[2024-01-24 13:36:45,494] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:45,497] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:45,497] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3d8901c-bcab-4182-8e91-4030799126db/dqc_reference
[2024-01-24 13:36:46,714] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:46,715] [INFO] Task started: Prodigal
[2024-01-24 13:36:46,715] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f42e682-c509-4a20-b350-70814595a6e7/GCF_013248975.1_ASM1324897v1_genomic.fna.gz | prodigal -d GCF_013248975.1_ASM1324897v1_genomic.fna/cds.fna -a GCF_013248975.1_ASM1324897v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:59,016] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:59,016] [INFO] Task started: HMMsearch
[2024-01-24 13:36:59,016] [INFO] Running command: hmmsearch --tblout GCF_013248975.1_ASM1324897v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3d8901c-bcab-4182-8e91-4030799126db/dqc_reference/reference_markers.hmm GCF_013248975.1_ASM1324897v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:59,342] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:59,343] [INFO] Found 6/6 markers.
[2024-01-24 13:36:59,393] [INFO] Query marker FASTA was written to GCF_013248975.1_ASM1324897v1_genomic.fna/markers.fasta
[2024-01-24 13:36:59,393] [INFO] Task started: Blastn
[2024-01-24 13:36:59,394] [INFO] Running command: blastn -query GCF_013248975.1_ASM1324897v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3d8901c-bcab-4182-8e91-4030799126db/dqc_reference/reference_markers.fasta -out GCF_013248975.1_ASM1324897v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:59,978] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:59,981] [INFO] Selected 21 target genomes.
[2024-01-24 13:36:59,982] [INFO] Target genome list was writen to GCF_013248975.1_ASM1324897v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:59,997] [INFO] Task started: fastANI
[2024-01-24 13:36:59,997] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f42e682-c509-4a20-b350-70814595a6e7/GCF_013248975.1_ASM1324897v1_genomic.fna.gz --refList GCF_013248975.1_ASM1324897v1_genomic.fna/target_genomes.txt --output GCF_013248975.1_ASM1324897v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:19,073] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:19,074] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3d8901c-bcab-4182-8e91-4030799126db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:19,074] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3d8901c-bcab-4182-8e91-4030799126db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:19,089] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:19,089] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:19,089] [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
Neobacillus endophyticus	strain=BRMEA1	GCA_013248975.1	2738405	2738405	type	True	100.0	1874	1876	95	conclusive
Neobacillus mesonae	strain=FJAT-13985	GCA_001636315.1	1193713	1193713	type	True	79.1295	367	1876	95	below_threshold
Neobacillus fumarioli	strain=NBRC 102428	GCA_001591485.1	105229	105229	type	True	79.0128	488	1876	95	below_threshold
Bacillus dafuensis	strain=FJAT-25496	GCA_007995155.1	1742359	1742359	type	True	78.9813	185	1876	95	below_threshold
Neobacillus novalis	strain=FJAT-14227	GCA_001636395.1	220687	220687	type	True	78.8651	410	1876	95	below_threshold
Neobacillus soli	strain=DSM 15604	GCA_002335815.1	220688	220688	type	True	78.7939	387	1876	95	below_threshold
Neobacillus massiliamazoniensis	strain=LF1	GCA_001048695.1	1499688	1499688	type	True	78.7361	380	1876	95	below_threshold
Neobacillus rhizophilus	strain=FJAT-49825	GCA_018343535.1	2833579	2833579	type	True	78.6304	397	1876	95	below_threshold
Bacillus salipaludis	strain=WN066	GCA_004358205.1	2547811	2547811	type	True	78.5387	410	1876	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	78.2682	358	1876	95	below_threshold
Neobacillus novalis	strain=NBRC 102450	GCA_001591805.1	220687	220687	type	True	78.1787	392	1876	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	78.1513	348	1876	95	below_threshold
Neobacillus jeddahensis	strain=JCE	GCA_000612625.1	1461580	1461580	type	True	78.1232	344	1876	95	below_threshold
Neobacillus sedimentimangrovi	strain=FJAT-2464	GCA_010614825.1	2699460	2699460	type	True	78.1232	279	1876	95	below_threshold
Neobacillus soli	strain=NBRC 102451	GCA_001591665.1	220688	220688	type	True	78.0673	360	1876	95	below_threshold
Gottfriedia endophyticus	strain=RG28	GCA_017814275.1	2820819	2820819	type	True	77.6427	93	1876	95	below_threshold
Bacillus yapensis	strain=XXST-01	GCA_003966255.1	2492960	2492960	type	True	77.3202	127	1876	95	below_threshold
Bacillus yapensis	strain=XXST-01	GCA_005280205.1	2492960	2492960	type	True	77.2998	128	1876	95	below_threshold
