[2023-06-05 01:18:29,064] [INFO] DFAST_QC pipeline started.
[2023-06-05 01:18:29,067] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 01:18:29,068] [INFO] DQC Reference Directory: /var/lib/cwl/stged24c2d0-8140-47b7-8f1f-230acec3e1c4/dqc_reference
[2023-06-05 01:18:30,499] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 01:18:30,500] [INFO] Task started: Prodigal
[2023-06-05 01:18:30,500] [INFO] Running command: gunzip -c /var/lib/cwl/stgd8499aeb-65c9-4d53-977e-88de3281af38/GCA_010027185.1_ASM1002718v1_genomic.fna.gz | prodigal -d GCA_010027185.1_ASM1002718v1_genomic.fna/cds.fna -a GCA_010027185.1_ASM1002718v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 01:18:33,892] [INFO] Task succeeded: Prodigal
[2023-06-05 01:18:33,892] [INFO] Task started: HMMsearch
[2023-06-05 01:18:33,892] [INFO] Running command: hmmsearch --tblout GCA_010027185.1_ASM1002718v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged24c2d0-8140-47b7-8f1f-230acec3e1c4/dqc_reference/reference_markers.hmm GCA_010027185.1_ASM1002718v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 01:18:34,163] [INFO] Task succeeded: HMMsearch
[2023-06-05 01:18:34,165] [INFO] Found 6/6 markers.
[2023-06-05 01:18:34,184] [INFO] Query marker FASTA was written to GCA_010027185.1_ASM1002718v1_genomic.fna/markers.fasta
[2023-06-05 01:18:34,184] [INFO] Task started: Blastn
[2023-06-05 01:18:34,184] [INFO] Running command: blastn -query GCA_010027185.1_ASM1002718v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged24c2d0-8140-47b7-8f1f-230acec3e1c4/dqc_reference/reference_markers.fasta -out GCA_010027185.1_ASM1002718v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:18:34,819] [INFO] Task succeeded: Blastn
[2023-06-05 01:18:34,824] [INFO] Selected 18 target genomes.
[2023-06-05 01:18:34,824] [INFO] Target genome list was writen to GCA_010027185.1_ASM1002718v1_genomic.fna/target_genomes.txt
[2023-06-05 01:18:34,826] [INFO] Task started: fastANI
[2023-06-05 01:18:34,826] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8499aeb-65c9-4d53-977e-88de3281af38/GCA_010027185.1_ASM1002718v1_genomic.fna.gz --refList GCA_010027185.1_ASM1002718v1_genomic.fna/target_genomes.txt --output GCA_010027185.1_ASM1002718v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 01:18:41,915] [INFO] Task succeeded: fastANI
[2023-06-05 01:18:41,916] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged24c2d0-8140-47b7-8f1f-230acec3e1c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 01:18:41,916] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged24c2d0-8140-47b7-8f1f-230acec3e1c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 01:18:41,927] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 01:18:41,927] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 01:18:41,928] [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 acidiphobus	strain=MWH-PoolGreenA3	GCA_003065385.1	556053	556053	type	True	85.3873	290	333	95	below_threshold
Polynucleobacter difficilis	strain=AM-8B5	GCA_003065365.1	556054	556054	type	True	77.2079	55	333	95	below_threshold
Polynucleobacter paludilacus	strain=MWH-Mekk-C3	GCA_018687595.1	1855895	1855895	type	True	76.6059	50	333	95	below_threshold
Polynucleobacter nymphae	strain=AP-Mumm-500A-B3	GCA_018882155.1	2081043	2081043	type	True	76.6044	53	333	95	below_threshold
Polynucleobacter alcilacus	strain=UK-Pondora-W15	GCA_018881545.1	1819739	1819739	type	True	76.4599	53	333	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 01:18:41,930] [INFO] DFAST Taxonomy check result was written to GCA_010027185.1_ASM1002718v1_genomic.fna/tc_result.tsv
[2023-06-05 01:18:41,930] [INFO] ===== Taxonomy check completed =====
[2023-06-05 01:18:41,930] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 01:18:41,931] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged24c2d0-8140-47b7-8f1f-230acec3e1c4/dqc_reference/checkm_data
[2023-06-05 01:18:41,932] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 01:18:41,955] [INFO] Task started: CheckM
[2023-06-05 01:18:41,956] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_010027185.1_ASM1002718v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_010027185.1_ASM1002718v1_genomic.fna/checkm_input GCA_010027185.1_ASM1002718v1_genomic.fna/checkm_result
[2023-06-05 01:19:00,199] [INFO] Task succeeded: CheckM
[2023-06-05 01:19:00,201] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.25%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-05 01:19:00,222] [INFO] ===== Completeness check finished =====
[2023-06-05 01:19:00,222] [INFO] ===== Start GTDB Search =====
[2023-06-05 01:19:00,222] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_010027185.1_ASM1002718v1_genomic.fna/markers.fasta)
[2023-06-05 01:19:00,223] [INFO] Task started: Blastn
[2023-06-05 01:19:00,223] [INFO] Running command: blastn -query GCA_010027185.1_ASM1002718v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged24c2d0-8140-47b7-8f1f-230acec3e1c4/dqc_reference/reference_markers_gtdb.fasta -out GCA_010027185.1_ASM1002718v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:19:01,229] [INFO] Task succeeded: Blastn
[2023-06-05 01:19:01,235] [INFO] Selected 12 target genomes.
[2023-06-05 01:19:01,235] [INFO] Target genome list was writen to GCA_010027185.1_ASM1002718v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 01:19:01,237] [INFO] Task started: fastANI
[2023-06-05 01:19:01,237] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8499aeb-65c9-4d53-977e-88de3281af38/GCA_010027185.1_ASM1002718v1_genomic.fna.gz --refList GCA_010027185.1_ASM1002718v1_genomic.fna/target_genomes_gtdb.txt --output GCA_010027185.1_ASM1002718v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 01:19:04,890] [INFO] Task succeeded: fastANI
[2023-06-05 01:19:04,899] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 01:19:04,899] [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_018687475.1	s__Polynucleobacter sp009928245	97.5368	322	333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	97.52	97.29	0.97	0.94	13	conclusive
GCA_016867965.1	s__Polynucleobacter sp016867965	94.3805	288	333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003065385.1	s__Polynucleobacter acidiphobus	85.3873	290	333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002359975.1	s__Polynucleobacter sp002359975	79.7073	75	333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	98.53	97.93	0.70	0.67	7	-
GCA_002292975.1	s__Polynucleobacter sp002292975	78.4484	127	333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	98.75	98.63	0.92	0.90	4	-
GCA_009924985.1	s__Polynucleobacter sp009924985	78.0297	104	333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882085.1	s__Polynucleobacter sp018882085	76.8763	52	333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 01:19:04,901] [INFO] GTDB search result was written to GCA_010027185.1_ASM1002718v1_genomic.fna/result_gtdb.tsv
[2023-06-05 01:19:04,902] [INFO] ===== GTDB Search completed =====
[2023-06-05 01:19:04,906] [INFO] DFAST_QC result json was written to GCA_010027185.1_ASM1002718v1_genomic.fna/dqc_result.json
[2023-06-05 01:19:04,906] [INFO] DFAST_QC completed!
[2023-06-05 01:19:04,906] [INFO] Total running time: 0h0m36s