[2024-01-24 12:30:33,643] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:33,645] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:33,645] [INFO] DQC Reference Directory: /var/lib/cwl/stg106dd04e-1180-4637-b96b-dfeb688e0dc2/dqc_reference
[2024-01-24 12:30:34,930] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:34,931] [INFO] Task started: Prodigal
[2024-01-24 12:30:34,932] [INFO] Running command: gunzip -c /var/lib/cwl/stg641aa3e3-6893-4e3c-b4b2-fef9d58e0a0b/GCF_019656455.1_ASM1965645v1_genomic.fna.gz | prodigal -d GCF_019656455.1_ASM1965645v1_genomic.fna/cds.fna -a GCF_019656455.1_ASM1965645v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:48,404] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:48,405] [INFO] Task started: HMMsearch
[2024-01-24 12:30:48,405] [INFO] Running command: hmmsearch --tblout GCF_019656455.1_ASM1965645v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg106dd04e-1180-4637-b96b-dfeb688e0dc2/dqc_reference/reference_markers.hmm GCF_019656455.1_ASM1965645v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:48,724] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:48,726] [INFO] Found 6/6 markers.
[2024-01-24 12:30:48,771] [INFO] Query marker FASTA was written to GCF_019656455.1_ASM1965645v1_genomic.fna/markers.fasta
[2024-01-24 12:30:48,772] [INFO] Task started: Blastn
[2024-01-24 12:30:48,772] [INFO] Running command: blastn -query GCF_019656455.1_ASM1965645v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg106dd04e-1180-4637-b96b-dfeb688e0dc2/dqc_reference/reference_markers.fasta -out GCF_019656455.1_ASM1965645v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:49,885] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:49,889] [INFO] Selected 16 target genomes.
[2024-01-24 12:30:49,889] [INFO] Target genome list was writen to GCF_019656455.1_ASM1965645v1_genomic.fna/target_genomes.txt
[2024-01-24 12:30:49,896] [INFO] Task started: fastANI
[2024-01-24 12:30:49,896] [INFO] Running command: fastANI --query /var/lib/cwl/stg641aa3e3-6893-4e3c-b4b2-fef9d58e0a0b/GCF_019656455.1_ASM1965645v1_genomic.fna.gz --refList GCF_019656455.1_ASM1965645v1_genomic.fna/target_genomes.txt --output GCF_019656455.1_ASM1965645v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:08,016] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:08,017] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg106dd04e-1180-4637-b96b-dfeb688e0dc2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:08,017] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg106dd04e-1180-4637-b96b-dfeb688e0dc2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:08,031] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:08,031] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:08,031] [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
Noviherbaspirillum aridicola	strain=NCCP-691	GCA_019656455.1	2849687	2849687	type	True	100.0	1483	1484	95	conclusive
Noviherbaspirillum malthae	strain=CC-AFH3	GCA_015352985.1	1260987	1260987	type	True	81.6256	839	1484	95	below_threshold
Noviherbaspirillum humi	strain=U15	GCA_900188095.1	1688639	1688639	type	True	81.5797	711	1484	95	below_threshold
Noviherbaspirillum galbum	strain=17J57-3	GCA_010974945.1	2709383	2709383	type	True	81.3201	753	1484	95	below_threshold
Noviherbaspirillum aerium	strain=122213-3	GCA_008929045.1	2588497	2588497	type	True	81.2678	802	1484	95	below_threshold
Noviherbaspirillum denitrificans	strain=TSA40	GCA_002211445.1	1968433	1968433	type	True	81.1588	748	1484	95	below_threshold
Herbaspirillum robiniae	strain=HZ10	GCA_002213415.1	2014887	2014887	type	True	80.5573	585	1484	95	below_threshold
Noviherbaspirillum cavernae	strain=K2R10-39	GCA_003590875.1	2320862	2320862	type	True	80.062	603	1484	95	below_threshold
Noviherbaspirillum saxi	strain=K1R23-30	GCA_003591035.1	2320863	2320863	type	True	79.9962	601	1484	95	below_threshold
Noviherbaspirillum pedocola	strain=DKR-6	GCA_016632335.1	2801341	2801341	type	True	79.8121	619	1484	95	below_threshold
Massilia agilis	strain=JCM 31605	GCA_024756255.1	1811226	1811226	type	True	79.8018	562	1484	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	79.7107	571	1484	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	79.7057	428	1484	95	below_threshold
Herbaspirillum frisingense	strain=GSF30	GCA_000300975.2	92645	92645	type	True	79.6935	485	1484	95	below_threshold
Massilia eurypsychrophila	strain=JCM 30074	GCA_002760655.1	1485217	1485217	type	True	79.6489	577	1484	95	below_threshold
