[2024-01-24 13:09:49,412] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:49,414] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:49,414] [INFO] DQC Reference Directory: /var/lib/cwl/stg53fce2e1-6c7c-45df-aad2-17a086f2dc4a/dqc_reference
[2024-01-24 13:09:50,695] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:50,696] [INFO] Task started: Prodigal
[2024-01-24 13:09:50,696] [INFO] Running command: gunzip -c /var/lib/cwl/stg66429d62-9ed0-4a61-9e4c-dbf525b21990/GCF_024518835.1_ASM2451883v1_genomic.fna.gz | prodigal -d GCF_024518835.1_ASM2451883v1_genomic.fna/cds.fna -a GCF_024518835.1_ASM2451883v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:03,493] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:03,493] [INFO] Task started: HMMsearch
[2024-01-24 13:10:03,493] [INFO] Running command: hmmsearch --tblout GCF_024518835.1_ASM2451883v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53fce2e1-6c7c-45df-aad2-17a086f2dc4a/dqc_reference/reference_markers.hmm GCF_024518835.1_ASM2451883v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:03,798] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:03,800] [INFO] Found 6/6 markers.
[2024-01-24 13:10:03,831] [INFO] Query marker FASTA was written to GCF_024518835.1_ASM2451883v1_genomic.fna/markers.fasta
[2024-01-24 13:10:03,831] [INFO] Task started: Blastn
[2024-01-24 13:10:03,831] [INFO] Running command: blastn -query GCF_024518835.1_ASM2451883v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53fce2e1-6c7c-45df-aad2-17a086f2dc4a/dqc_reference/reference_markers.fasta -out GCF_024518835.1_ASM2451883v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:04,574] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:04,578] [INFO] Selected 22 target genomes.
[2024-01-24 13:10:04,578] [INFO] Target genome list was writen to GCF_024518835.1_ASM2451883v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:04,620] [INFO] Task started: fastANI
[2024-01-24 13:10:04,621] [INFO] Running command: fastANI --query /var/lib/cwl/stg66429d62-9ed0-4a61-9e4c-dbf525b21990/GCF_024518835.1_ASM2451883v1_genomic.fna.gz --refList GCF_024518835.1_ASM2451883v1_genomic.fna/target_genomes.txt --output GCF_024518835.1_ASM2451883v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:22,429] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:22,429] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53fce2e1-6c7c-45df-aad2-17a086f2dc4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:22,430] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53fce2e1-6c7c-45df-aad2-17a086f2dc4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:22,447] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:22,447] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:22,447] [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
Limnobacter humi	strain=NBRC 111650	GCA_024518835.1	1778671	1778671	type	True	100.0	1067	1068	95	conclusive
Limnobacter alexandrii	strain=LZ-4	GCA_005871185.1	2570352	2570352	type	True	78.6069	380	1068	95	below_threshold
Cupriavidus taiwanensis	strain=LMG 19424	GCA_000069785.1	164546	164546	suspected-type	True	76.4969	71	1068	95	below_threshold
Noviherbaspirillum pedocola	strain=DKR-6	GCA_016632335.1	2801341	2801341	type	True	76.4106	53	1068	95	below_threshold
Achromobacter insolitus	strain=NCTC13520	GCA_900637265.1	217204	217204	type	True	76.3865	65	1068	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	76.3805	64	1068	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	76.3778	75	1068	95	below_threshold
Noviherbaspirillum humi	strain=U15	GCA_900188095.1	1688639	1688639	type	True	76.2668	74	1068	95	below_threshold
Roseateles terrae	strain=CECT 7247	GCA_014192155.1	431060	431060	type	True	76.2568	64	1068	95	below_threshold
Pseudoduganella namucuonensis	strain=CGMCC 1.11014	GCA_900116645.1	1035707	1035707	type	True	76.251	73	1068	95	below_threshold
Achromobacter aloeverae	strain=AVA-1	GCA_004121055.1	1750518	1750518	type	True	76.0931	55	1068	95	below_threshold
Pseudoduganella umbonata	strain=CECT 7753	GCA_014192225.1	864828	864828	type	True	76.0103	56	1068	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:22,449] [INFO] DFAST Taxonomy check result was written to GCF_024518835.1_ASM2451883v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:22,450] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:22,450] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:22,450] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53fce2e1-6c7c-45df-aad2-17a086f2dc4a/dqc_reference/checkm_data
[2024-01-24 13:10:22,451] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:22,483] [INFO] Task started: CheckM
[2024-01-24 13:10:22,483] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024518835.1_ASM2451883v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024518835.1_ASM2451883v1_genomic.fna/checkm_input GCF_024518835.1_ASM2451883v1_genomic.fna/checkm_result
[2024-01-24 13:11:07,473] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:07,474] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:07,504] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:07,504] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:07,505] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024518835.1_ASM2451883v1_genomic.fna/markers.fasta)
[2024-01-24 13:11:07,505] [INFO] Task started: Blastn
[2024-01-24 13:11:07,505] [INFO] Running command: blastn -query GCF_024518835.1_ASM2451883v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53fce2e1-6c7c-45df-aad2-17a086f2dc4a/dqc_reference/reference_markers_gtdb.fasta -out GCF_024518835.1_ASM2451883v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:08,767] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:08,771] [INFO] Selected 18 target genomes.
[2024-01-24 13:11:08,771] [INFO] Target genome list was writen to GCF_024518835.1_ASM2451883v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:08,971] [INFO] Task started: fastANI
[2024-01-24 13:11:08,971] [INFO] Running command: fastANI --query /var/lib/cwl/stg66429d62-9ed0-4a61-9e4c-dbf525b21990/GCF_024518835.1_ASM2451883v1_genomic.fna.gz --refList GCF_024518835.1_ASM2451883v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024518835.1_ASM2451883v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:21,912] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:21,933] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:11:21,934] [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_902506325.1	s__Limnobacter sp902506325	78.7056	340	1068	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004291335.1	s__Limnobacter thiooxidans	78.6866	345	1068	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005871185.1	s__Limnobacter alexandrii	78.6069	380	1068	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000170915.1	s__Limnobacter sp000170915	78.5695	323	1068	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	98.10	98.01	0.88	0.86	5	-
GCA_018815245.1	s__Limnobacter sp018815245	78.4377	375	1068	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	99.98	99.93	0.99	0.98	9	-
GCF_013004065.1	s__Limnobacter sp002954425	78.3781	356	1068	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	97.67	96.02	0.92	0.87	19	-
GCF_004340105.1	s__Variovorax sp004340105	76.4492	57	1068	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002261225.1	s__Bordetella_C sp002261225	76.3998	58	1068	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003058055.1	s__Acidovorax sp003058055	76.3373	88	1068	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.89	97.89	0.93	0.93	2	-
GCF_008119665.1	s__Pigmentiphaga aceris	76.2282	68	1068	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017356245.1	s__Bordetella_A petrii_D	76.0914	76	1068	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903928495.1	s__UBA2334 sp903928495	76.0714	74	1068	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA2334	95.0	99.91	99.91	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:21,936] [INFO] GTDB search result was written to GCF_024518835.1_ASM2451883v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:21,936] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:21,942] [INFO] DFAST_QC result json was written to GCF_024518835.1_ASM2451883v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:21,942] [INFO] DFAST_QC completed!
[2024-01-24 13:11:21,943] [INFO] Total running time: 0h1m33s