[2024-01-24 11:44:22,867] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:22,872] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:22,872] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a5a1c0c-f320-4bea-8c9c-d85d658a7270/dqc_reference
[2024-01-24 11:44:26,344] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:26,350] [INFO] Task started: Prodigal
[2024-01-24 11:44:26,351] [INFO] Running command: gunzip -c /var/lib/cwl/stge26514a9-f8bf-4a3a-873f-7782084a8e35/GCF_013359935.1_ASM1335993v1_genomic.fna.gz | prodigal -d GCF_013359935.1_ASM1335993v1_genomic.fna/cds.fna -a GCF_013359935.1_ASM1335993v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:46,297] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:46,298] [INFO] Task started: HMMsearch
[2024-01-24 11:44:46,298] [INFO] Running command: hmmsearch --tblout GCF_013359935.1_ASM1335993v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a5a1c0c-f320-4bea-8c9c-d85d658a7270/dqc_reference/reference_markers.hmm GCF_013359935.1_ASM1335993v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:46,676] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:46,678] [INFO] Found 6/6 markers.
[2024-01-24 11:44:46,758] [INFO] Query marker FASTA was written to GCF_013359935.1_ASM1335993v1_genomic.fna/markers.fasta
[2024-01-24 11:44:46,759] [INFO] Task started: Blastn
[2024-01-24 11:44:46,759] [INFO] Running command: blastn -query GCF_013359935.1_ASM1335993v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a5a1c0c-f320-4bea-8c9c-d85d658a7270/dqc_reference/reference_markers.fasta -out GCF_013359935.1_ASM1335993v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:47,380] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:47,384] [INFO] Selected 29 target genomes.
[2024-01-24 11:44:47,384] [INFO] Target genome list was writen to GCF_013359935.1_ASM1335993v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:47,406] [INFO] Task started: fastANI
[2024-01-24 11:44:47,406] [INFO] Running command: fastANI --query /var/lib/cwl/stge26514a9-f8bf-4a3a-873f-7782084a8e35/GCF_013359935.1_ASM1335993v1_genomic.fna.gz --refList GCF_013359935.1_ASM1335993v1_genomic.fna/target_genomes.txt --output GCF_013359935.1_ASM1335993v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:45:16,468] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:16,469] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a5a1c0c-f320-4bea-8c9c-d85d658a7270/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:45:16,469] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a5a1c0c-f320-4bea-8c9c-d85d658a7270/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:45:16,483] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:45:16,483] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:45:16,483] [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 xylanilyticus	strain=LMG 21957	GCA_013359935.1	248903	248903	type	True	100.0	2413	2416	95	conclusive
Paenibacillus illinoisensis	strain=NBRC 15959	GCA_004000925.1	59845	59845	type	True	87.3422	1826	2416	95	below_threshold
Paenibacillus pabuli	strain=NBRC 13638	GCA_001514495.1	1472	1472	suspected-type	True	83.2657	1460	2416	95	below_threshold
Paenibacillus xylanivorans	strain=A59	GCA_001280595.1	1705561	1705561	type	True	83.0176	1394	2416	95	below_threshold
Paenibacillus taichungensis	strain=DSM 19942	GCA_013359905.1	484184	484184	type	True	82.9287	1421	2416	95	below_threshold
Paenibacillus amylolyticus	strain=NBRC 15957	GCA_004001025.1	1451	1451	suspected-type	True	82.5253	1303	2416	95	below_threshold
Paenibacillus xylanexedens	strain=DSM 21292	GCA_017874615.1	528191	528191	suspected-type	True	82.4546	1305	2416	95	below_threshold
Paenibacillus barcinonensis	strain=CECT 7022	GCA_003217495.1	198119	198119	type	True	80.9989	897	2416	95	below_threshold
Paenibacillus polysaccharolyticus	strain=BL9	GCA_900102085.1	582692	582692	type	True	80.9549	942	2416	95	below_threshold
Paenibacillus segetis	strain=CGMCC 1.12769	GCA_014639155.1	1325360	1325360	type	True	77.9238	119	2416	95	below_threshold
Paenibacillus faecalis	strain=Marseille-P3787	GCA_900289175.1	2079532	2079532	type	True	77.7346	137	2416	95	below_threshold
Paenibacillus agri	strain=JW14	GCA_013359945.1	2744309	2744309	type	True	77.6619	173	2416	95	below_threshold
Paenibacillus selenitireducens	strain=ES3-24	GCA_002021565.1	1324314	1324314	type	True	77.5533	118	2416	95	below_threshold
Paenibacillus plantarum	strain=LMG 31461	GCA_013141695.1	2654975	2654975	type	True	77.1827	75	2416	95	below_threshold
Paenibacillus swuensis	strain=DY6	GCA_001644605.1	1178515	1178515	type	True	76.6252	63	2416	95	below_threshold
Paenibacillus lignilyticus	strain=DLE-14	GCA_017942085.1	1172615	1172615	type	True	76.601	88	2416	95	below_threshold
Paenibacillus foliorum	strain=LMG 31456	GCA_013141765.1	2654974	2654974	type	True	76.4893	69	2416	95	below_threshold
Paenibacillus curdlanolyticus	strain=YK9	GCA_000179615.1	59840	59840	type	True	76.3348	73	2416	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:45:16,485] [INFO] DFAST Taxonomy check result was written to GCF_013359935.1_ASM1335993v1_genomic.fna/tc_result.tsv
[2024-01-24 11:45:16,485] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:45:16,485] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:45:16,486] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a5a1c0c-f320-4bea-8c9c-d85d658a7270/dqc_reference/checkm_data
