[2024-01-24 13:49:54,865] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:54,866] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:54,866] [INFO] DQC Reference Directory: /var/lib/cwl/stgfcc76d6c-21db-4ab2-b833-c494cec948e8/dqc_reference
[2024-01-24 13:49:55,948] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:55,949] [INFO] Task started: Prodigal
[2024-01-24 13:49:55,949] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c0a3abe-7788-4615-b0ca-683f10dba98e/GCF_003217495.1_ASM321749v1_genomic.fna.gz | prodigal -d GCF_003217495.1_ASM321749v1_genomic.fna/cds.fna -a GCF_003217495.1_ASM321749v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:11,826] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:11,826] [INFO] Task started: HMMsearch
[2024-01-24 13:50:11,826] [INFO] Running command: hmmsearch --tblout GCF_003217495.1_ASM321749v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfcc76d6c-21db-4ab2-b833-c494cec948e8/dqc_reference/reference_markers.hmm GCF_003217495.1_ASM321749v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:12,099] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:12,100] [INFO] Found 6/6 markers.
[2024-01-24 13:50:12,144] [INFO] Query marker FASTA was written to GCF_003217495.1_ASM321749v1_genomic.fna/markers.fasta
[2024-01-24 13:50:12,144] [INFO] Task started: Blastn
[2024-01-24 13:50:12,144] [INFO] Running command: blastn -query GCF_003217495.1_ASM321749v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfcc76d6c-21db-4ab2-b833-c494cec948e8/dqc_reference/reference_markers.fasta -out GCF_003217495.1_ASM321749v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:12,686] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:12,688] [INFO] Selected 17 target genomes.
[2024-01-24 13:50:12,688] [INFO] Target genome list was writen to GCF_003217495.1_ASM321749v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:12,693] [INFO] Task started: fastANI
[2024-01-24 13:50:12,693] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c0a3abe-7788-4615-b0ca-683f10dba98e/GCF_003217495.1_ASM321749v1_genomic.fna.gz --refList GCF_003217495.1_ASM321749v1_genomic.fna/target_genomes.txt --output GCF_003217495.1_ASM321749v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:33,306] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:33,306] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfcc76d6c-21db-4ab2-b833-c494cec948e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:33,306] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfcc76d6c-21db-4ab2-b833-c494cec948e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:33,317] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:33,317] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:33,317] [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
Paenibacillus barcinonensis	strain=CECT 7022	GCA_003217495.1	198119	198119	type	True	100.0	2051	2052	95	conclusive
Paenibacillus silvae	strain=CGMCC 1.12770	GCA_014639235.1	1325358	1325358	type	True	89.9087	1740	2052	95	below_threshold
Paenibacillus polysaccharolyticus	strain=BL9	GCA_900102085.1	582692	582692	type	True	83.8752	1504	2052	95	below_threshold
Paenibacillus xylanexedens	strain=DSM 21292	GCA_017874615.1	528191	528191	suspected-type	True	81.5343	1146	2052	95	below_threshold
Paenibacillus amylolyticus	strain=NBRC 15957	GCA_004001025.1	1451	1451	suspected-type	True	81.3781	1140	2052	95	below_threshold
Paenibacillus xylanivorans	strain=A59	GCA_001280595.1	1705561	1705561	type	True	81.0152	944	2052	95	below_threshold
Paenibacillus pabuli	strain=NBRC 13638	GCA_001514495.1	1472	1472	suspected-type	True	81.0127	950	2052	95	below_threshold
Paenibacillus xylanilyticus	strain=LMG 21957	GCA_013359935.1	248903	248903	type	True	80.9957	888	2052	95	below_threshold
Paenibacillus illinoisensis	strain=NBRC 15959	GCA_004000925.1	59845	59845	type	True	80.8825	889	2052	95	below_threshold
Paenibacillus etheri	strain=SH7	GCA_001012825.2	1306852	1306852	type	True	77.2867	117	2052	95	below_threshold
Paenibacillus algicola	strain=HB172198	GCA_005577435.1	2565926	2565926	type	True	77.2367	127	2052	95	below_threshold
Paenibacillus roseus	strain=MAHUQ-46	GCA_016424485.1	2798579	2798579	type	True	76.9372	71	2052	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	76.8908	120	2052	95	below_threshold