Oxalicibacterium solurbis	strain=CCM 7664	GCA_014635845.1	69280	69280	type	True	79.5888	421	1484	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:08,033] [INFO] DFAST Taxonomy check result was written to GCF_019656455.1_ASM1965645v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:08,033] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:08,034] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:08,034] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg106dd04e-1180-4637-b96b-dfeb688e0dc2/dqc_reference/checkm_data
[2024-01-24 12:31:08,035] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:08,079] [INFO] Task started: CheckM
[2024-01-24 12:31:08,079] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019656455.1_ASM1965645v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019656455.1_ASM1965645v1_genomic.fna/checkm_input GCF_019656455.1_ASM1965645v1_genomic.fna/checkm_result
[2024-01-24 12:31:51,782] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:51,783] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:51,809] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:51,809] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:51,810] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019656455.1_ASM1965645v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:51,810] [INFO] Task started: Blastn
[2024-01-24 12:31:51,810] [INFO] Running command: blastn -query GCF_019656455.1_ASM1965645v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg106dd04e-1180-4637-b96b-dfeb688e0dc2/dqc_reference/reference_markers_gtdb.fasta -out GCF_019656455.1_ASM1965645v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:54,106] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:54,110] [INFO] Selected 15 target genomes.
[2024-01-24 12:31:54,110] [INFO] Target genome list was writen to GCF_019656455.1_ASM1965645v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:54,121] [INFO] Task started: fastANI
[2024-01-24 12:31:54,122] [INFO] Running command: fastANI --query /var/lib/cwl/stg641aa3e3-6893-4e3c-b4b2-fef9d58e0a0b/GCF_019656455.1_ASM1965645v1_genomic.fna.gz --refList GCF_019656455.1_ASM1965645v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019656455.1_ASM1965645v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:09,551] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:09,566] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:32:09,567] [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_015352985.1	s__Noviherbaspirillum malthae	81.5951	842	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188095.1	s__Noviherbaspirillum humi	81.5448	715	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010974945.1	s__Noviherbaspirillum galbum	81.3112	754	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004570315.1	s__Noviherbaspirillum sp004570315	81.3079	609	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008929045.1	s__Noviherbaspirillum aerium	81.2715	801	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002211445.1	s__Noviherbaspirillum denitrificans	81.1259	751	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007874125.1	s__Noviherbaspirillum sp007874125	81.0947	703	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744395.1	s__Herbaspirillum sp017744395	80.8368	524	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002213415.1	s__Herbaspirillum robiniae	80.5485	587	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	98.55	98.54	0.93	0.92	3	-
GCF_000818395.1	s__Noviherbaspirillum autotrophicum	80.4405	676	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009914615.1	s__Herbaspirillum frisingense_B	80.4225	488	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017814915.1	s__Herbaspirillum sp017814915	80.3152	551	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014379395.1	s__Janthinobacterium sp014379395	80.0916	362	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590875.1	s__Noviherbaspirillum sp003590875	80.0697	601	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000261365.1	s__Herbaspirillum sp000261365	79.8482	469	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	98.65	98.65	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:09,569] [INFO] GTDB search result was written to GCF_019656455.1_ASM1965645v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:09,570] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:09,574] [INFO] DFAST_QC result json was written to GCF_019656455.1_ASM1965645v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:09,574] [INFO] DFAST_QC completed!
[2024-01-24 12:32:09,575] [INFO] Total running time: 0h1m36s