[2024-01-24 10:47:11,671] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:11,673] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:11,673] [INFO] DQC Reference Directory: /var/lib/cwl/stg293635bc-29e2-4a9e-b7da-74c4b125da2e/dqc_reference
[2024-01-24 10:47:16,943] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:16,945] [INFO] Task started: Prodigal
[2024-01-24 10:47:16,945] [INFO] Running command: gunzip -c /var/lib/cwl/stg091a56a0-de67-4ced-b98c-18b612bd8295/GCF_011008805.1_ASM1100880v1_genomic.fna.gz | prodigal -d GCF_011008805.1_ASM1100880v1_genomic.fna/cds.fna -a GCF_011008805.1_ASM1100880v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:29,434] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:29,434] [INFO] Task started: HMMsearch
[2024-01-24 10:47:29,434] [INFO] Running command: hmmsearch --tblout GCF_011008805.1_ASM1100880v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg293635bc-29e2-4a9e-b7da-74c4b125da2e/dqc_reference/reference_markers.hmm GCF_011008805.1_ASM1100880v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:29,737] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:29,739] [INFO] Found 6/6 markers.
[2024-01-24 10:47:29,792] [INFO] Query marker FASTA was written to GCF_011008805.1_ASM1100880v1_genomic.fna/markers.fasta
[2024-01-24 10:47:29,792] [INFO] Task started: Blastn
[2024-01-24 10:47:29,793] [INFO] Running command: blastn -query GCF_011008805.1_ASM1100880v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg293635bc-29e2-4a9e-b7da-74c4b125da2e/dqc_reference/reference_markers.fasta -out GCF_011008805.1_ASM1100880v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:30,441] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:30,446] [INFO] Selected 25 target genomes.
[2024-01-24 10:47:30,446] [INFO] Target genome list was writen to GCF_011008805.1_ASM1100880v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:39,601] [INFO] Task started: fastANI
[2024-01-24 10:47:39,602] [INFO] Running command: fastANI --query /var/lib/cwl/stg091a56a0-de67-4ced-b98c-18b612bd8295/GCF_011008805.1_ASM1100880v1_genomic.fna.gz --refList GCF_011008805.1_ASM1100880v1_genomic.fna/target_genomes.txt --output GCF_011008805.1_ASM1100880v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:58,318] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:58,319] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg293635bc-29e2-4a9e-b7da-74c4b125da2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:58,320] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg293635bc-29e2-4a9e-b7da-74c4b125da2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:58,340] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:47:58,340] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:58,340] [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
Margalitia shackletonii	strain=LMG 18435	GCA_011008805.1	157838	157838	type	True	100.0	1664	1671	95	conclusive
Margalitia shackletonii	strain=LMG 18435	GCA_001420715.1	157838	157838	type	True	99.9892	1670	1671	95	conclusive
Margalitia camelliae	strain=7578-1	GCA_002844575.1	1707093	1707093	type	True	82.6591	1038	1671	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_025263665.1	38875	38875	type	True	78.9139	323	1671	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_017809215.1	38875	38875	type	True	78.9124	326	1671	95	below_threshold
Heyndrickxia sporothermodurans	strain=DSM 10599	GCA_016785185.1	46224	46224	type	True	78.2023	265	1671	95	below_threshold
Heyndrickxia sporothermodurans	strain=DSM 10599	GCA_003055085.1	46224	46224	type	True	78.079	244	1671	95	below_threshold
Bacillus subtilis subsp. subtilis	strain=168	GCA_002009135.1	135461	1423	type	True	77.5415	53	1671	95	below_threshold
Bacillus subtilis subsp. subtilis	strain=168	GCA_024917115.1	135461	1423	type	True	77.532	52	1671	95	below_threshold
Bacillus subtilis subsp. subtilis	strain=168	GCA_002009095.1	135461	1423	type	True	77.5047	51	1671	95	below_threshold
Neobacillus mesonae	strain=FJAT-13985	GCA_001636315.1	1193713	1193713	type	True	77.41	128	1671	95	below_threshold
Neobacillus dielmonensis	strain=FF4	GCA_000612665.1	1347369	1347369	type	True	77.2836	89	1671	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	77.0095	112	1671	95	below_threshold
Rossellomorea aquimaris	strain=TF12	GCA_001648555.1	189382	189382	suspected-type	True	76.9158	103	1671	95	below_threshold
Bacillus enclensis	strain=SGD-1123	GCA_001456935.1	1402860	1402860	type	True	76.8693	69	1671	95	below_threshold
Peribacillus acanthi	strain=L28	GCA_003073175.1	2171554	2171554	type	True	76.8427	82	1671	95	below_threshold
Lederbergia lenta	strain=NCTC4824	GCA_900478165.1	1467	1467	type	True	76.7286	93	1671	95	below_threshold
Sutcliffiella deserti	strain=DG-18	GCA_020037475.1	2875501	2875501	type	True	76.5905	61	1671	95	below_threshold
Ureibacillus chungkukjangi	strain=2RL32	GCA_003049615.1	1202712	1202712	type	True	76.4263	54	1671	95	below_threshold
Lederbergia lenta	strain=NBRC 16444	GCA_001591545.1	1467	1467	type	True	76.3277	93	1671	95	below_threshold
Cytobacillus firmus	strain=NBRC 15306	GCA_001591465.1	1399	1399	suspected-type	True	76.3019	68	1671	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:58,342] [INFO] DFAST Taxonomy check result was written to GCF_011008805.1_ASM1100880v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:58,342] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:58,343] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:58,343] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg293635bc-29e2-4a9e-b7da-74c4b125da2e/dqc_reference/checkm_data