[2024-01-24 11:45:16,487] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:45:16,554] [INFO] Task started: CheckM
[2024-01-24 11:45:16,554] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013359935.1_ASM1335993v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013359935.1_ASM1335993v1_genomic.fna/checkm_input GCF_013359935.1_ASM1335993v1_genomic.fna/checkm_result
[2024-01-24 11:46:15,254] [INFO] Task succeeded: CheckM
[2024-01-24 11:46:15,255] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:46:15,278] [INFO] ===== Completeness check finished =====
[2024-01-24 11:46:15,278] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:46:15,278] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013359935.1_ASM1335993v1_genomic.fna/markers.fasta)
[2024-01-24 11:46:15,279] [INFO] Task started: Blastn
[2024-01-24 11:46:15,279] [INFO] Running command: blastn -query GCF_013359935.1_ASM1335993v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a5a1c0c-f320-4bea-8c9c-d85d658a7270/dqc_reference/reference_markers_gtdb.fasta -out GCF_013359935.1_ASM1335993v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:46:16,066] [INFO] Task succeeded: Blastn
[2024-01-24 11:46:16,071] [INFO] Selected 29 target genomes.
[2024-01-24 11:46:16,071] [INFO] Target genome list was writen to GCF_013359935.1_ASM1335993v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:46:16,109] [INFO] Task started: fastANI
[2024-01-24 11:46:16,110] [INFO] Running command: fastANI --query /var/lib/cwl/stge26514a9-f8bf-4a3a-873f-7782084a8e35/GCF_013359935.1_ASM1335993v1_genomic.fna.gz --refList GCF_013359935.1_ASM1335993v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013359935.1_ASM1335993v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:50,862] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:50,888] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:46:50,888] [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_013359935.1	s__Paenibacillus xylanilyticus	100.0	2413	2416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004000925.1	s__Paenibacillus illinoisensis	87.3326	1828	2416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	95.55	95.10	0.89	0.77	9	-
GCF_000499205.1	s__Paenibacillus sp000499205	83.7949	1488	2416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.89	98.31	0.94	0.92	4	-
GCF_014844075.1	s__Paenibacillus sp014844075	83.3466	1452	2416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514495.1	s__Paenibacillus pabuli	83.2584	1462	2416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109515.1	s__Paenibacillus sp900109515	83.0996	1323	2416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	95.23	95.20	0.85	0.85	7	-
GCF_001280595.1	s__Paenibacillus xylanivorans	83.0261	1392	2416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013359905.1	s__Paenibacillus taichungensis	82.937	1419	2416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.85	95.16	0.90	0.85	6	-
GCF_003287275.1	s__Paenibacillus taichungensis_A	82.9191	1427	2416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101225.1	s__Paenibacillus sp900101225	82.7263	1366	2416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.22	98.17	98.17	0.94	0.94	2	-
GCF_018614975.1	s__Paenibacillus polymyxa_E	82.6107	1262	2416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570725.1	s__Paenibacillus amylolyticus_A	82.561	1313	2416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.59	97.52	0.92	0.91	3	-
GCF_000316035.1	s__Paenibacillus sp000316035	82.5411	1227	2416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.8348	N/A	N/A	N/A	N/A	1	-
GCF_004001025.1	s__Paenibacillus amylolyticus	82.5191	1304	2416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	96.2155	97.25	97.08	0.90	0.88	9	-
GCF_008386395.1	s__Paenibacillus amylolyticus_B	82.5169	1343	2416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.96	95.65	0.92	0.85	8	-
GCF_012912005.1	s__Paenibacillus sp012912005	82.4849	1263	2416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003268635.1	s__Paenibacillus sp003268635	81.6481	1040	2416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426865.1	s__Paenibacillus sp001426865	81.535	1047	2416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.30	96.30	0.92	0.92	2	-
GCF_014639155.1	s__Paenibacillus_A segetis	77.9238	119	2416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013359945.1	s__Paenibacillus sp013359945	77.6796	172	2416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002021565.1	s__Paenibacillus_K selenitireducens	77.5403	116	2416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003991425.1	s__Paenibacillus_A lutimineralis	77.4395	120	2416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001637205.1	s__Paenibacillus glacialis	77.418	100	2416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013141695.1	s__Paenibacillus_E plantarum	77.1072	74	2416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428045.1	s__Paenibacillus_E sp001428045	77.0218	80	2416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:46:50,890] [INFO] GTDB search result was written to GCF_013359935.1_ASM1335993v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:50,890] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:50,895] [INFO] DFAST_QC result json was written to GCF_013359935.1_ASM1335993v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:50,895] [INFO] DFAST_QC completed!
[2024-01-24 11:46:50,895] [INFO] Total running time: 0h2m28s