[2024-01-24 13:56:12,780] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:56:12,785] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:56:12,785] [INFO] DQC Reference Directory: /var/lib/cwl/stgb223318f-f2ba-4ac8-900e-dad74d39da07/dqc_reference
[2024-01-24 13:56:14,422] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:56:14,423] [INFO] Task started: Prodigal
[2024-01-24 13:56:14,424] [INFO] Running command: gunzip -c /var/lib/cwl/stgf512e572-aa91-4643-8e30-07185db747ac/GCF_013307225.1_ASM1330722v1_genomic.fna.gz | prodigal -d GCF_013307225.1_ASM1330722v1_genomic.fna/cds.fna -a GCF_013307225.1_ASM1330722v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:19,741] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:19,742] [INFO] Task started: HMMsearch
[2024-01-24 13:56:19,742] [INFO] Running command: hmmsearch --tblout GCF_013307225.1_ASM1330722v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb223318f-f2ba-4ac8-900e-dad74d39da07/dqc_reference/reference_markers.hmm GCF_013307225.1_ASM1330722v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:20,022] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:20,024] [INFO] Found 6/6 markers.
[2024-01-24 13:56:20,049] [INFO] Query marker FASTA was written to GCF_013307225.1_ASM1330722v1_genomic.fna/markers.fasta
[2024-01-24 13:56:20,049] [INFO] Task started: Blastn
[2024-01-24 13:56:20,049] [INFO] Running command: blastn -query GCF_013307225.1_ASM1330722v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb223318f-f2ba-4ac8-900e-dad74d39da07/dqc_reference/reference_markers.fasta -out GCF_013307225.1_ASM1330722v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:20,685] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:20,690] [INFO] Selected 11 target genomes.
[2024-01-24 13:56:20,691] [INFO] Target genome list was writen to GCF_013307225.1_ASM1330722v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:20,697] [INFO] Task started: fastANI
[2024-01-24 13:56:20,697] [INFO] Running command: fastANI --query /var/lib/cwl/stgf512e572-aa91-4643-8e30-07185db747ac/GCF_013307225.1_ASM1330722v1_genomic.fna.gz --refList GCF_013307225.1_ASM1330722v1_genomic.fna/target_genomes.txt --output GCF_013307225.1_ASM1330722v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:25,461] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:25,461] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb223318f-f2ba-4ac8-900e-dad74d39da07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:25,461] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb223318f-f2ba-4ac8-900e-dad74d39da07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:25,471] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:25,471] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:25,471] [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
Polynucleobacter tropicus	strain=MWH-UH21B	GCA_013307225.1	1743174	1743174	type	True	100.0	680	680	95	conclusive
Polynucleobacter parvulilacunae	strain=Ross1-W9	GCA_018881715.1	1855631	1855631	type	True	80.8902	340	680	95	below_threshold
Polynucleobacter yangtzensis	strain=MWH-JaK3	GCA_001595965.1	1743159	1743159	type	True	80.6078	358	680	95	below_threshold
Polynucleobacter wuianus	strain=QLW-P1FAT50C-4	GCA_001659725.1	1743168	1743168	type	True	80.5442	411	680	95	below_threshold
Polynucleobacter hirudinilacicola	strain=MWH-EgelM1-30-B4	GCA_002192535.1	1743166	1743166	type	True	80.4562	325	680	95	below_threshold
Polynucleobacter ibericus	strain=es-MAR-2	GCA_018687955.1	1819725	1819725	type	True	80.3962	325	680	95	below_threshold
Polynucleobacter asymbioticus	strain=QLW-P1DMWA-1	GCA_000016345.1	576611	576611	type	True	80.0697	338	680	95	below_threshold
Polynucleobacter nymphae	strain=AP-Mumm-500A-B3	GCA_018882155.1	2081043	2081043	type	True	79.8454	316	680	95	below_threshold
Polynucleobacter alcilacus	strain=UK-Pondora-W15	GCA_018881545.1	1819739	1819739	type	True	79.595	295	680	95	below_threshold
Polynucleobacter finlandensis	strain=MWH-Mekk-B1	GCA_018881755.1	1855894	1855894	type	True	79.359	300	680	95	below_threshold
