[2024-01-25 17:37:20,490] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:37:20,491] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:37:20,491] [INFO] DQC Reference Directory: /var/lib/cwl/stgba42b724-9280-4127-82ef-6b596cc92234/dqc_reference
[2024-01-25 17:37:21,633] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:37:21,634] [INFO] Task started: Prodigal
[2024-01-25 17:37:21,634] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a6f47f0-833e-43a8-b443-0b218ac8f3bb/GCF_028595345.1_ASM2859534v1_genomic.fna.gz | prodigal -d GCF_028595345.1_ASM2859534v1_genomic.fna/cds.fna -a GCF_028595345.1_ASM2859534v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:37:46,398] [INFO] Task succeeded: Prodigal
[2024-01-25 17:37:46,399] [INFO] Task started: HMMsearch
[2024-01-25 17:37:46,399] [INFO] Running command: hmmsearch --tblout GCF_028595345.1_ASM2859534v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba42b724-9280-4127-82ef-6b596cc92234/dqc_reference/reference_markers.hmm GCF_028595345.1_ASM2859534v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:37:46,664] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:37:46,665] [INFO] Found 6/6 markers.
[2024-01-25 17:37:46,711] [INFO] Query marker FASTA was written to GCF_028595345.1_ASM2859534v1_genomic.fna/markers.fasta
[2024-01-25 17:37:46,711] [INFO] Task started: Blastn
[2024-01-25 17:37:46,711] [INFO] Running command: blastn -query GCF_028595345.1_ASM2859534v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba42b724-9280-4127-82ef-6b596cc92234/dqc_reference/reference_markers.fasta -out GCF_028595345.1_ASM2859534v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:37:47,641] [INFO] Task succeeded: Blastn
[2024-01-25 17:37:47,647] [INFO] Selected 21 target genomes.
[2024-01-25 17:37:47,648] [INFO] Target genome list was writen to GCF_028595345.1_ASM2859534v1_genomic.fna/target_genomes.txt
[2024-01-25 17:37:47,653] [INFO] Task started: fastANI
[2024-01-25 17:37:47,653] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a6f47f0-833e-43a8-b443-0b218ac8f3bb/GCF_028595345.1_ASM2859534v1_genomic.fna.gz --refList GCF_028595345.1_ASM2859534v1_genomic.fna/target_genomes.txt --output GCF_028595345.1_ASM2859534v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:38:05,559] [INFO] Task succeeded: fastANI
[2024-01-25 17:38:05,560] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba42b724-9280-4127-82ef-6b596cc92234/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:38:05,560] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba42b724-9280-4127-82ef-6b596cc92234/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:38:05,574] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:38:05,575] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:38:05,575] [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
Paucibacter toxinivorans	strain=DSM 16998	GCA_004362525.1	270368	270368	type	True	79.2072	695	1806	95	below_threshold
Pelomonas saccharophila	strain=DSM 654	GCA_004342485.1	304	304	type	True	78.9213	601	1806	95	below_threshold
Mitsuaria chitinivorans	strain=HWN-4	GCA_002761755.1	2917965	2917965	type	True	78.4528	560	1806	95	below_threshold
Roseateles depolymerans	strain=DSM 11813	GCA_003387155.1	76731	76731	type	True	78.4397	501	1806	95	below_threshold
Pelomonas puraquae	strain=CCUG 52769	GCA_002205845.1	431059	431059	type	True	78.3302	562	1806	95	below_threshold
Ideonella azotifigens	strain=DSM 21438	GCA_006519715.1	513160	513160	type	True	78.3262	377	1806	95	below_threshold
Roseateles terrae	strain=CECT 7247	GCA_014192155.1	431060	431060	type	True	78.1345	474	1806	95	below_threshold
Aquabacterium olei	strain=NBRC 110486	GCA_003100395.1	1296669	1296669	type	True	78.0659	305	1806	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	77.9869	362	1806	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	77.9704	395	1806	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_003349825.1	215580	215580	type	True	77.9606	367	1806	95	below_threshold
Sphaerotilus natans	strain=ATCC 13338	GCA_900156335.1	34103	34103	type	True	77.9408	428	1806	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	77.8629	370	1806	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	77.8233	310	1806	95	below_threshold
Malikia granosa	strain=P1	GCA_002980595.1	263067	263067	type	True	77.7541	322	1806	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_001517325.1	363952	363952	type	True	77.2634	239	1806	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_001418295.1	363952	363952	type	True	77.2633	239	1806	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_000964545.1	363952	363952	type	True	77.2592	249	1806	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	77.2508	269	1806	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	77.2452	318	1806	95	below_threshold
