[2024-01-24 14:20:15,716] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:20:15,721] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:20:15,721] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ce37dcb-d278-44e4-abb4-8cc272d29200/dqc_reference
[2024-01-24 14:20:17,642] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:20:17,643] [INFO] Task started: Prodigal
[2024-01-24 14:20:17,643] [INFO] Running command: gunzip -c /var/lib/cwl/stg3648cb1b-4d15-4468-8e57-7089ab2b9cfe/GCF_005116465.1_ASM511646v1_genomic.fna.gz | prodigal -d GCF_005116465.1_ASM511646v1_genomic.fna/cds.fna -a GCF_005116465.1_ASM511646v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:28,737] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:28,738] [INFO] Task started: HMMsearch
[2024-01-24 14:20:28,738] [INFO] Running command: hmmsearch --tblout GCF_005116465.1_ASM511646v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ce37dcb-d278-44e4-abb4-8cc272d29200/dqc_reference/reference_markers.hmm GCF_005116465.1_ASM511646v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:29,121] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:29,122] [INFO] Found 6/6 markers.
[2024-01-24 14:20:29,175] [INFO] Query marker FASTA was written to GCF_005116465.1_ASM511646v1_genomic.fna/markers.fasta
[2024-01-24 14:20:29,175] [INFO] Task started: Blastn
[2024-01-24 14:20:29,175] [INFO] Running command: blastn -query GCF_005116465.1_ASM511646v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ce37dcb-d278-44e4-abb4-8cc272d29200/dqc_reference/reference_markers.fasta -out GCF_005116465.1_ASM511646v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:32,222] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:32,227] [INFO] Selected 18 target genomes.
[2024-01-24 14:20:32,227] [INFO] Target genome list was writen to GCF_005116465.1_ASM511646v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:32,239] [INFO] Task started: fastANI
[2024-01-24 14:20:32,240] [INFO] Running command: fastANI --query /var/lib/cwl/stg3648cb1b-4d15-4468-8e57-7089ab2b9cfe/GCF_005116465.1_ASM511646v1_genomic.fna.gz --refList GCF_005116465.1_ASM511646v1_genomic.fna/target_genomes.txt --output GCF_005116465.1_ASM511646v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:47,325] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:47,325] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ce37dcb-d278-44e4-abb4-8cc272d29200/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:47,326] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ce37dcb-d278-44e4-abb4-8cc272d29200/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:47,359] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:20:47,359] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:20:47,359] [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
Bacillus yapensis	strain=XXST-01	GCA_005280205.1	2492960	2492960	type	True	90.3801	1241	1565	95	below_threshold
Bacillus yapensis	strain=XXST-01	GCA_003966255.1	2492960	2492960	type	True	90.3672	1242	1565	95	below_threshold
Robertmurraya massiliosenegalensis	strain=JC6	GCA_000311725.1	1287657	1287657	type	True	79.6594	493	1565	95	below_threshold
Robertmurraya siralis	strain=171544	GCA_005502275.1	77777	77777	type	True	78.9102	413	1565	95	below_threshold
Cytobacillus horneckiae	strain=1P01SC	GCA_002835735.1	549687	549687	type	True	78.7793	162	1565	95	below_threshold
Peribacillus acanthi	strain=L28	GCA_003073175.1	2171554	2171554	type	True	78.186	97	1565	95	below_threshold
Cytobacillus praedii	strain=FJAT-25547	GCA_001439605.1	1742358	1742358	type	True	77.4881	184	1565	95	below_threshold
Neobacillus jeddahensis	strain=JCE	GCA_000612625.1	1461580	1461580	type	True	77.4413	148	1565	95	below_threshold
Neobacillus mesonae	strain=FJAT-13985	GCA_001636315.1	1193713	1193713	type	True	77.3811	135	1565	95	below_threshold
Sutcliffiella halmapala	strain=DSM 8723	GCA_002019665.1	79882	79882	type	True	77.2663	102	1565	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	77.2207	130	1565	95	below_threshold
Bacillus gaemokensis	strain=KCTC 13318	GCA_001590835.1	574375	574375	type	True	77.1453	89	1565	95	below_threshold
Bacillus gaemokensis	strain=JCM 15801	GCA_000712615.1	574375	574375	type	True	77.038	89	1565	95	below_threshold
Niallia nealsonii	strain=FO-92	GCA_002835805.1	115979	115979	type	True	77.0299	132	1565	95	below_threshold
Peribacillus asahii	strain=MA001	GCA_003570725.1	228899	228899	suspected-type	True	76.9374	122	1565	95	below_threshold
Lederbergia wuyishanensis	strain=CGMCC 1.12709	GCA_022900255.1	1347903	1347903	type	True	76.4918	80	1565	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:47,363] [INFO] DFAST Taxonomy check result was written to GCF_005116465.1_ASM511646v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:47,364] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:47,364] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:47,364] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ce37dcb-d278-44e4-abb4-8cc272d29200/dqc_reference/checkm_data
