[2024-01-24 13:36:45,536] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:45,538] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:45,538] [INFO] DQC Reference Directory: /var/lib/cwl/stgc7970f7b-2421-4e5b-a6e4-b42e781fd7a5/dqc_reference
[2024-01-24 13:36:46,873] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:46,875] [INFO] Task started: Prodigal
[2024-01-24 13:36:46,875] [INFO] Running command: gunzip -c /var/lib/cwl/stg467aa2ab-ca24-49e4-87c3-ddb23400df13/GCF_014640295.1_ASM1464029v1_genomic.fna.gz | prodigal -d GCF_014640295.1_ASM1464029v1_genomic.fna/cds.fna -a GCF_014640295.1_ASM1464029v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:01,423] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:01,423] [INFO] Task started: HMMsearch
[2024-01-24 13:37:01,423] [INFO] Running command: hmmsearch --tblout GCF_014640295.1_ASM1464029v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc7970f7b-2421-4e5b-a6e4-b42e781fd7a5/dqc_reference/reference_markers.hmm GCF_014640295.1_ASM1464029v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:01,709] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:01,710] [INFO] Found 6/6 markers.
[2024-01-24 13:37:01,752] [INFO] Query marker FASTA was written to GCF_014640295.1_ASM1464029v1_genomic.fna/markers.fasta
[2024-01-24 13:37:01,752] [INFO] Task started: Blastn
[2024-01-24 13:37:01,752] [INFO] Running command: blastn -query GCF_014640295.1_ASM1464029v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7970f7b-2421-4e5b-a6e4-b42e781fd7a5/dqc_reference/reference_markers.fasta -out GCF_014640295.1_ASM1464029v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:02,368] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:02,373] [INFO] Selected 26 target genomes.
[2024-01-24 13:37:02,374] [INFO] Target genome list was writen to GCF_014640295.1_ASM1464029v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:02,384] [INFO] Task started: fastANI
[2024-01-24 13:37:02,385] [INFO] Running command: fastANI --query /var/lib/cwl/stg467aa2ab-ca24-49e4-87c3-ddb23400df13/GCF_014640295.1_ASM1464029v1_genomic.fna.gz --refList GCF_014640295.1_ASM1464029v1_genomic.fna/target_genomes.txt --output GCF_014640295.1_ASM1464029v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:29,071] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:29,071] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc7970f7b-2421-4e5b-a6e4-b42e781fd7a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:29,072] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc7970f7b-2421-4e5b-a6e4-b42e781fd7a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:29,089] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:29,089] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:29,090] [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 abyssi	strain=CGMCC 1.12987	GCA_014640295.1	1340531	1340531	type	True	100.0	1724	1725	95	conclusive
Paenibacillus roseus	strain=MAHUQ-46	GCA_016424485.1	2798579	2798579	type	True	77.8765	197	1725	95	below_threshold
Paenibacillus pinihumi	strain=DSM 23905	GCA_000422505.1	669462	669462	type	True	77.7824	218	1725	95	below_threshold
Paenibacillus phyllosphaerae	strain=CECT 5862	GCA_014192105.1	274593	274593	type	True	77.5489	188	1725	95	below_threshold
Paenibacillus oenotherae	strain=DT7-4	GCA_019443105.1	1435645	1435645	type	True	77.5344	180	1725	95	below_threshold
Paenibacillus pinisoli	strain=JCM 19203	GCA_003605435.1	1276110	1276110	type	True	77.433	161	1725	95	below_threshold
Paenibacillus harenae	strain=DSM 16969	GCA_000422465.1	306543	306543	type	True	77.3765	200	1725	95	below_threshold
Paenibacillus daejeonensis	strain=DSM 15491	GCA_000378385.1	135193	135193	type	True	77.3324	195	1725	95	below_threshold
Paenibacillus protaetiae	strain=FW100M-2	GCA_004135365.1	2509456	2509456	type	True	77.3084	156	1725	95	below_threshold
Paenibacillus algicola	strain=HB172198	GCA_005577435.1	2565926	2565926	type	True	77.2793	88	1725	95	below_threshold
Paenibacillus albus	strain=18JY67-1	GCA_003952225.1	2495582	2495582	type	True	77.2712	171	1725	95	below_threshold
Paenibacillus lignilyticus	strain=DLE-14	GCA_017942085.1	1172615	1172615	type	True	77.2241	175	1725	95	below_threshold
Paenibacillus alkaliterrae	strain=DSM 17040	GCA_021532375.1	320909	320909	type	True	77.2241	188	1725	95	below_threshold
Paenibacillus taihuensis	strain=CGMCC 1.10966	GCA_003386535.1	1156355	1156355	type	True	77.2193	177	1725	95	below_threshold
Paenibacillus radicis	strain=CGMCC 1.15286	GCA_014641555.1	1737354	1737354	type	True	77.1119	193	1725	95	below_threshold
Paenibacillus glycanilyticus subsp. hiroshimensis	strain=CCI5	GCA_015473105.1	2805378	126569	type	True	77.054	180	1725	95	below_threshold
Paenibacillus tarimensis	strain=DSM 19409	GCA_021532315.1	416012	416012	type	True	77.0483	185	1725	95	below_threshold
Paenibacillus gorillae		GCA_000513275.1	1243662	1243662	type	True	76.9379	181	1725	95	below_threshold
Paenibacillus cellulosilyticus	strain=CECT 5696	GCA_003182255.1	375489	375489	type	True	76.8946	147	1725	95	below_threshold
Paenibacillus nasutitermitis	strain=CGMCC 1.15178	GCA_014641075.1	1652958	1652958	type	True	76.8815	187	1725	95	below_threshold
Paenibacillus kobensis	strain=NBRC 15729	GCA_004000825.1	59841	59841	type	True	76.8601	150	1725	95	below_threshold
Paenibacillus baekrokdamisoli	strain=KCTC 33723	GCA_003945345.1	1712516	1712516	type	True	76.6979	152	1725	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:29,091] [INFO] DFAST Taxonomy check result was written to GCF_014640295.1_ASM1464029v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:29,092] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:29,092] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:29,092] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc7970f7b-2421-4e5b-a6e4-b42e781fd7a5/dqc_reference/checkm_data
