbbcf6a40-aa47-48e5-b11b-e6b6abf77666/dqc_reference/checkm_data
[2024-01-24 11:59:41,856] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:41,896] [INFO] Task started: CheckM
[2024-01-24 11:59:41,896] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016765795.1_ASM1676579v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016765795.1_ASM1676579v1_genomic.fna/checkm_input GCF_016765795.1_ASM1676579v1_genomic.fna/checkm_result
[2024-01-24 12:00:22,807] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:22,808] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:22,830] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:22,831] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:22,831] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016765795.1_ASM1676579v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:22,832] [INFO] Task started: Blastn
[2024-01-24 12:00:22,832] [INFO] Running command: blastn -query GCF_016765795.1_ASM1676579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbcf6a40-aa47-48e5-b11b-e6b6abf77666/dqc_reference/reference_markers_gtdb.fasta -out GCF_016765795.1_ASM1676579v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:24,684] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:24,687] [INFO] Selected 13 target genomes.
[2024-01-24 12:00:24,688] [INFO] Target genome list was writen to GCF_016765795.1_ASM1676579v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:24,697] [INFO] Task started: fastANI
[2024-01-24 12:00:24,697] [INFO] Running command: fastANI --query /var/lib/cwl/stgfda13189-972a-40b6-bdf6-7175c5c400d3/GCF_016765795.1_ASM1676579v1_genomic.fna.gz --refList GCF_016765795.1_ASM1676579v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016765795.1_ASM1676579v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:35,340] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:35,356] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:35,356] [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_016765795.1	s__UBA1943 sp016765795	100.0	1255	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002336845.1	s__UBA1943 sp002336845	87.4861	904	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859945.1	s__UBA1943 sp014859945	81.8546	601	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013328815.1	s__UBA1943 sp013328815	81.6652	824	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	97.27	97.27	0.97	0.97	2	-
GCA_011008935.1	s__KMS-5 sp011008935	80.1431	670	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__KMS-5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869835.1	s__KMS-5 sp016869835	79.6349	502	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__KMS-5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110025.1	s__Gemmobacter aquatilis	79.5535	660	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018798885.1	s__Gemmobacter sp018798885	79.4832	615	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003054195.1	s__Gemmobacter caeni	79.2002	585	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	98.77	98.23	0.88	0.79	5	-
GCF_002900965.1	s__ETT8 sp002900965	78.9179	529	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010915705.1	s__ETT8 sp010915705	78.902	526	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002794355.1	s__ETT8 sp002794355	78.7834	524	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013824045.1	s__Gemmobacter_B sp013824045	78.5139	384	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:35,358] [INFO] GTDB search result was written to GCF_016765795.1_ASM1676579v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:35,360] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:35,364] [INFO] DFAST_QC result json was written to GCF_016765795.1_ASM1676579v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:35,365] [INFO] DFAST_QC completed!
[2024-01-24 12:00:35,365] [INFO] Total running time: 0h1m23s