[2024-01-24 12:53:56,857] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:56,859] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:56,859] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d9501e9-f1bf-4831-9cb2-b512070095f3/dqc_reference
[2024-01-24 12:53:58,270] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:58,271] [INFO] Task started: Prodigal
[2024-01-24 12:53:58,271] [INFO] Running command: gunzip -c /var/lib/cwl/stg4c96b4f3-fcf8-4dad-9acc-b9a56a91555d/GCF_002192535.1_ASM219253v1_genomic.fna.gz | prodigal -d GCF_002192535.1_ASM219253v1_genomic.fna/cds.fna -a GCF_002192535.1_ASM219253v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:03,229] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:03,230] [INFO] Task started: HMMsearch
[2024-01-24 12:54:03,230] [INFO] Running command: hmmsearch --tblout GCF_002192535.1_ASM219253v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d9501e9-f1bf-4831-9cb2-b512070095f3/dqc_reference/reference_markers.hmm GCF_002192535.1_ASM219253v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:03,474] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:03,476] [INFO] Found 6/6 markers.
[2024-01-24 12:54:03,505] [INFO] Query marker FASTA was written to GCF_002192535.1_ASM219253v1_genomic.fna/markers.fasta
[2024-01-24 12:54:03,505] [INFO] Task started: Blastn
[2024-01-24 12:54:03,506] [INFO] Running command: blastn -query GCF_002192535.1_ASM219253v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d9501e9-f1bf-4831-9cb2-b512070095f3/dqc_reference/reference_markers.fasta -out GCF_002192535.1_ASM219253v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:04,086] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:04,090] [INFO] Selected 13 target genomes.
[2024-01-24 12:54:04,090] [INFO] Target genome list was writen to GCF_002192535.1_ASM219253v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:04,097] [INFO] Task started: fastANI
[2024-01-24 12:54:04,097] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c96b4f3-fcf8-4dad-9acc-b9a56a91555d/GCF_002192535.1_ASM219253v1_genomic.fna.gz --refList GCF_002192535.1_ASM219253v1_genomic.fna/target_genomes.txt --output GCF_002192535.1_ASM219253v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:10,835] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:10,835] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d9501e9-f1bf-4831-9cb2-b512070095f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:10,835] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d9501e9-f1bf-4831-9cb2-b512070095f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:10,846] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:10,847] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:10,847] [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 hirudinilacicola	strain=MWH-EgelM1-30-B4	GCA_002192535.1	1743166	1743166	type	True	100.0	666	666	95	conclusive
Polynucleobacter campilacus	strain=MWH-Feld-100	GCA_002206625.1	1743163	1743163	type	True	83.4283	470	666	95	below_threshold
Polynucleobacter nymphae	strain=AP-Mumm-500A-B3	GCA_018882155.1	2081043	2081043	type	True	82.8327	466	666	95	below_threshold
Polynucleobacter ibericus	strain=es-MAR-2	GCA_018687955.1	1819725	1819725	type	True	81.9477	370	666	95	below_threshold
Polynucleobacter parvulilacunae	strain=Ross1-W9	GCA_018881715.1	1855631	1855631	type	True	81.723	369	666	95	below_threshold
Polynucleobacter yangtzensis	strain=MWH-JaK3	GCA_001595965.1	1743159	1743159	type	True	81.5985	375	666	95	below_threshold
Polynucleobacter wuianus	strain=QLW-P1FAT50C-4	GCA_001659725.1	1743168	1743168	type	True	81.4883	387	666	95	below_threshold
Polynucleobacter alcilacus	strain=UK-Pondora-W15	GCA_018881545.1	1819739	1819739	type	True	81.1822	407	666	95	below_threshold
Polynucleobacter asymbioticus	strain=QLW-P1DMWA-1	GCA_000016345.1	576611	576611	type	True	80.9499	353	666	95	below_threshold
Polynucleobacter tropicus	strain=MWH-UH21B	GCA_013307225.1	1743174	1743174	type	True	80.7133	324	666	95	below_threshold
Polynucleobacter corsicus	strain=AP-Melu-1000-A1	GCA_018688255.1	2081042	2081042	type	True	80.2667	296	666	95	below_threshold
Polynucleobacter bastaniensis	strain=AP-Basta-1000A-D1	GCA_018882205.1	2081039	2081039	type	True	79.9606	315	666	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:10,849] [INFO] DFAST Taxonomy check result was written to GCF_002192535.1_ASM219253v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:10,849] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:10,849] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:10,849] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d9501e9-f1bf-4831-9cb2-b512070095f3/dqc_reference/checkm_data
[2024-01-24 12:54:10,851] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:10,933] [INFO] Task started: CheckM
[2024-01-24 12:54:10,933] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002192535.1_ASM219253v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002192535.1_ASM219253v1_genomic.fna/checkm_input GCF_002192535.1_ASM219253v1_genomic.fna/checkm_result
[2024-01-24 12:54:32,735] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:32,738] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:32,754] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:32,754] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:32,754] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002192535.1_ASM219253v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:32,755] [INFO] Task started: Blastn
[2024-01-24 12:54:32,755] [INFO] Running command: blastn -query GCF_002192535.1_ASM219253v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d9501e9-f1bf-4831-9cb2-b512070095f3/dqc_reference/reference_markers_gtdb.fasta -out GCF_002192535.1_ASM219253v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:33,566] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:33,569] [INFO] Selected 11 target genomes.
[2024-01-24 12:54:33,569] [INFO] Target genome list was writen to GCF_002192535.1_ASM219253v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:33,600] [INFO] Task started: fastANI
[2024-01-24 12:54:33,600] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c96b4f3-fcf8-4dad-9acc-b9a56a91555d/GCF_002192535.1_ASM219253v1_genomic.fna.gz --refList GCF_002192535.1_ASM219253v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002192535.1_ASM219253v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:38,426] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:38,435] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:38,436] [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_002192535.1	s__Polynucleobacter hirudinilacicola	100.0	666	666	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_018882465.1	s__Polynucleobacter sp018882465	93.9688	570	666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903995005.1	s__Polynucleobacter sp903995005	92.5425	364	666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881855.1	s__Polynucleobacter sp018881855	89.4269	538	666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881635.1	s__Polynucleobacter sp018881635	83.4768	456	666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002206625.1	s__Polynucleobacter campilacus	83.4093	471	666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018687735.1	s__Polynucleobacter sp018687735	83.3059	465	666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	98.63	98.63	0.93	0.93	2	-
GCF_018882155.1	s__Polynucleobacter sp018882155	82.8152	467	666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018688315.1	s__Polynucleobacter sp018688315	81.885	377	666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903843315.1	s__Polynucleobacter sp903843315	81.5153	329	666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.21	99.08	0.85	0.77	17	-
GCF_018881545.1	s__Polynucleobacter sp018881545	81.1662	408	666	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 12:54:38,437] [INFO] GTDB search result was written to GCF_002192535.1_ASM219253v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:38,438] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:38,441] [INFO] DFAST_QC result json was written to GCF_002192535.1_ASM219253v1_genomic.fna/dqc_result.json
[2024-01-24 12:54:38,441] [INFO] DFAST_QC completed!
[2024-01-24 12:54:38,441] [INFO] Total running time: 0h0m42s