[2024-01-24 11:02:49,212] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:02:49,214] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:02:49,214] [INFO] DQC Reference Directory: /var/lib/cwl/stg0234c2a7-81e2-49ed-b642-2009adcf88b8/dqc_reference
[2024-01-24 11:02:50,434] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:02:50,435] [INFO] Task started: Prodigal
[2024-01-24 11:02:50,435] [INFO] Running command: gunzip -c /var/lib/cwl/stg22e614c7-4f5a-457c-913b-5229bde415d6/GCF_014202215.1_ASM1420221v1_genomic.fna.gz | prodigal -d GCF_014202215.1_ASM1420221v1_genomic.fna/cds.fna -a GCF_014202215.1_ASM1420221v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:03:02,603] [INFO] Task succeeded: Prodigal
[2024-01-24 11:03:02,604] [INFO] Task started: HMMsearch
[2024-01-24 11:03:02,604] [INFO] Running command: hmmsearch --tblout GCF_014202215.1_ASM1420221v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0234c2a7-81e2-49ed-b642-2009adcf88b8/dqc_reference/reference_markers.hmm GCF_014202215.1_ASM1420221v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:03:02,917] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:03:02,919] [INFO] Found 6/6 markers.
[2024-01-24 11:03:02,961] [INFO] Query marker FASTA was written to GCF_014202215.1_ASM1420221v1_genomic.fna/markers.fasta
[2024-01-24 11:03:02,962] [INFO] Task started: Blastn
[2024-01-24 11:03:02,962] [INFO] Running command: blastn -query GCF_014202215.1_ASM1420221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0234c2a7-81e2-49ed-b642-2009adcf88b8/dqc_reference/reference_markers.fasta -out GCF_014202215.1_ASM1420221v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:03:03,890] [INFO] Task succeeded: Blastn
[2024-01-24 11:03:03,894] [INFO] Selected 31 target genomes.
[2024-01-24 11:03:03,894] [INFO] Target genome list was writen to GCF_014202215.1_ASM1420221v1_genomic.fna/target_genomes.txt
[2024-01-24 11:03:03,919] [INFO] Task started: fastANI
[2024-01-24 11:03:03,919] [INFO] Running command: fastANI --query /var/lib/cwl/stg22e614c7-4f5a-457c-913b-5229bde415d6/GCF_014202215.1_ASM1420221v1_genomic.fna.gz --refList GCF_014202215.1_ASM1420221v1_genomic.fna/target_genomes.txt --output GCF_014202215.1_ASM1420221v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:03:28,883] [INFO] Task succeeded: fastANI
[2024-01-24 11:03:28,884] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0234c2a7-81e2-49ed-b642-2009adcf88b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:03:28,885] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0234c2a7-81e2-49ed-b642-2009adcf88b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:03:28,908] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:03:28,908] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:03:28,908] [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	78.3542	432	1411	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_003349825.1	215580	215580	type	True	78.3093	438	1411	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	78.2439	445	1411	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	77.8336	442	1411	95	below_threshold
Sphaerotilus natans	strain=ATCC 13338	GCA_900156335.1	34103	34103	type	True	77.6706	465	1411	95	below_threshold
Sphaerotilus natans subsp. natans	strain=DSM 6575	GCA_000689195.1	882627	34103	type	True	77.6697	447	1411	95	below_threshold
Bordetella pertussis	strain=18323	GCA_000306945.1	520	520	type	True	77.6269	313	1411	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	77.6244	395	1411	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	77.6118	474	1411	95	below_threshold
Bordetella pertussis	strain=FDAARGOS_1543	GCA_020736265.1	520	520	type	True	77.5849	316	1411	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	77.5258	384	1411	95	below_threshold
Cupriavidus malaysiensis	strain=USMAA1020	GCA_001854325.1	367825	367825	type	True	77.4381	525	1411	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	77.4095	349	1411	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_004340905.1	28068	28068	suspected-type	True	77.3907	493	1411	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	77.3891	491	1411	95	below_threshold
Pigmentiphaga kullae	strain=K24	GCA_004216695.1	151784	151784	type	True	77.3762	366	1411	95	below_threshold
Verticiella sediminum	strain=DSM 27279	GCA_007558815.1	1247510	1247510	type	True	77.3644	367	1411	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	77.3542	379	1411	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	77.3063	344	1411	95	below_threshold
Sulfuritortus calidifontis	strain=DSM 103923	GCA_004346085.1	1914471	1914471	type	True	77.2511	232	1411	95	below_threshold
Sulfuritortus calidifontis	strain=J1A	GCA_003967275.1	1914471	1914471	type	True	77.198	237	1411	95	below_threshold
Derxia lacustris	strain=HL-12	GCA_002105195.1	764842	764842	type	True	77.1297	420	1411	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	77.068	481	1411	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	77.027	317	1411	95	below_threshold
Duganella callida	strain=DN04	GCA_004614165.1	2561932	2561932	type	True	76.9721	329	1411	95	below_threshold
Achromobacter veterisilvae	strain=LMG 30378	GCA_900496975.1	2069367	2069367	type	True	76.8987	376	1411	95	below_threshold
Achromobacter aloeverae	strain=AVA-1	GCA_004121055.1	1750518	1750518	type	True	76.8625	305	1411	95	below_threshold
