[2024-01-24 13:49:30,820] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:30,822] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:30,822] [INFO] DQC Reference Directory: /var/lib/cwl/stgdcc8b861-013a-493d-80b9-3c44620aa8ae/dqc_reference
[2024-01-24 13:49:32,148] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:32,149] [INFO] Task started: Prodigal
[2024-01-24 13:49:32,150] [INFO] Running command: gunzip -c /var/lib/cwl/stg123d6045-4137-4885-a451-8e530ede56bd/GCF_014641555.1_ASM1464155v1_genomic.fna.gz | prodigal -d GCF_014641555.1_ASM1464155v1_genomic.fna/cds.fna -a GCF_014641555.1_ASM1464155v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:49,583] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:49,584] [INFO] Task started: HMMsearch
[2024-01-24 13:49:49,584] [INFO] Running command: hmmsearch --tblout GCF_014641555.1_ASM1464155v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdcc8b861-013a-493d-80b9-3c44620aa8ae/dqc_reference/reference_markers.hmm GCF_014641555.1_ASM1464155v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:50,021] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:50,023] [INFO] Found 6/6 markers.
[2024-01-24 13:49:50,076] [INFO] Query marker FASTA was written to GCF_014641555.1_ASM1464155v1_genomic.fna/markers.fasta
[2024-01-24 13:49:50,076] [INFO] Task started: Blastn
[2024-01-24 13:49:50,076] [INFO] Running command: blastn -query GCF_014641555.1_ASM1464155v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdcc8b861-013a-493d-80b9-3c44620aa8ae/dqc_reference/reference_markers.fasta -out GCF_014641555.1_ASM1464155v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:50,748] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:50,751] [INFO] Selected 14 target genomes.
[2024-01-24 13:49:50,752] [INFO] Target genome list was writen to GCF_014641555.1_ASM1464155v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:50,757] [INFO] Task started: fastANI
[2024-01-24 13:49:50,757] [INFO] Running command: fastANI --query /var/lib/cwl/stg123d6045-4137-4885-a451-8e530ede56bd/GCF_014641555.1_ASM1464155v1_genomic.fna.gz --refList GCF_014641555.1_ASM1464155v1_genomic.fna/target_genomes.txt --output GCF_014641555.1_ASM1464155v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:08,149] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:08,150] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdcc8b861-013a-493d-80b9-3c44620aa8ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:08,150] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdcc8b861-013a-493d-80b9-3c44620aa8ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:08,163] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:08,163] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:08,163] [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 radicis	strain=CGMCC 1.15286	GCA_014641555.1	1737354	1737354	type	True	100.0	2141	2145	95	conclusive
Paenibacillus gorillae		GCA_000513275.1	1243662	1243662	type	True	88.8934	1717	2145	95	below_threshold
Paenibacillus glycanilyticus subsp. hiroshimensis	strain=CCI5	GCA_015473105.1	2805378	126569	type	True	78.7605	462	2145	95	below_threshold
Paenibacillus lupini	strain=CECT 8235	GCA_011761355.1	1450204	1450204	type	True	78.6479	410	2145	95	below_threshold
Paenibacillus catalpae	strain=CGMCC 1.10784	GCA_900112695.1	1045775	1045775	type	True	78.6319	442	2145	95	below_threshold
Paenibacillus glycanilyticus	strain=NBRC 16618	GCA_004000805.1	126569	126569	type	True	78.6111	478	2145	95	below_threshold
Paenibacillus algorifonticola	strain=CGMCC 1.10223	GCA_900112925.1	684063	684063	type	True	78.2948	366	2145	95	below_threshold
Paenibacillus algorifonticola	strain=XJ259	GCA_000971975.1	684063	684063	type	True	78.2365	371	2145	95	below_threshold
Paenibacillus prosopidis	strain=CECT 7506	GCA_003337375.1	630520	630520	type	True	78.0599	313	2145	95	below_threshold
Cohnella herbarum	strain=MFER-1	GCA_012849095.1	2728023	2728023	type	True	76.9595	151	2145	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	76.5703	94	2145	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	76.3051	130	2145	95	below_threshold
Paenibacillus oceani	strain=IB182363	GCA_014705615.1	2772510	2772510	type	True	76.2358	119	2145	95	below_threshold
Paenibacillus tianjinensis	strain=TB2019	GCA_017086365.1	2810347	2810347	type	True	76.2332	93	2145	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:08,165] [INFO] DFAST Taxonomy check result was written to GCF_014641555.1_ASM1464155v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:08,166] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:08,166] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:08,166] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdcc8b861-013a-493d-80b9-3c44620aa8ae/dqc_reference/checkm_data
[2024-01-24 13:50:08,167] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:08,237] [INFO] Task started: CheckM
[2024-01-24 13:50:08,238] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014641555.1_ASM1464155v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014641555.1_ASM1464155v1_genomic.fna/checkm_input GCF_014641555.1_ASM1464155v1_genomic.fna/checkm_result
[2024-01-24 13:51:01,284] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:01,285] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:01,317] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:01,317] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:01,318] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014641555.1_ASM1464155v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:01,318] [INFO] Task started: Blastn
[2024-01-24 13:51:01,319] [INFO] Running command: blastn -query GCF_014641555.1_ASM1464155v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdcc8b861-013a-493d-80b9-3c44620aa8ae/dqc_reference/reference_markers_gtdb.fasta -out GCF_014641555.1_ASM1464155v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:02,173] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:02,177] [INFO] Selected 9 target genomes.
[2024-01-24 13:51:02,178] [INFO] Target genome list was writen to GCF_014641555.1_ASM1464155v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:02,196] [INFO] Task started: fastANI
[2024-01-24 13:51:02,196] [INFO] Running command: fastANI --query /var/lib/cwl/stg123d6045-4137-4885-a451-8e530ede56bd/GCF_014641555.1_ASM1464155v1_genomic.fna.gz --refList GCF_014641555.1_ASM1464155v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014641555.1_ASM1464155v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:13,181] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:13,193] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:13,193] [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_014641555.1	s__Paenibacillus_C radicis	100.0	2141	2145	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000513275.1	s__Paenibacillus_C gorillae	88.8934	1717	2145	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_009737085.1	s__Paenibacillus_C sp009737085	80.4658	623	2145	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_000023585.1	s__Paenibacillus_C sp000023585	78.6951	486	2145	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_011761355.1	s__Paenibacillus_C lupini	78.6584	409	2145	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_900112695.1	s__Paenibacillus_C catalpae	78.6383	443	2145	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_004000805.1	s__Paenibacillus_C glycanilyticus	78.6194	477	2145	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_004345425.1	s__Paenibacillus_C sp004345425	78.5322	457	2145	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	99.19	99.19	0.96	0.96	2	-
GCF_000971975.1	s__Paenibacillus_C algorifonticola	78.2364	371	2145	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	99.98	99.98	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:13,195] [INFO] GTDB search result was written to GCF_014641555.1_ASM1464155v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:13,195] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:13,199] [INFO] DFAST_QC result json was written to GCF_014641555.1_ASM1464155v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:13,199] [INFO] DFAST_QC completed!
[2024-01-24 13:51:13,199] [INFO] Total running time: 0h1m42s