[2024-01-24 14:19:20,342] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:20,344] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:20,344] [INFO] DQC Reference Directory: /var/lib/cwl/stgc542223d-3786-498d-90de-5033fc4e4ce8/dqc_reference
[2024-01-24 14:19:23,549] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:23,551] [INFO] Task started: Prodigal
[2024-01-24 14:19:23,551] [INFO] Running command: gunzip -c /var/lib/cwl/stg9c0735f8-5f2d-46f9-8565-75e044d98caa/GCF_020169515.1_ASM2016951v1_genomic.fna.gz | prodigal -d GCF_020169515.1_ASM2016951v1_genomic.fna/cds.fna -a GCF_020169515.1_ASM2016951v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:41,665] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:41,665] [INFO] Task started: HMMsearch
[2024-01-24 14:19:41,665] [INFO] Running command: hmmsearch --tblout GCF_020169515.1_ASM2016951v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc542223d-3786-498d-90de-5033fc4e4ce8/dqc_reference/reference_markers.hmm GCF_020169515.1_ASM2016951v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:42,147] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:42,148] [INFO] Found 6/6 markers.
[2024-01-24 14:19:42,202] [INFO] Query marker FASTA was written to GCF_020169515.1_ASM2016951v1_genomic.fna/markers.fasta
[2024-01-24 14:19:42,203] [INFO] Task started: Blastn
[2024-01-24 14:19:42,203] [INFO] Running command: blastn -query GCF_020169515.1_ASM2016951v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc542223d-3786-498d-90de-5033fc4e4ce8/dqc_reference/reference_markers.fasta -out GCF_020169515.1_ASM2016951v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:44,804] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:44,808] [INFO] Selected 21 target genomes.
[2024-01-24 14:19:44,808] [INFO] Target genome list was writen to GCF_020169515.1_ASM2016951v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:44,855] [INFO] Task started: fastANI
[2024-01-24 14:19:44,855] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c0735f8-5f2d-46f9-8565-75e044d98caa/GCF_020169515.1_ASM2016951v1_genomic.fna.gz --refList GCF_020169515.1_ASM2016951v1_genomic.fna/target_genomes.txt --output GCF_020169515.1_ASM2016951v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:12,421] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:12,423] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc542223d-3786-498d-90de-5033fc4e4ce8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:12,423] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc542223d-3786-498d-90de-5033fc4e4ce8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:12,438] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:20:12,438] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:20:12,438] [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 alkaliterrae	strain=DSM 17040	GCA_021532375.1	320909	320909	type	True	80.6393	718	2081	95	below_threshold
Paenibacillus prosopidis	strain=CECT 7506	GCA_003337375.1	630520	630520	type	True	80.3143	677	2081	95	below_threshold
Paenibacillus harenae	strain=DSM 16969	GCA_000422465.1	306543	306543	type	True	80.0248	787	2081	95	below_threshold
Paenibacillus endophyticus	strain=CECT 8234	GCA_014192395.1	1294268	1294268	type	True	79.0825	551	2081	95	below_threshold
Paenibacillus paridis	strain=py1325	GCA_006345825.1	2583376	2583376	type	True	79.0197	511	2081	95	below_threshold
Paenibacillus luteus	strain=R-3	GCA_006542765.1	2545753	2545753	type	True	79.0163	542	2081	95	below_threshold
Paenibacillus sinopodophylli	strain=CCTCC AB 2016047	GCA_005930355.1	1837342	1837342	type	True	78.9783	457	2081	95	below_threshold
Paenibacillus pinisoli	strain=JCM 19203	GCA_003605435.1	1276110	1276110	type	True	78.2663	356	2081	95	below_threshold
Paenibacillus beijingensis	strain=DSM 24997	GCA_000961095.1	1126833	1126833	type	True	77.843	289	2081	95	below_threshold
Paenibacillus oenotherae	strain=DT7-4	GCA_019443105.1	1435645	1435645	type	True	77.4024	191	2081	95	below_threshold
Paenibacillus lycopersici	strain=12200R-189	GCA_010119935.1	2704462	2704462	type	True	77.2122	351	2081	95	below_threshold
Paenibacillus lignilyticus	strain=DLE-14	GCA_017942085.1	1172615	1172615	type	True	77.1176	219	2081	95	below_threshold
Paenibacillus taihuensis	strain=CGMCC 1.10966	GCA_003386535.1	1156355	1156355	type	True	77.0135	236	2081	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	76.9175	247	2081	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	76.7438	163	2081	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	76.7191	132	2081	95	below_threshold