[2024-01-24 13:37:29,094] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:29,148] [INFO] Task started: CheckM
[2024-01-24 13:37:29,149] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014640295.1_ASM1464029v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014640295.1_ASM1464029v1_genomic.fna/checkm_input GCF_014640295.1_ASM1464029v1_genomic.fna/checkm_result
[2024-01-24 13:38:13,590] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:13,591] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:13,609] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:13,609] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:13,609] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014640295.1_ASM1464029v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:13,610] [INFO] Task started: Blastn
[2024-01-24 13:38:13,610] [INFO] Running command: blastn -query GCF_014640295.1_ASM1464029v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7970f7b-2421-4e5b-a6e4-b42e781fd7a5/dqc_reference/reference_markers_gtdb.fasta -out GCF_014640295.1_ASM1464029v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:14,381] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:14,384] [INFO] Selected 24 target genomes.
[2024-01-24 13:38:14,384] [INFO] Target genome list was writen to GCF_014640295.1_ASM1464029v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:14,418] [INFO] Task started: fastANI
[2024-01-24 13:38:14,418] [INFO] Running command: fastANI --query /var/lib/cwl/stg467aa2ab-ca24-49e4-87c3-ddb23400df13/GCF_014640295.1_ASM1464029v1_genomic.fna.gz --refList GCF_014640295.1_ASM1464029v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014640295.1_ASM1464029v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:39,635] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:39,654] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:39,654] [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_014640295.1	s__Paenibacillus_D abyssi	100.0	1724	1725	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_D	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016424485.1	s__Paenibacillus_D sp016424485	77.947	196	1725	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422505.1	s__Paenibacillus_D pinihumi	77.7834	218	1725	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_D	95.0	99.89	99.89	1.00	1.00	2	-
GCF_009737085.1	s__Paenibacillus_C sp009737085	77.7023	174	1725	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004134985.1	s__Paenibacillus_D sp004134985	77.532	217	1725	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003605435.1	s__Paenibacillus_C pinisoli	77.433	161	1725	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_000422465.1	s__Paenibacillus_C harenae	77.3765	200	1725	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_014705655.1	s__Paenibacillus_C sp014705655	77.3402	203	1725	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_000378385.1	s__Paenibacillus_D daejeonensis	77.3324	195	1725	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135365.1	s__Paenibacillus_C protaetiae	77.3175	157	1725	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_004342525.1	s__Paenibacillus_Z sp004342525	77.2918	166	1725	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428245.1	s__Paenibacillus_C sp001428245	77.2409	213	1725	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_003952225.1	s__Paenibacillus_Z albus	77.232	170	1725	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386535.1	s__Paenibacillus_Z taihuensis	77.2251	178	1725	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741035.1	s__Paenibacillus_C sp002741035	77.1582	179	1725	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	95.68	95.68	0.84	0.84	2	-
GCF_900106745.1	s__Paenibacillus_Z sp900106745	77.1313	162	1725	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004000805.1	s__Paenibacillus_C glycanilyticus	77.095	175	1725	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	97.79	97.79	0.90	0.90	2	-
GCF_900116125.1	s__Paenibacillus_Z sp900116125	77.0563	181	1725	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	95.31	95.31	0.87	0.87	2	-
GCF_003217535.1	s__Paenibacillus_C sp003217535	77.034	200	1725	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_900110075.1	s__Paenibacillus_Z sp900110075	76.9864	167	1725	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014534655.1	s__Paenibacillus_E sp014534655	76.9399	122	1725	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_014641075.1	s__Paenibacillus_Z nasutitermitis	76.8597	185	1725	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779765.1	s__Paenibacillus_T sp014779765	76.6467	142	1725	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_T	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004307995.1	s__Paenibacillus_AF thalictri	76.604	114	1725	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AF	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:39,656] [INFO] GTDB search result was written to GCF_014640295.1_ASM1464029v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:39,657] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:39,661] [INFO] DFAST_QC result json was written to GCF_014640295.1_ASM1464029v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:39,662] [INFO] DFAST_QC completed!
[2024-01-24 13:38:39,662] [INFO] Total running time: 0h1m54s