[2024-01-24 11:05:27,863] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:27,867] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:27,868] [INFO] DQC Reference Directory: /var/lib/cwl/stge0a84bea-101f-44f0-87bc-cbae6ff7a9b7/dqc_reference
[2024-01-24 11:05:29,294] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:29,295] [INFO] Task started: Prodigal
[2024-01-24 11:05:29,295] [INFO] Running command: gunzip -c /var/lib/cwl/stg5ae14f92-56be-437f-8cd6-5cb34d536a1a/GCF_030160815.1_ASM3016081v1_genomic.fna.gz | prodigal -d GCF_030160815.1_ASM3016081v1_genomic.fna/cds.fna -a GCF_030160815.1_ASM3016081v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:44,497] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:44,498] [INFO] Task started: HMMsearch
[2024-01-24 11:05:44,498] [INFO] Running command: hmmsearch --tblout GCF_030160815.1_ASM3016081v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0a84bea-101f-44f0-87bc-cbae6ff7a9b7/dqc_reference/reference_markers.hmm GCF_030160815.1_ASM3016081v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:44,812] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:44,813] [INFO] Found 6/6 markers.
[2024-01-24 11:05:44,867] [INFO] Query marker FASTA was written to GCF_030160815.1_ASM3016081v1_genomic.fna/markers.fasta
[2024-01-24 11:05:44,868] [INFO] Task started: Blastn
[2024-01-24 11:05:44,868] [INFO] Running command: blastn -query GCF_030160815.1_ASM3016081v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0a84bea-101f-44f0-87bc-cbae6ff7a9b7/dqc_reference/reference_markers.fasta -out GCF_030160815.1_ASM3016081v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:46,002] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:46,005] [INFO] Selected 22 target genomes.
[2024-01-24 11:05:46,005] [INFO] Target genome list was writen to GCF_030160815.1_ASM3016081v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:46,013] [INFO] Task started: fastANI
[2024-01-24 11:05:46,013] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ae14f92-56be-437f-8cd6-5cb34d536a1a/GCF_030160815.1_ASM3016081v1_genomic.fna.gz --refList GCF_030160815.1_ASM3016081v1_genomic.fna/target_genomes.txt --output GCF_030160815.1_ASM3016081v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:09,475] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:09,475] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0a84bea-101f-44f0-87bc-cbae6ff7a9b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:09,476] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0a84bea-101f-44f0-87bc-cbae6ff7a9b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:09,492] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:06:09,492] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:06:09,493] [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
Hydrogenophaga pseudoflava	strain=NBRC 102511	GCA_001592285.1	47421	47421	type	True	84.1072	905	1503	95	below_threshold
Hydrogenophaga flava	strain=NBRC 102514	GCA_001571145.1	65657	65657	type	True	83.8194	923	1503	95	below_threshold
Hydrogenophaga aromaticivorans	strain=D2P1	GCA_013387465.1	2610898	2610898	type	True	82.8963	894	1503	95	below_threshold
Hydrogenophaga taeniospiralis	strain=NBRC 102512	GCA_001592305.1	65656	65656	type	True	82.5137	878	1503	95	below_threshold
Hydrogenophaga palleronii	strain=NBRC 102513	GCA_001571225.1	65655	65655	type	True	82.4927	779	1503	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	82.4488	788	1503	95	below_threshold
Hydrogenophaga borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	82.1239	777	1503	95	below_threshold
Hydrogenophaga intermedia	strain=S1	GCA_000723405.1	65786	65786	type	True	81.7918	783	1503	95	below_threshold
Hydrogenophaga intermedia	strain=DSM 5680	GCA_005938115.1	65786	65786	type	True	81.7627	771	1503	95	below_threshold
Hydrogenophaga intermedia	strain=NBRC 102510	GCA_001571205.1	65786	65786	type	True	81.7614	766	1503	95	below_threshold
Tepidicella baoligensis	strain=B18-50	GCA_013432195.1	2707016	2707016	type	True	80.2767	485	1503	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	80.1946	592	1503	95	below_threshold
Comamonas phosphati	strain=CGMCC 1.12294	GCA_014637085.1	1211803	1211803	type	True	80.1904	530	1503	95	below_threshold
Acidovorax delafieldii	strain=DSM 64	GCA_007993815.1	47920	47920	type	True	79.9472	585	1503	95	below_threshold
Comamonas aquatica	strain=NBRC 14918	GCA_000739875.1	225991	225991	type	True	79.9175	477	1503	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	79.9171	614	1503	95	below_threshold
Brachymonas denitrificans	strain=DSM 15123	GCA_900110225.1	28220	28220	type	True	79.8178	395	1503	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	79.6292	436	1503	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_000964545.1	363952	363952	type	True	78.9768	453	1503	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	78.9507	450	1503	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_001418295.1	363952	363952	type	True	78.9262	451	1503	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_001517325.1	363952	363952	type	True	78.9207	451	1503	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:09,494] [INFO] DFAST Taxonomy check result was written to GCF_030160815.1_ASM3016081v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:09,495] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:09,495] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:09,495] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0a84bea-101f-44f0-87bc-cbae6ff7a9b7/dqc_reference/checkm_data
