[2024-01-25 18:05:50,572] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:05:50,574] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:05:50,574] [INFO] DQC Reference Directory: /var/lib/cwl/stgda931494-e9cd-4c34-9034-3d50a403592a/dqc_reference
[2024-01-25 18:05:51,719] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:05:51,719] [INFO] Task started: Prodigal
[2024-01-25 18:05:51,720] [INFO] Running command: gunzip -c /var/lib/cwl/stg4d1fd282-20fb-4a57-96fd-d3170fa831ac/GCF_001866005.1_ASM186600v1_genomic.fna.gz | prodigal -d GCF_001866005.1_ASM186600v1_genomic.fna/cds.fna -a GCF_001866005.1_ASM186600v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:05:57,988] [INFO] Task succeeded: Prodigal
[2024-01-25 18:05:57,988] [INFO] Task started: HMMsearch
[2024-01-25 18:05:57,988] [INFO] Running command: hmmsearch --tblout GCF_001866005.1_ASM186600v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda931494-e9cd-4c34-9034-3d50a403592a/dqc_reference/reference_markers.hmm GCF_001866005.1_ASM186600v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:05:58,214] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:05:58,215] [INFO] Found 6/6 markers.
[2024-01-25 18:05:58,245] [INFO] Query marker FASTA was written to GCF_001866005.1_ASM186600v1_genomic.fna/markers.fasta
[2024-01-25 18:05:58,245] [INFO] Task started: Blastn
[2024-01-25 18:05:58,245] [INFO] Running command: blastn -query GCF_001866005.1_ASM186600v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda931494-e9cd-4c34-9034-3d50a403592a/dqc_reference/reference_markers.fasta -out GCF_001866005.1_ASM186600v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:05:58,788] [INFO] Task succeeded: Blastn
[2024-01-25 18:05:58,791] [INFO] Selected 18 target genomes.
[2024-01-25 18:05:58,791] [INFO] Target genome list was writen to GCF_001866005.1_ASM186600v1_genomic.fna/target_genomes.txt
[2024-01-25 18:05:58,804] [INFO] Task started: fastANI
[2024-01-25 18:05:58,804] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d1fd282-20fb-4a57-96fd-d3170fa831ac/GCF_001866005.1_ASM186600v1_genomic.fna.gz --refList GCF_001866005.1_ASM186600v1_genomic.fna/target_genomes.txt --output GCF_001866005.1_ASM186600v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:06:18,403] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:18,404] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda931494-e9cd-4c34-9034-3d50a403592a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:06:18,404] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda931494-e9cd-4c34-9034-3d50a403592a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:06:18,415] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:06:18,415] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:06:18,415] [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
Anaerobacillus alkalilacustris	strain=DSM 18345	GCA_001866005.1	393763	393763	type	True	100.0	1317	1322	95	conclusive
Anaerobacillus alkalidiazotrophicus	strain=DSM 22531	GCA_001866055.1	472963	472963	type	True	94.1866	947	1322	95	below_threshold
Anaerobacillus isosaccharinicus	strain=NB2006	GCA_001866075.3	1532552	1532552	type	True	79.1698	360	1322	95	below_threshold
Niallia alba	strain=UniB3	GCA_012933555.1	2729105	2729105	type	True	78.7079	88	1322	95	below_threshold
Anaerobacillus arseniciselenatis	strain=DSM 15340	GCA_001865995.1	85682	85682	type	True	78.6958	316	1322	95	below_threshold
Anaerobacillus alkaliphilus	strain=B16-10	GCA_004116265.1	1548597	1548597	type	True	78.4207	293	1322	95	below_threshold
Bacillus shivajii	strain=JCM 32183	GCA_020519665.1	1983719	1983719	type	True	78.202	85	1322	95	below_threshold
Sutcliffiella cohnii	strain=DSM 6307	GCA_002250055.1	33932	33932	type	True	78.0064	80	1322	95	below_threshold
Desertibacillus haloalkaliphilus	strain=KJ1-10-99	GCA_019039105.1	1328930	1328930	type	True	77.3599	94	1322	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_022221345.1	1392	1392	type	True	77.2018	69	1322	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	77.1378	77	1322	95	below_threshold
Bacillus sanguinis	strain=BML-BC004	GCA_018332475.1	2817476	2817476	type	True	76.8714	61	1322	95	below_threshold
Alkalihalobacterium elongatum	strain=MEB199	GCA_019024285.1	2675466	2675466	type	True	76.7293	112	1322	95	below_threshold
Alkalihalophilus marmarensis	strain=DSM 21297	GCA_000474275.2	521377	521377	type	True	76.6222	72	1322	95	below_threshold
Alkalihalobacillus akibai	strain=JCM 9157	GCA_001315085.1	1411	1411	type	True	76.5953	105	1322	95	below_threshold
Alkalihalobacillus akibai	strain=JCM 9157	GCA_000513135.1	1411	1411	type	True	76.5697	104	1322	95	below_threshold
Bacillus gaemokensis	strain=JCM 15801	GCA_000712615.1	574375	574375	type	True	76.0415	67	1322	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:06:18,417] [INFO] DFAST Taxonomy check result was written to GCF_001866005.1_ASM186600v1_genomic.fna/tc_result.tsv