[2024-01-24 14:20:47,365] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:47,519] [INFO] Task started: CheckM
[2024-01-24 14:20:47,519] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005116465.1_ASM511646v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005116465.1_ASM511646v1_genomic.fna/checkm_input GCF_005116465.1_ASM511646v1_genomic.fna/checkm_result
[2024-01-24 14:21:28,950] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:28,952] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:28,975] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:28,975] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:28,976] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005116465.1_ASM511646v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:28,976] [INFO] Task started: Blastn
[2024-01-24 14:21:28,976] [INFO] Running command: blastn -query GCF_005116465.1_ASM511646v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ce37dcb-d278-44e4-abb4-8cc272d29200/dqc_reference/reference_markers_gtdb.fasta -out GCF_005116465.1_ASM511646v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:30,466] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:30,471] [INFO] Selected 17 target genomes.
[2024-01-24 14:21:30,471] [INFO] Target genome list was writen to GCF_005116465.1_ASM511646v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:30,484] [INFO] Task started: fastANI
[2024-01-24 14:21:30,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg3648cb1b-4d15-4468-8e57-7089ab2b9cfe/GCF_005116465.1_ASM511646v1_genomic.fna.gz --refList GCF_005116465.1_ASM511646v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005116465.1_ASM511646v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:48,333] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:48,409] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:48,409] [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_005116465.1	s__Robertmurraya kyonggiensis	100.0	1565	1565	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005280205.1	s__Robertmurraya yapensis	90.3801	1241	1565	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000311725.1	s__Robertmurraya massiliosenegalensis	79.6488	494	1565	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	100.00	100.00	0.99	0.99	2	-
GCF_005502275.1	s__Robertmurraya siralis	78.9152	414	1565	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	99.13	99.00	0.93	0.92	3	-
GCF_014837155.1	s__Litchfieldia sp014837155	78.8104	153	1565	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Litchfieldia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009917645.1	s__Robertmurraya sp009917645	77.9158	207	1565	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001509555.1	s__Cytobacillus sp001509555	77.5768	169	1565	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613035.1	s__Cytobacillus sp018613035	77.4997	162	1565	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.97	99.97	0.97	0.97	2	-
GCF_001439605.1	s__Cytobacillus praedii	77.486	185	1565	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.20	99.20	0.93	0.93	2	-
GCF_900115925.1	s__CL95 sp900115925	77.4779	140	1565	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__CL95	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003182355.1	s__Cytobacillus oceanisediminis_A	77.4415	157	1565	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000612625.1	s__Neobacillus jeddahensis	77.4257	148	1565	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	-
GCA_011524525.1	s__Robertmurraya sp011524525	77.3482	147	1565	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000686805.1	s__Neobacillus sp000686805	77.2146	159	1565	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_002272245.1	s__Neobacillus sp002272245	77.1236	150	1565	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	97.06	97.06	0.86	0.86	2	-
GCF_902374955.1	s__Bacillus_AD massilioanorexius	76.9674	105	1565	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_AD	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007679095.1	s__DE0126 sp007679095	76.8024	83	1565	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__DE0126	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:48,411] [INFO] GTDB search result was written to GCF_005116465.1_ASM511646v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:48,411] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:48,416] [INFO] DFAST_QC result json was written to GCF_005116465.1_ASM511646v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:48,416] [INFO] DFAST_QC completed!
[2024-01-24 14:21:48,416] [INFO] Total running time: 0h1m33s