[2024-01-24 11:06:09,497] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:09,543] [INFO] Task started: CheckM
[2024-01-24 11:06:09,544] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030160815.1_ASM3016081v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030160815.1_ASM3016081v1_genomic.fna/checkm_input GCF_030160815.1_ASM3016081v1_genomic.fna/checkm_result
[2024-01-24 11:07:45,394] [INFO] Task succeeded: CheckM
[2024-01-24 11:07:45,396] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 11:07:45,420] [INFO] ===== Completeness check finished =====
[2024-01-24 11:07:45,421] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:07:45,421] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030160815.1_ASM3016081v1_genomic.fna/markers.fasta)
[2024-01-24 11:07:45,422] [INFO] Task started: Blastn
[2024-01-24 11:07:45,422] [INFO] Running command: blastn -query GCF_030160815.1_ASM3016081v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0a84bea-101f-44f0-87bc-cbae6ff7a9b7/dqc_reference/reference_markers_gtdb.fasta -out GCF_030160815.1_ASM3016081v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:07:47,581] [INFO] Task succeeded: Blastn
[2024-01-24 11:07:47,586] [INFO] Selected 21 target genomes.
[2024-01-24 11:07:47,586] [INFO] Target genome list was writen to GCF_030160815.1_ASM3016081v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:07:47,608] [INFO] Task started: fastANI
[2024-01-24 11:07:47,608] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ae14f92-56be-437f-8cd6-5cb34d536a1a/GCF_030160815.1_ASM3016081v1_genomic.fna.gz --refList GCF_030160815.1_ASM3016081v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030160815.1_ASM3016081v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:08:05,985] [INFO] Task succeeded: fastANI
[2024-01-24 11:08:06,006] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:08:06,007] [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_001592285.1	s__Hydrogenophaga pseudoflava	84.045	911	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	97.77	97.69	0.91	0.91	4	-
GCF_001571145.1	s__Hydrogenophaga flava	83.8338	922	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790705.1	s__Hydrogenophaga sp016790705	83.5331	716	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013387465.1	s__Hydrogenophaga aromaticivorans	82.8578	901	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	96.00	95.64	0.87	0.82	12	-
GCA_018780075.1	s__Hydrogenophaga sp018780075	82.7891	841	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001770905.1	s__Hydrogenophaga sp001770905	82.6568	853	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	99.83	99.75	0.90	0.90	3	-
GCA_013823655.1	s__Hydrogenophaga sp013823655	82.5034	532	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011388215.1	s__Hydrogenophaga sp011388215	82.4541	787	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	99.06	99.06	0.95	0.95	2	-
GCA_018993155.1	s__Hydrogenophaga sp018993155	82.3088	765	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018903185.1	s__Hydrogenophaga sp018903185	82.2833	406	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	99.34	99.34	0.82	0.82	2	-
GCF_002127215.1	s__Hydrogenophaga sp002127215	82.2341	656	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003417535.1	s__Hydrogenophaga borbori	82.13	776	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	96.89	96.31	0.93	0.91	7	-
GCA_006227825.1	s__Hydrogenophaga sp006227825	82.0675	553	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016741995.1	s__Hydrogenophaga sp016741995	82.0379	682	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011772445.1	s__Hydrogenophaga sp011772445	81.8509	721	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	100.00	100.00	1.00	1.00	9	-
GCA_013823485.1	s__Hydrogenophaga sp013823485	81.8323	588	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	98.29	98.29	0.80	0.80	2	-
GCF_000723405.1	s__Hydrogenophaga intermedia	81.7986	781	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	99.52	98.31	0.93	0.83	5	-
GCF_014637085.1	s__Comamonas phosphati	80.2182	527	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739875.1	s__Comamonas aquatica	79.9105	478	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	96.97	96.57	0.89	0.87	7	-
GCF_000964545.1	s__Comamonas thiooxydans	78.9812	453	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	97.51	95.23	0.90	0.87	29	-
GCF_000241525.1	s__Comamonas testosteroni	78.9629	459	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	99.74	98.70	0.99	0.94	6	-
--------------------------------------------------------------------------------
[2024-01-24 11:08:06,008] [INFO] GTDB search result was written to GCF_030160815.1_ASM3016081v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:08:06,009] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:08:06,013] [INFO] DFAST_QC result json was written to GCF_030160815.1_ASM3016081v1_genomic.fna/dqc_result.json
[2024-01-24 11:08:06,013] [INFO] DFAST_QC completed!
[2024-01-24 11:08:06,013] [INFO] Total running time: 0h2m38s