[2024-01-24 13:23:10,744] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:23:10,745] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:23:10,745] [INFO] DQC Reference Directory: /var/lib/cwl/stg27064682-c00c-4ddb-a33f-f98f86670464/dqc_reference
[2024-01-24 13:23:11,990] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:23:11,991] [INFO] Task started: Prodigal
[2024-01-24 13:23:11,991] [INFO] Running command: gunzip -c /var/lib/cwl/stg866fadd8-24f2-4507-953e-7f209ffb3881/GCF_003892345.1_ASM389234v1_genomic.fna.gz | prodigal -d GCF_003892345.1_ASM389234v1_genomic.fna/cds.fna -a GCF_003892345.1_ASM389234v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:23:25,056] [INFO] Task succeeded: Prodigal
[2024-01-24 13:23:25,057] [INFO] Task started: HMMsearch
[2024-01-24 13:23:25,057] [INFO] Running command: hmmsearch --tblout GCF_003892345.1_ASM389234v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg27064682-c00c-4ddb-a33f-f98f86670464/dqc_reference/reference_markers.hmm GCF_003892345.1_ASM389234v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:23:25,297] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:23:25,299] [INFO] Found 6/6 markers.
[2024-01-24 13:23:25,332] [INFO] Query marker FASTA was written to GCF_003892345.1_ASM389234v1_genomic.fna/markers.fasta
[2024-01-24 13:23:25,332] [INFO] Task started: Blastn
[2024-01-24 13:23:25,332] [INFO] Running command: blastn -query GCF_003892345.1_ASM389234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg27064682-c00c-4ddb-a33f-f98f86670464/dqc_reference/reference_markers.fasta -out GCF_003892345.1_ASM389234v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:26,164] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:26,168] [INFO] Selected 20 target genomes.
[2024-01-24 13:23:26,169] [INFO] Target genome list was writen to GCF_003892345.1_ASM389234v1_genomic.fna/target_genomes.txt
[2024-01-24 13:23:26,173] [INFO] Task started: fastANI
[2024-01-24 13:23:26,174] [INFO] Running command: fastANI --query /var/lib/cwl/stg866fadd8-24f2-4507-953e-7f209ffb3881/GCF_003892345.1_ASM389234v1_genomic.fna.gz --refList GCF_003892345.1_ASM389234v1_genomic.fna/target_genomes.txt --output GCF_003892345.1_ASM389234v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:44,543] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:44,543] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg27064682-c00c-4ddb-a33f-f98f86670464/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:44,544] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg27064682-c00c-4ddb-a33f-f98f86670464/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:44,558] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:23:44,559] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:44,559] [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
Lautropia dentalis	strain=KCOM 2505	GCA_003892345.1	2490857	2490857	type	True	99.9996	1266	1270	95	conclusive
Lautropia mirabilis	strain=ATCC 51599	GCA_000186425.1	47671	47671	type	True	83.9613	792	1270	95	below_threshold
Lautropia mirabilis	strain=NCTC12852	GCA_900637555.1	47671	47671	type	True	83.8748	806	1270	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	77.5414	238	1270	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	77.5179	231	1270	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	77.5163	236	1270	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	77.4653	238	1270	95	below_threshold
Cupriavidus taiwanensis	strain=LMG 19424	GCA_000069785.1	164546	164546	suspected-type	True	77.3541	254	1270	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	77.3305	238	1270	95	below_threshold
Candidimonas humi	strain=DSM 25336	GCA_019166065.1	683355	683355	type	True	77.327	160	1270	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	77.318	252	1270	95	below_threshold
Cupriavidus malaysiensis	strain=USMAA1020	GCA_001854325.1	367825	367825	type	True	77.2947	248	1270	95	below_threshold
Achromobacter denitrificans	strain=LMG 1231	GCA_902859715.1	32002	32002	type	True	77.1805	239	1270	95	below_threshold
Achromobacter denitrificans	strain=NBRC 15125	GCA_001571365.1	32002	32002	type	True	77.1418	232	1270	95	below_threshold
Pigmentiphaga kullae	strain=K24	GCA_004216695.1	151784	151784	type	True	77.1091	232	1270	95	below_threshold
Noviherbaspirillum aridicola	strain=NCCP-691	GCA_019656455.1	2849687	2849687	type	True	77.1017	167	1270	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	77.0754	259	1270	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	77.0616	242	1270	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	76.9752	202	1270	95	below_threshold
