[2024-01-25 17:49:20,956] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:49:20,957] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:49:20,957] [INFO] DQC Reference Directory: /var/lib/cwl/stg3adaed4f-8b52-4a78-b3aa-5c8e052cc742/dqc_reference
[2024-01-25 17:49:22,127] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:49:22,131] [INFO] Task started: Prodigal
[2024-01-25 17:49:22,132] [INFO] Running command: gunzip -c /var/lib/cwl/stg4773e031-e8ea-4d61-9f73-c741ce8cf718/GCF_026013905.1_ASM2601390v1_genomic.fna.gz | prodigal -d GCF_026013905.1_ASM2601390v1_genomic.fna/cds.fna -a GCF_026013905.1_ASM2601390v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:49:32,865] [INFO] Task succeeded: Prodigal
[2024-01-25 17:49:32,866] [INFO] Task started: HMMsearch
[2024-01-25 17:49:32,866] [INFO] Running command: hmmsearch --tblout GCF_026013905.1_ASM2601390v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3adaed4f-8b52-4a78-b3aa-5c8e052cc742/dqc_reference/reference_markers.hmm GCF_026013905.1_ASM2601390v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:49:33,089] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:49:33,090] [INFO] Found 6/6 markers.
[2024-01-25 17:49:33,126] [INFO] Query marker FASTA was written to GCF_026013905.1_ASM2601390v1_genomic.fna/markers.fasta
[2024-01-25 17:49:33,126] [INFO] Task started: Blastn
[2024-01-25 17:49:33,127] [INFO] Running command: blastn -query GCF_026013905.1_ASM2601390v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3adaed4f-8b52-4a78-b3aa-5c8e052cc742/dqc_reference/reference_markers.fasta -out GCF_026013905.1_ASM2601390v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:49:34,161] [INFO] Task succeeded: Blastn
[2024-01-25 17:49:34,164] [INFO] Selected 15 target genomes.
[2024-01-25 17:49:34,164] [INFO] Target genome list was writen to GCF_026013905.1_ASM2601390v1_genomic.fna/target_genomes.txt
[2024-01-25 17:49:34,170] [INFO] Task started: fastANI
[2024-01-25 17:49:34,171] [INFO] Running command: fastANI --query /var/lib/cwl/stg4773e031-e8ea-4d61-9f73-c741ce8cf718/GCF_026013905.1_ASM2601390v1_genomic.fna.gz --refList GCF_026013905.1_ASM2601390v1_genomic.fna/target_genomes.txt --output GCF_026013905.1_ASM2601390v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:49:48,805] [INFO] Task succeeded: fastANI
[2024-01-25 17:49:48,805] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3adaed4f-8b52-4a78-b3aa-5c8e052cc742/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:49:48,806] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3adaed4f-8b52-4a78-b3aa-5c8e052cc742/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:49:48,816] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:49:48,816] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:49:48,816] [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
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	83.0547	715	1116	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	83.008	733	1116	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_003349825.1	215580	215580	type	True	82.9724	727	1116	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	80.7893	669	1116	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	80.2196	579	1116	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	79.9998	598	1116	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	79.9748	595	1116	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	79.9629	492	1116	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	79.9004	500	1116	95	below_threshold
Mitsuaria chitinivorans	strain=HWN-4	GCA_002761755.1	2917965	2917965	type	True	79.7927	497	1116	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	79.6319	460	1116	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	79.6287	482	1116	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.4919	499	1116	95	below_threshold
Pelomonas puraquae	strain=CCUG 52769	GCA_002205845.1	431059	431059	type	True	79.4426	487	1116	95	below_threshold
Ramlibacter alkalitolerans	strain=KACC 19305	GCA_016722765.1	2039631	2039631	type	True	79.2875	489	1116	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:49:48,817] [INFO] DFAST Taxonomy check result was written to GCF_026013905.1_ASM2601390v1_genomic.fna/tc_result.tsv
[2024-01-25 17:49:48,817] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:49:48,817] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:49:48,818] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3adaed4f-8b52-4a78-b3aa-5c8e052cc742/dqc_reference/checkm_data
[2024-01-25 17:49:48,818] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:49:48,858] [INFO] Task started: CheckM