Pandoraea morbifera	strain=LMG 31116	GCA_902459575.1	2508300	2508300	type	True	76.6086	238	1411	95	below_threshold
Pandoraea nosoerga	strain=LMG 31109	GCA_902459585.1	2508296	2508296	type	True	76.5161	270	1411	95	below_threshold
Pandoraea eparura	strain=LMG 31012	GCA_902459725.1	2508291	2508291	type	True	76.2922	233	1411	95	below_threshold
Pandoraea capi	strain=LMG 20602	GCA_902459735.1	2508286	2508286	type	True	76.2498	198	1411	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:03:28,910] [INFO] DFAST Taxonomy check result was written to GCF_014202215.1_ASM1420221v1_genomic.fna/tc_result.tsv
[2024-01-24 11:03:28,911] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:03:28,911] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:03:28,911] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0234c2a7-81e2-49ed-b642-2009adcf88b8/dqc_reference/checkm_data
[2024-01-24 11:03:28,912] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:03:28,955] [INFO] Task started: CheckM
[2024-01-24 11:03:28,956] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014202215.1_ASM1420221v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014202215.1_ASM1420221v1_genomic.fna/checkm_input GCF_014202215.1_ASM1420221v1_genomic.fna/checkm_result
[2024-01-24 11:04:16,907] [INFO] Task succeeded: CheckM
[2024-01-24 11:04:16,909] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:04:16,933] [INFO] ===== Completeness check finished =====
[2024-01-24 11:04:16,933] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:04:16,934] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014202215.1_ASM1420221v1_genomic.fna/markers.fasta)
[2024-01-24 11:04:16,934] [INFO] Task started: Blastn
[2024-01-24 11:04:16,934] [INFO] Running command: blastn -query GCF_014202215.1_ASM1420221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0234c2a7-81e2-49ed-b642-2009adcf88b8/dqc_reference/reference_markers_gtdb.fasta -out GCF_014202215.1_ASM1420221v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:04:18,656] [INFO] Task succeeded: Blastn
[2024-01-24 11:04:18,660] [INFO] Selected 14 target genomes.
[2024-01-24 11:04:18,660] [INFO] Target genome list was writen to GCF_014202215.1_ASM1420221v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:04:18,675] [INFO] Task started: fastANI
[2024-01-24 11:04:18,675] [INFO] Running command: fastANI --query /var/lib/cwl/stg22e614c7-4f5a-457c-913b-5229bde415d6/GCF_014202215.1_ASM1420221v1_genomic.fna.gz --refList GCF_014202215.1_ASM1420221v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014202215.1_ASM1420221v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:04:31,202] [INFO] Task succeeded: fastANI
[2024-01-24 11:04:31,221] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:04:31,221] [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_014202215.1	s__Quisquiliibacterium transsilvanicum	100.0	1410	1411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Quisquiliibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008039575.1	s__SCN-69-89 sp008039575	80.404	659	1411	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	80.3962	425	1411	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_001724855.1	s__SCN-69-89 sp001724855	80.0219	531	1411	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_003577305.1	s__SCN-69-89 sp003577305	79.8587	480	1411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	99.77	99.54	0.93	0.87	4	-
GCA_001898645.1	s__SCN-69-89 sp001898645	79.8086	597	1411	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	-
GCA_018970865.1	s__CAIZPE01 sp018970865	79.6994	580	1411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAIZPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903934795.1	s__CAIZPE01 sp903934795	79.6052	554	1411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAIZPE01	95.0	99.53	99.52	0.90	0.89	3	-
GCA_903934295.1	s__CAIZPE01 sp903934295	79.4494	590	1411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAIZPE01	95.0	99.93	99.93	0.98	0.98	2	-
GCA_016710525.1	s__CAIZPE01 sp016710525	79.2452	603	1411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAIZPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003818495.1	s__UBA4615 sp003818495	79.1308	538	1411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA4615	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015476235.1	s__Schlegelella thermodepolymerans	78.2275	448	1411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Schlegelella	95.0	99.89	99.68	0.98	0.95	4	-
GCA_016716275.1	s__JADJWR01 sp016716275	78.0868	394	1411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JADJWR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016583785.1	s__Rubrivivax gelatinosus_B	77.4189	480	1411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.02	99.02	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:04:31,223] [INFO] GTDB search result was written to GCF_014202215.1_ASM1420221v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:04:31,223] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:04:31,227] [INFO] DFAST_QC result json was written to GCF_014202215.1_ASM1420221v1_genomic.fna/dqc_result.json
[2024-01-24 11:04:31,228] [INFO] DFAST_QC completed!
[2024-01-24 11:04:31,228] [INFO] Total running time: 0h1m42s