[2024-01-24 13:22:01,486] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:01,490] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:01,490] [INFO] DQC Reference Directory: /var/lib/cwl/stgf925dabd-1418-4f90-bbbd-150db13531b7/dqc_reference
[2024-01-24 13:22:02,929] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:02,930] [INFO] Task started: Prodigal
[2024-01-24 13:22:02,931] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2a7d5e2-9735-4351-9db3-026c8a96e870/GCF_026794045.1_ASM2679404v1_genomic.fna.gz | prodigal -d GCF_026794045.1_ASM2679404v1_genomic.fna/cds.fna -a GCF_026794045.1_ASM2679404v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:26,760] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:26,760] [INFO] Task started: HMMsearch
[2024-01-24 13:22:26,760] [INFO] Running command: hmmsearch --tblout GCF_026794045.1_ASM2679404v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf925dabd-1418-4f90-bbbd-150db13531b7/dqc_reference/reference_markers.hmm GCF_026794045.1_ASM2679404v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:27,216] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:27,218] [INFO] Found 6/6 markers.
[2024-01-24 13:22:27,269] [INFO] Query marker FASTA was written to GCF_026794045.1_ASM2679404v1_genomic.fna/markers.fasta
[2024-01-24 13:22:27,269] [INFO] Task started: Blastn
[2024-01-24 13:22:27,269] [INFO] Running command: blastn -query GCF_026794045.1_ASM2679404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf925dabd-1418-4f90-bbbd-150db13531b7/dqc_reference/reference_markers.fasta -out GCF_026794045.1_ASM2679404v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:27,883] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:27,887] [INFO] Selected 30 target genomes.
[2024-01-24 13:22:27,887] [INFO] Target genome list was writen to GCF_026794045.1_ASM2679404v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:27,910] [INFO] Task started: fastANI
[2024-01-24 13:22:27,911] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2a7d5e2-9735-4351-9db3-026c8a96e870/GCF_026794045.1_ASM2679404v1_genomic.fna.gz --refList GCF_026794045.1_ASM2679404v1_genomic.fna/target_genomes.txt --output GCF_026794045.1_ASM2679404v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:55,063] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:55,064] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf925dabd-1418-4f90-bbbd-150db13531b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:55,064] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf925dabd-1418-4f90-bbbd-150db13531b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:55,080] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:22:55,080] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:22:55,080] [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 thiaminolyticus	strain=NRRL B-4156	GCA_007066085.1	49283	49283	type	True	80.1422	741	2087	95	below_threshold
Paenibacillus thiaminolyticus	strain=NRRL B-4156	GCA_002161855.1	49283	49283	type	True	80.0564	743	2087	95	below_threshold
Paenibacillus thiaminolyticus	strain=NBRC 15656	GCA_004001005.1	49283	49283	type	True	79.9908	716	2087	95	below_threshold
Paenibacillus alvei	strain=DSM 29	GCA_000293805.1	44250	44250	type	True	79.9346	522	2087	95	below_threshold
Paenibacillus popilliae	strain=ATCC 14706	GCA_000315235.1	78057	78057	type	True	78.6121	355	2087	95	below_threshold
Paenibacillus arenosi	strain=CAU 1523	GCA_014841135.1	2774142	2774142	type	True	77.5481	157	2087	95	below_threshold
Paenibacillus caui	strain=81-11	GCA_019904135.1	2873927	2873927	type	True	77.0448	86	2087	95	below_threshold
Paenibacillus paeoniae	strain=M4BSY-1	GCA_003388735.1	2292705	2292705	type	True	76.632	78	2087	95	below_threshold
Paenibacillus protaetiae	strain=FW100M-2	GCA_004135365.1	2509456	2509456	type	True	76.4886	97	2087	95	below_threshold
Paenibacillus tianjinensis	strain=TB2019	GCA_017086365.1	2810347	2810347	type	True	76.4844	78	2087	95	below_threshold
Paenibacillus barengoltzii	strain=NBRC 101215	GCA_004000745.1	343517	343517	type	True	76.474	97	2087	95	below_threshold
Paenibacillus senegalimassiliensis	strain=SIT18	GCA_001486585.1	1737426	1737426	type	True	76.4524	66	2087	95	below_threshold
Paenibacillus pinisoli	strain=JCM 19203	GCA_003605435.1	1276110	1276110	type	True	76.4513	95	2087	95	below_threshold
Paenibacillus hemerocallicola	strain=KCTC 33185	GCA_006265175.1	1172614	1172614	type	True	76.3442	109	2087	95	below_threshold
Paenibacillus allorhizosphaerae	strain=CIP 111802	GCA_910594985.1	2849866	2849866	type	True	76.316	120	2087	95	below_threshold
Saccharibacillus deserti	strain=KCTC 33693	GCA_013185225.1	1634444	1634444	type	True	76.2446	81	2087	95	below_threshold
Saccharibacillus deserti	strain=WLJ055	GCA_013618475.1	1634444	1634444	type	True	76.2446	81	2087	95	below_threshold
Paenibacillus mesophilus	strain=SYSU K30004	GCA_005938385.1	2582849	2582849	type	True	76.2428	114	2087	95	below_threshold