[2024-01-25 17:49:48,858] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026013905.1_ASM2601390v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026013905.1_ASM2601390v1_genomic.fna/checkm_input GCF_026013905.1_ASM2601390v1_genomic.fna/checkm_result
[2024-01-25 17:51:22,494] [INFO] Task succeeded: CheckM
[2024-01-25 17:51:22,495] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:51:22,511] [INFO] ===== Completeness check finished =====
[2024-01-25 17:51:22,512] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:51:22,513] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026013905.1_ASM2601390v1_genomic.fna/markers.fasta)
[2024-01-25 17:51:22,513] [INFO] Task started: Blastn
[2024-01-25 17:51:22,513] [INFO] Running command: blastn -query GCF_026013905.1_ASM2601390v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3adaed4f-8b52-4a78-b3aa-5c8e052cc742/dqc_reference/reference_markers_gtdb.fasta -out GCF_026013905.1_ASM2601390v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:51:24,629] [INFO] Task succeeded: Blastn
[2024-01-25 17:51:24,632] [INFO] Selected 20 target genomes.
[2024-01-25 17:51:24,632] [INFO] Target genome list was writen to GCF_026013905.1_ASM2601390v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:51:24,661] [INFO] Task started: fastANI
[2024-01-25 17:51:24,662] [INFO] Running command: fastANI --query /var/lib/cwl/stg4773e031-e8ea-4d61-9f73-c741ce8cf718/GCF_026013905.1_ASM2601390v1_genomic.fna.gz --refList GCF_026013905.1_ASM2601390v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026013905.1_ASM2601390v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:51:46,669] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:46,682] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:51:46,682] [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_015476235.1	s__Schlegelella thermodepolymerans	82.9903	735	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Schlegelella	95.0	99.89	99.68	0.98	0.95	4	-
GCF_003569765.1	s__Aquabacterium_B tepidiphilum	81.1175	669	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002930615.1	s__Zhizhongheella caldifontis	81.0953	613	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Zhizhongheella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006386545.1	s__Pseudorivibacter rhizosphaerae	80.9337	630	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudorivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001017435.1	s__Polyangium_A brachysporum	80.7986	668	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polyangium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003265685.1	s__Piscinibacter caeni	80.7011	609	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007994965.1	s__Piscinibacter aquaticus	80.6823	578	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014873965.1	s__VBDL01 sp014873965	80.535	597	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__VBDL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430725.1	s__Azohydromonas australica	80.2046	581	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016219375.1	s__Aquabacterium sp016219375	80.1933	533	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826655.1	s__Methylibium sp902826655	80.1215	530	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Methylibium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302505.1	s__Rubrivivax sp017302505	80.0868	440	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381125.1	s__Caldimonas manganoxidans	80.0284	521	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caldimonas	95.0	98.73	98.73	0.91	0.91	2	-
GCF_012927045.1	s__Azohydromonas caseinilytica	80.0223	591	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009760915.1	s__Azohydromonas aeria	79.9942	598	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598255.1	s__Mitsuaria chitosanitabida	79.6164	531	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	99.05	99.05	0.96	0.96	2	-
GCF_002205645.1	s__Mitsuaria aquatilis	79.5234	538	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016467315.1	s__OAE585 sp016467315	79.3741	540	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__OAE585	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019232985.1	s__JAFAMW01 sp019232985	79.1114	346	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAFAMW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016789955.1	s__Rubrivivax sp016789955	79.0647	453	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:51:46,685] [INFO] GTDB search result was written to GCF_026013905.1_ASM2601390v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:51:46,686] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:51:46,690] [INFO] DFAST_QC result json was written to GCF_026013905.1_ASM2601390v1_genomic.fna/dqc_result.json
[2024-01-25 17:51:46,690] [INFO] DFAST_QC completed!
[2024-01-25 17:51:46,690] [INFO] Total running time: 0h2m26s