[2024-01-24 10:47:58,344] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:58,397] [INFO] Task started: CheckM
[2024-01-24 10:47:58,397] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011008805.1_ASM1100880v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011008805.1_ASM1100880v1_genomic.fna/checkm_input GCF_011008805.1_ASM1100880v1_genomic.fna/checkm_result
[2024-01-24 10:48:33,384] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:33,385] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:33,413] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:33,413] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:33,414] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011008805.1_ASM1100880v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:33,414] [INFO] Task started: Blastn
[2024-01-24 10:48:33,414] [INFO] Running command: blastn -query GCF_011008805.1_ASM1100880v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg293635bc-29e2-4a9e-b7da-74c4b125da2e/dqc_reference/reference_markers_gtdb.fasta -out GCF_011008805.1_ASM1100880v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:34,307] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:34,311] [INFO] Selected 21 target genomes.
[2024-01-24 10:48:34,311] [INFO] Target genome list was writen to GCF_011008805.1_ASM1100880v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:34,378] [INFO] Task started: fastANI
[2024-01-24 10:48:34,379] [INFO] Running command: fastANI --query /var/lib/cwl/stg091a56a0-de67-4ced-b98c-18b612bd8295/GCF_011008805.1_ASM1100880v1_genomic.fna.gz --refList GCF_011008805.1_ASM1100880v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011008805.1_ASM1100880v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:51,698] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:51,725] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:51,725] [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_001420715.1	s__Margalitia shackletonii	99.9892	1670	1671	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Margalitia	95.0	99.16	98.74	0.93	0.89	4	conclusive
GCF_002844575.1	s__Margalitia camelliae	82.6591	1038	1671	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Margalitia	95.0	99.53	99.53	0.93	0.93	2	-
GCF_018343615.1	s__Margalitia sp018343615	80.4193	742	1671	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Margalitia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017809215.1	s__Heyndrickxia oleronia	78.9257	325	1671	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Heyndrickxia	95.0	98.68	97.33	0.92	0.89	7	-
GCA_018333075.1	s__Heyndrickxia sporothermodurans_A	78.282	332	1671	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Heyndrickxia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016772275.1	s__Heyndrickxia vini	78.2443	308	1671	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Heyndrickxia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016756695.1	s__Heyndrickxia sporothermodurans	78.1421	291	1671	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Heyndrickxia	95.0	99.73	97.95	0.95	0.84	38	-
GCF_000009045.1	s__Bacillus subtilis	77.4562	50	1671	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.63	95.03	0.95	0.86	485	-
GCF_002860255.1	s__Neobacillus cucumis_A	77.2909	147	1671	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002560985.1	s__Bacillus_A sp002560985	77.2086	99	1671	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002582035.1	s__Bacillus_A pseudomycoides_B	77.0285	94	1671	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001648555.1	s__Rossellomorea aquimaris	76.9158	103	1671	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Rossellomorea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008710145.1	s__Bacillus_BD endozanthoxylicus	76.9073	108	1671	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BD	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799755.1	s__Fredinandcohnia timonensis_A	76.8581	90	1671	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003073175.1	s__Bacillus_BN acanthi	76.8427	82	1671	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_BN	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900240995.1	s__OESV01 sp900240995	76.7814	91	1671	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_C;f__Bacillaceae_J;g__OESV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006861795.1	s__Psychrobacillus lasiicapitis	76.7142	61	1671	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	99.99	99.99	0.99	0.99	2	-
GCA_016841285.1	s__Calidifontibacillus sp016841285	76.4489	68	1671	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_C;f__Bacillaceae_J;g__Calidifontibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591545.1	s__Bacillus_AH lentus	76.3277	93	1671	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Bacillus_AH	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012843435.1	s__Psychrobacillus sp012843435	76.158	56	1671	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:51,727] [INFO] GTDB search result was written to GCF_011008805.1_ASM1100880v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:51,727] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:51,731] [INFO] DFAST_QC result json was written to GCF_011008805.1_ASM1100880v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:51,732] [INFO] DFAST_QC completed!
[2024-01-24 10:48:51,732] [INFO] Total running time: 0h1m40s