Paenibacillus brevis	strain=MSJ-6	GCA_018919145.1	2841508	2841508	type	True	76.3489	79	2081	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:12,440] [INFO] DFAST Taxonomy check result was written to GCF_020169515.1_ASM2016951v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:12,440] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:12,441] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:12,441] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc542223d-3786-498d-90de-5033fc4e4ce8/dqc_reference/checkm_data
[2024-01-24 14:20:12,442] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:12,514] [INFO] Task started: CheckM
[2024-01-24 14:20:12,514] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020169515.1_ASM2016951v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020169515.1_ASM2016951v1_genomic.fna/checkm_input GCF_020169515.1_ASM2016951v1_genomic.fna/checkm_result
[2024-01-24 14:21:05,342] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:05,344] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:05,367] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:05,367] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:05,368] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020169515.1_ASM2016951v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:05,368] [INFO] Task started: Blastn
[2024-01-24 14:21:05,368] [INFO] Running command: blastn -query GCF_020169515.1_ASM2016951v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc542223d-3786-498d-90de-5033fc4e4ce8/dqc_reference/reference_markers_gtdb.fasta -out GCF_020169515.1_ASM2016951v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:08,547] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:08,552] [INFO] Selected 21 target genomes.
[2024-01-24 14:21:08,552] [INFO] Target genome list was writen to GCF_020169515.1_ASM2016951v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:08,589] [INFO] Task started: fastANI
[2024-01-24 14:21:08,589] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c0735f8-5f2d-46f9-8565-75e044d98caa/GCF_020169515.1_ASM2016951v1_genomic.fna.gz --refList GCF_020169515.1_ASM2016951v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020169515.1_ASM2016951v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:34,762] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:34,811] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:21:34,812] [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_014705655.1	s__Paenibacillus_C sp014705655	80.8523	913	2081	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_003337375.1	s__Paenibacillus_C prosopidis	80.3059	678	2081	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	80.0456	784	2081	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_001428245.1	s__Paenibacillus_C sp001428245	79.8711	686	2081	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_003217535.1	s__Paenibacillus_C sp003217535	79.8267	751	2081	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_012935325.2	s__Paenibacillus_C sp012935325	79.4549	661	2081	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_001682865.1	s__Paenibacillus_C sp001682865	79.3275	592	2081	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	99.12	99.12	0.94	0.94	2	-
GCF_005222705.1	s__Paenibacillus_C sp005222705	79.1347	566	2081	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_014192395.1	s__Paenibacillus_C endophyticus	79.088	549	2081	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_006345825.1	s__Paenibacillus_C paridis	79.0335	509	2081	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_005930355.1	s__Paenibacillus_C sinopodophylli	78.9883	456	2081	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_003605435.1	s__Paenibacillus_C pinisoli	78.2767	355	2081	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_003112455.1	s__Paenibacillus_C agaridevorans	78.2659	376	2081	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	96.67	95.87	0.80	0.78	4	-
GCF_000961095.1	s__Paenibacillus_O beijingensis	77.8283	287	2081	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010119935.1	s__Paenibacillus_Z lycopersici	77.2124	351	2081	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_900106745.1	s__Paenibacillus_Z sp900106745	77.0964	205	2081	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	76.9805	236	2081	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:34,814] [INFO] GTDB search result was written to GCF_020169515.1_ASM2016951v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:34,815] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:34,819] [INFO] DFAST_QC result json was written to GCF_020169515.1_ASM2016951v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:34,819] [INFO] DFAST_QC completed!
[2024-01-24 14:21:34,819] [INFO] Total running time: 0h2m14s