Leeia aquatica	strain=IMCC25680	GCA_012641365.1	2725557	2725557	type	True	76.7384	80	1270	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:44,562] [INFO] DFAST Taxonomy check result was written to GCF_003892345.1_ASM389234v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:44,564] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:44,564] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:44,564] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg27064682-c00c-4ddb-a33f-f98f86670464/dqc_reference/checkm_data
[2024-01-24 13:23:44,565] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:44,603] [INFO] Task started: CheckM
[2024-01-24 13:23:44,603] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003892345.1_ASM389234v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003892345.1_ASM389234v1_genomic.fna/checkm_input GCF_003892345.1_ASM389234v1_genomic.fna/checkm_result
[2024-01-24 13:24:39,741] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:39,742] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:39,760] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:39,760] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:39,760] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003892345.1_ASM389234v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:39,761] [INFO] Task started: Blastn
[2024-01-24 13:24:39,761] [INFO] Running command: blastn -query GCF_003892345.1_ASM389234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg27064682-c00c-4ddb-a33f-f98f86670464/dqc_reference/reference_markers_gtdb.fasta -out GCF_003892345.1_ASM389234v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:41,163] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:41,167] [INFO] Selected 15 target genomes.
[2024-01-24 13:24:41,167] [INFO] Target genome list was writen to GCF_003892345.1_ASM389234v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:41,251] [INFO] Task started: fastANI
[2024-01-24 13:24:41,251] [INFO] Running command: fastANI --query /var/lib/cwl/stg866fadd8-24f2-4507-953e-7f209ffb3881/GCF_003892345.1_ASM389234v1_genomic.fna.gz --refList GCF_003892345.1_ASM389234v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003892345.1_ASM389234v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:52,571] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:52,583] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:52,584] [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_003892345.1	s__Lautropia dentalis	99.9996	1266	1270	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lautropia	95.0	98.32	98.32	0.98	0.98	2	conclusive
GCF_900637555.1	s__Lautropia mirabilis	83.8864	805	1270	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lautropia	95.0	97.31	96.25	0.97	0.95	6	-
GCF_008039575.1	s__SCN-69-89 sp008039575	78.0282	232	1270	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724315.1	s__SCN-69-89 sp001724315	77.8906	164	1270	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012513675.1	s__Lautropia sp012513675	77.8326	178	1270	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lautropia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970865.1	s__CAIZPE01 sp018970865	77.6627	214	1270	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAIZPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898645.1	s__SCN-69-89 sp001898645	77.6313	257	1270	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	99.96	99.96	0.96	0.96	2	-
GCF_002188465.1	s__Pigmentiphaga sp002188465	77.5124	187	1270	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003854895.1	s__Pigmentiphaga sp003854895	77.4792	220	1270	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000069785.1	s__Cupriavidus taiwanensis	77.3186	252	1270	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.86	98.78	0.92	0.91	9	-
GCA_013813615.1	s__Lautropia sp013813615	77.2489	144	1270	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lautropia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004016515.1	s__Rubrivivax albus	77.2264	228	1270	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016703325.1	s__JADJCH01 sp016703325	76.9136	184	1270	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JADJCH01	95.0	99.29	99.29	0.91	0.91	2	-
GCA_903898725.1	s__UBA4615 sp903898725	76.9134	212	1270	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA4615	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713125.1	s__SZAS-79 sp016713125	76.4401	154	1270	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__SZAS-79	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:52,585] [INFO] GTDB search result was written to GCF_003892345.1_ASM389234v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:52,586] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:52,589] [INFO] DFAST_QC result json was written to GCF_003892345.1_ASM389234v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:52,590] [INFO] DFAST_QC completed!
[2024-01-24 13:24:52,590] [INFO] Total running time: 0h1m42s