Serpentinimonas barnesii	strain=H1	GCA_000696225.1	1458427	1458427	type	True	76.6156	191	1806	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:38:05,578] [INFO] DFAST Taxonomy check result was written to GCF_028595345.1_ASM2859534v1_genomic.fna/tc_result.tsv
[2024-01-25 17:38:05,579] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:38:05,579] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:38:05,579] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba42b724-9280-4127-82ef-6b596cc92234/dqc_reference/checkm_data
[2024-01-25 17:38:05,580] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:38:05,631] [INFO] Task started: CheckM
[2024-01-25 17:38:05,631] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028595345.1_ASM2859534v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028595345.1_ASM2859534v1_genomic.fna/checkm_input GCF_028595345.1_ASM2859534v1_genomic.fna/checkm_result
[2024-01-25 17:39:14,922] [INFO] Task succeeded: CheckM
[2024-01-25 17:39:14,923] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:39:14,942] [INFO] ===== Completeness check finished =====
[2024-01-25 17:39:14,942] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:39:14,943] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028595345.1_ASM2859534v1_genomic.fna/markers.fasta)
[2024-01-25 17:39:14,943] [INFO] Task started: Blastn
[2024-01-25 17:39:14,943] [INFO] Running command: blastn -query GCF_028595345.1_ASM2859534v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba42b724-9280-4127-82ef-6b596cc92234/dqc_reference/reference_markers_gtdb.fasta -out GCF_028595345.1_ASM2859534v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:16,691] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:16,694] [INFO] Selected 12 target genomes.
[2024-01-25 17:39:16,694] [INFO] Target genome list was writen to GCF_028595345.1_ASM2859534v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:39:16,703] [INFO] Task started: fastANI
[2024-01-25 17:39:16,703] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a6f47f0-833e-43a8-b443-0b218ac8f3bb/GCF_028595345.1_ASM2859534v1_genomic.fna.gz --refList GCF_028595345.1_ASM2859534v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028595345.1_ASM2859534v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:39:29,446] [INFO] Task succeeded: fastANI
[2024-01-25 17:39:29,454] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:39:29,455] [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
GCA_018780415.1	s__Paucibacter_A sp018780415	84.6149	1106	1806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001477625.1	s__Paucibacter_A sp001477625	80.6479	853	1806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002255955.1	s__Paucibacter_A sp002255955	80.4521	875	1806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005503085.1	s__Paucibacter_A sp005503085	80.3813	794	1806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002885975.1	s__Paucibacter_A aquatile	80.3556	883	1806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204525.1	s__Paucibacter_A oligotrophus	80.2892	841	1806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003852425.1	s__Paucibacter_A sp003852425	80.0791	833	1806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019234815.1	s__WAJ17 sp019234815	79.2456	467	1806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__WAJ17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903820745.1	s__Paucibacter_A sp903820745	79.0892	463	1806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter_A	95.0	99.77	99.75	0.91	0.91	3	-
GCF_014192585.1	s__Variovorax sp014192585	77.0167	266	1806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001464055.1	s__Rubrivivax sp001464055	76.8731	333	1806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016467405.1	s__Lacisediminimonas sp016467405	76.5201	166	1806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lacisediminimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:39:29,456] [INFO] GTDB search result was written to GCF_028595345.1_ASM2859534v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:39:29,457] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:39:29,461] [INFO] DFAST_QC result json was written to GCF_028595345.1_ASM2859534v1_genomic.fna/dqc_result.json
[2024-01-25 17:39:29,461] [INFO] DFAST_QC completed!
[2024-01-25 17:39:29,461] [INFO] Total running time: 0h2m9s