Paenibacillus frigoriresistens	strain=LMG 31322	GCA_013266765.1	1143711	1143711	type	True	76.8462	52	2052	95	below_threshold
Paenibacillus sonchi	strain=LMG 24727	GCA_016772475.1	373687	373687	type	True	76.8169	142	2052	95	below_threshold
Paenibacillus anseongense	strain=MAH-34	GCA_009757995.1	2682845	2682845	type	True	76.3406	56	2052	95	below_threshold
Paenibacillus chondroitinus	strain=NBRC 15376	GCA_004000765.1	59842	59842	type	True	76.1053	51	2052	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:33,318] [INFO] DFAST Taxonomy check result was written to GCF_003217495.1_ASM321749v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:33,319] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:33,319] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:33,319] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfcc76d6c-21db-4ab2-b833-c494cec948e8/dqc_reference/checkm_data
[2024-01-24 13:50:33,320] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:33,378] [INFO] Task started: CheckM
[2024-01-24 13:50:33,378] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003217495.1_ASM321749v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003217495.1_ASM321749v1_genomic.fna/checkm_input GCF_003217495.1_ASM321749v1_genomic.fna/checkm_result
[2024-01-24 13:51:20,602] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:20,603] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:20,617] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:20,617] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:20,618] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003217495.1_ASM321749v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:20,618] [INFO] Task started: Blastn
[2024-01-24 13:51:20,618] [INFO] Running command: blastn -query GCF_003217495.1_ASM321749v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfcc76d6c-21db-4ab2-b833-c494cec948e8/dqc_reference/reference_markers_gtdb.fasta -out GCF_003217495.1_ASM321749v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:21,403] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:21,434] [INFO] Selected 9 target genomes.
[2024-01-24 13:51:21,435] [INFO] Target genome list was writen to GCF_003217495.1_ASM321749v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:21,441] [INFO] Task started: fastANI
[2024-01-24 13:51:21,441] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c0a3abe-7788-4615-b0ca-683f10dba98e/GCF_003217495.1_ASM321749v1_genomic.fna.gz --refList GCF_003217495.1_ASM321749v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003217495.1_ASM321749v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:34,457] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:34,463] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:34,463] [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_003217495.1	s__Paenibacillus barcinonensis	100.0	2051	2052	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_014639235.1	s__Paenibacillus silvae	89.9087	1740	2052	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.52	95.24	0.88	0.86	5	-
GCF_003719335.1	s__Paenibacillus amylolyticus_D	84.0122	1488	2052	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007680605.1	s__Paenibacillus xylanexedens_B	83.8993	1525	2052	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.13	99.13	0.96	0.96	2	-
GCF_900102085.1	s__Paenibacillus polysaccharolyticus	83.8738	1504	2052	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.73	97.72	0.92	0.92	4	-
GCA_017512705.1	s__Paenibacillus sp017512705	83.1935	1155	2052	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004001025.1	s__Paenibacillus amylolyticus	81.372	1141	2052	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	96.2155	97.25	97.08	0.90	0.88	9	-
GCF_001514495.1	s__Paenibacillus pabuli	81.0127	950	2052	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003287275.1	s__Paenibacillus taichungensis_A	81.0118	976	2052	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:34,465] [INFO] GTDB search result was written to GCF_003217495.1_ASM321749v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:34,466] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:34,469] [INFO] DFAST_QC result json was written to GCF_003217495.1_ASM321749v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:34,469] [INFO] DFAST_QC completed!
[2024-01-24 13:51:34,469] [INFO] Total running time: 0h1m40s