Paenibacillus chibensis	strain=NBRC 15958	GCA_004001045.1	59846	59846	type	True	76.2212	123	2087	95	below_threshold
Paenibacillus flagellatus	strain=DXL2	GCA_003217775.1	2211139	2211139	type	True	76.2118	122	2087	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	76.1267	94	2087	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:55,083] [INFO] DFAST Taxonomy check result was written to GCF_026794045.1_ASM2679404v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:55,087] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:55,087] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:55,088] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf925dabd-1418-4f90-bbbd-150db13531b7/dqc_reference/checkm_data
[2024-01-24 13:22:55,090] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:55,155] [INFO] Task started: CheckM
[2024-01-24 13:22:55,156] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026794045.1_ASM2679404v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026794045.1_ASM2679404v1_genomic.fna/checkm_input GCF_026794045.1_ASM2679404v1_genomic.fna/checkm_result
[2024-01-24 13:24:00,713] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:00,715] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:00,736] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:00,736] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:00,737] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026794045.1_ASM2679404v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:00,737] [INFO] Task started: Blastn
[2024-01-24 13:24:00,737] [INFO] Running command: blastn -query GCF_026794045.1_ASM2679404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf925dabd-1418-4f90-bbbd-150db13531b7/dqc_reference/reference_markers_gtdb.fasta -out GCF_026794045.1_ASM2679404v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:01,505] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:01,510] [INFO] Selected 16 target genomes.
[2024-01-24 13:24:01,510] [INFO] Target genome list was writen to GCF_026794045.1_ASM2679404v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:01,576] [INFO] Task started: fastANI
[2024-01-24 13:24:01,576] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2a7d5e2-9735-4351-9db3-026c8a96e870/GCF_026794045.1_ASM2679404v1_genomic.fna.gz --refList GCF_026794045.1_ASM2679404v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026794045.1_ASM2679404v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:18,421] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:18,437] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:18,438] [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_017052585.1	s__Paenibacillus_B apiarius	98.4938	1958	2087	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	98.54	98.54	0.95	0.95	2	conclusive
GCF_000283315.1	s__Paenibacillus_B sp000283315	89.6227	1743	2087	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007066085.1	s__Paenibacillus_B thiaminolyticus	80.1621	741	2087	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	98.67	95.07	0.96	0.85	7	-
GCF_000245555.1	s__Paenibacillus_B dendritiformis_A	80.0761	677	2087	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	97.57	96.94	0.92	0.90	3	-
GCF_018403065.1	s__Paenibacillus_B dendritiformis_B	80.0469	672	2087	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000293805.1	s__Paenibacillus_B alvei	79.9343	522	2087	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	97.68	97.62	0.90	0.89	5	-
GCF_013266915.1	s__Paenibacillus_B sp900539405	79.4613	666	2087	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	99.54	99.32	0.96	0.95	4	-
GCF_015845845.1	s__Paenibacillus_B dendritiformis_C	79.431	670	2087	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001894745.1	s__Paenibacillus_B sp001894745	79.1256	481	2087	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	96.43	95.29	0.89	0.85	9	-
GCF_000315235.1	s__Paenibacillus_B popilliae	78.6121	355	2087	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014863545.1	s__Paenibacillus lautus_A	76.8364	125	2087	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.37	95.82	0.93	0.90	10	-
GCF_004135365.1	s__Paenibacillus_C protaetiae	76.5504	99	2087	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017086365.1	s__Paenibacillus sp017086365	76.4844	78	2087	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001486585.1	s__Paenibacillus_A senegalimassiliensis	76.4524	66	2087	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:18,439] [INFO] GTDB search result was written to GCF_026794045.1_ASM2679404v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:18,440] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:18,443] [INFO] DFAST_QC result json was written to GCF_026794045.1_ASM2679404v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:18,444] [INFO] DFAST_QC completed!
[2024-01-24 13:24:18,444] [INFO] Total running time: 0h2m17s