Polynucleobacter paneuropaeus	strain=MG-25-Pas1-D2	GCA_003261235.1	2527775	2527775	type	True	79.2387	195	680	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:25,473] [INFO] DFAST Taxonomy check result was written to GCF_013307225.1_ASM1330722v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:25,473] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:25,474] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:25,474] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb223318f-f2ba-4ac8-900e-dad74d39da07/dqc_reference/checkm_data
[2024-01-24 13:56:25,475] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:25,497] [INFO] Task started: CheckM
[2024-01-24 13:56:25,497] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013307225.1_ASM1330722v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013307225.1_ASM1330722v1_genomic.fna/checkm_input GCF_013307225.1_ASM1330722v1_genomic.fna/checkm_result
[2024-01-24 13:56:48,707] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:48,709] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:48,742] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:48,743] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:48,743] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013307225.1_ASM1330722v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:48,744] [INFO] Task started: Blastn
[2024-01-24 13:56:48,744] [INFO] Running command: blastn -query GCF_013307225.1_ASM1330722v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb223318f-f2ba-4ac8-900e-dad74d39da07/dqc_reference/reference_markers_gtdb.fasta -out GCF_013307225.1_ASM1330722v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:49,825] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:49,829] [INFO] Selected 14 target genomes.
[2024-01-24 13:56:49,829] [INFO] Target genome list was writen to GCF_013307225.1_ASM1330722v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:49,839] [INFO] Task started: fastANI
[2024-01-24 13:56:49,839] [INFO] Running command: fastANI --query /var/lib/cwl/stgf512e572-aa91-4643-8e30-07185db747ac/GCF_013307225.1_ASM1330722v1_genomic.fna.gz --refList GCF_013307225.1_ASM1330722v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013307225.1_ASM1330722v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:56,099] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:56,114] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:56,114] [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_013307225.1	s__Polynucleobacter sp013307225	100.0	680	680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018687095.1	s__Polynucleobacter sp018687095	88.3586	517	680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018687195.1	s__Polynucleobacter sp018687195	85.0438	537	680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881575.1	s__Polynucleobacter sp018881575	80.959	353	680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018687455.1	s__Polynucleobacter sp001870365	80.7432	363	680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	96.21	96.15	0.92	0.92	3	-
GCF_018688095.1	s__Polynucleobacter sp018688095	80.6692	394	680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001595965.1	s__Polynucleobacter yangtzensis	80.6078	358	680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900096755.1	s__Polynucleobacter necessarius_K	80.5885	326	680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001659725.1	s__Polynucleobacter wuianus	80.5295	412	680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	98.91	97.82	0.95	0.89	3	-
GCF_018881655.1	s__Polynucleobacter sp001889925	80.4873	347	680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	96.71	95.84	0.78	0.66	4	-
GCF_018687895.1	s__Polynucleobacter sp018687895	80.4543	341	680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881975.1	s__Polynucleobacter sp018881975	80.271	334	680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018687495.1	s__Polynucleobacter sp018687495	80.2291	322	680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	97.99	97.99	0.89	0.89	2	-
GCA_000342265.1	s__Polynucleobacter sp000342265	79.9235	285	680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:56:56,116] [INFO] GTDB search result was written to GCF_013307225.1_ASM1330722v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:56,116] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:56,129] [INFO] DFAST_QC result json was written to GCF_013307225.1_ASM1330722v1_genomic.fna/dqc_result.json
[2024-01-24 13:56:56,129] [INFO] DFAST_QC completed!
[2024-01-24 13:56:56,130] [INFO] Total running time: 0h0m43s