Anoxybacillus kestanbolensis	strain=NCIMB 13971	GCA_023653015.1	227476	227476	type	True	76.5092	60	1876	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:19,091] [INFO] DFAST Taxonomy check result was written to GCF_013248975.1_ASM1324897v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:19,092] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:19,092] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:19,092] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3d8901c-bcab-4182-8e91-4030799126db/dqc_reference/checkm_data
[2024-01-24 13:37:19,093] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:19,146] [INFO] Task started: CheckM
[2024-01-24 13:37:19,146] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013248975.1_ASM1324897v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013248975.1_ASM1324897v1_genomic.fna/checkm_input GCF_013248975.1_ASM1324897v1_genomic.fna/checkm_result
[2024-01-24 13:38:02,011] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:02,012] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:02,027] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:02,027] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:02,027] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013248975.1_ASM1324897v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:02,027] [INFO] Task started: Blastn
[2024-01-24 13:38:02,027] [INFO] Running command: blastn -query GCF_013248975.1_ASM1324897v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3d8901c-bcab-4182-8e91-4030799126db/dqc_reference/reference_markers_gtdb.fasta -out GCF_013248975.1_ASM1324897v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:02,858] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:02,865] [INFO] Selected 27 target genomes.
[2024-01-24 13:38:02,865] [INFO] Target genome list was writen to GCF_013248975.1_ASM1324897v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:02,902] [INFO] Task started: fastANI
[2024-01-24 13:38:02,902] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f42e682-c509-4a20-b350-70814595a6e7/GCF_013248975.1_ASM1324897v1_genomic.fna.gz --refList GCF_013248975.1_ASM1324897v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013248975.1_ASM1324897v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:29,001] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:29,016] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:29,017] [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_013248975.1	s__Neobacillus endophyticus	100.0	1872	1876	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	conclusive
GCF_001636315.1	s__Neobacillus mesonae	79.0819	366	1876	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	98.98	98.98	0.94	0.94	2	-
GCF_001591485.1	s__Neobacillus fumarioli	79.0079	489	1876	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_001048695.1	s__Neobacillus massiliamazoniensis	78.7624	377	1876	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_018343535.1	s__Neobacillus sp018343535	78.6211	392	1876	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	99.05	99.05	0.95	0.95	2	-
GCF_004358205.1	s__Neobacillus salipaludis	78.5304	411	1876	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_001026695.1	s__Neobacillus vireti	78.4004	366	1876	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001866655.1	s__Neobacillus sp001866655	78.3761	397	1876	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_002585305.1	s__Neobacillus sp002585305	78.2761	387	1876	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	97.64	95.53	0.90	0.84	3	-
GCF_001584325.1	s__Bacillus nakamurai	78.2189	54	1876	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	99.07	99.07	0.94	0.94	2	-
GCF_018613415.1	s__Neobacillus sp018613415	78.2144	366	1876	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_001591805.1	s__Neobacillus novalis	78.204	391	1876	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000482325.1	s__Neobacillus sp000482325	78.1983	375	1876	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	-
GCA_019219025.1	s__Neobacillus sp019219025	78.1836	381	1876	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_014656545.1	s__Neobacillus sp014656545	78.15	347	1876	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_000612625.1	s__Neobacillus jeddahensis	78.1227	344	1876	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	99.99	99.99	0.99	0.99	3	-
GCF_018613065.1	s__Neobacillus sp018613065	78.1133	394	1876	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	95.53	95.32	0.78	0.75	6	-
GCF_001591665.1	s__Neobacillus soli	78.0673	360	1876	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009928415.1	s__Neobacillus sp009928415	78.0281	332	1876	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_000380245.2	s__Bacillus_AD massiliogorillae	76.7113	100	1876	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_AD	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:29,018] [INFO] GTDB search result was written to GCF_013248975.1_ASM1324897v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:29,019] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:29,023] [INFO] DFAST_QC result json was written to GCF_013248975.1_ASM1324897v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:29,023] [INFO] DFAST_QC completed!
[2024-01-24 13:38:29,023] [INFO] Total running time: 0h1m44s