[2024-01-25 18:06:18,419] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:06:18,419] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:06:18,419] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda931494-e9cd-4c34-9034-3d50a403592a/dqc_reference/checkm_data
[2024-01-25 18:06:18,422] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:06:18,463] [INFO] Task started: CheckM
[2024-01-25 18:06:18,463] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001866005.1_ASM186600v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001866005.1_ASM186600v1_genomic.fna/checkm_input GCF_001866005.1_ASM186600v1_genomic.fna/checkm_result
[2024-01-25 18:06:41,875] [INFO] Task succeeded: CheckM
[2024-01-25 18:06:41,876] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:06:41,898] [INFO] ===== Completeness check finished =====
[2024-01-25 18:06:41,899] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:06:41,899] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001866005.1_ASM186600v1_genomic.fna/markers.fasta)
[2024-01-25 18:06:41,899] [INFO] Task started: Blastn
[2024-01-25 18:06:41,899] [INFO] Running command: blastn -query GCF_001866005.1_ASM186600v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda931494-e9cd-4c34-9034-3d50a403592a/dqc_reference/reference_markers_gtdb.fasta -out GCF_001866005.1_ASM186600v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:42,680] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:42,683] [INFO] Selected 16 target genomes.
[2024-01-25 18:06:42,683] [INFO] Target genome list was writen to GCF_001866005.1_ASM186600v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:06:42,692] [INFO] Task started: fastANI
[2024-01-25 18:06:42,692] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d1fd282-20fb-4a57-96fd-d3170fa831ac/GCF_001866005.1_ASM186600v1_genomic.fna.gz --refList GCF_001866005.1_ASM186600v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001866005.1_ASM186600v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:07:01,605] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:01,614] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:07:01,615] [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_001866005.1	s__Anaerobacillus alkalilacustris	100.0	1318	1322	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Anaerobacillaceae;g__Anaerobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001866055.1	s__Anaerobacillus alkalidiazotrophicus	94.2577	943	1322	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Anaerobacillaceae;g__Anaerobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001866075.3	s__Anaerobacillus isosaccharinicus	79.1387	357	1322	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Anaerobacillaceae;g__Anaerobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001865995.1	s__Anaerobacillus arseniciselenatis	78.6958	316	1322	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Anaerobacillaceae;g__Anaerobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007120055.1	s__Anaerobacillus sp007120055	78.5066	248	1322	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Anaerobacillaceae;g__Anaerobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004116265.1	s__Anaerobacillus alkaliphilus	78.428	295	1322	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Anaerobacillaceae;g__Anaerobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007118195.1	s__Anaerobacillus sp007118195	77.9862	225	1322	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Anaerobacillaceae;g__Anaerobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002335805.1	s__FJAT-45350 sp002335805	77.7519	151	1322	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__FJAT-45350	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002560985.1	s__Bacillus_A sp002560985	76.9456	53	1322	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_003318295.1	s__Maribacillus taeanensis	76.8351	85	1322	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__UBA6769;g__Maribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019024285.1	s__Bacillus_BH sp019024285	76.7519	113	1322	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_BH	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000474275.2	s__Bacillus_S marmarensis	76.6222	72	1322	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_S	95.9507	N/A	N/A	N/A	N/A	1	-
GCF_000513135.1	s__Bacillus_L akibai	76.5546	106	1322	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011008565.1	s__Weizmannia ginsengihum	76.4856	54	1322	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Weizmannia	95.0	99.62	99.53	0.95	0.92	4	-
GCF_002272245.1	s__Neobacillus sp002272245	76.0662	60	1322	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	-
--------------------------------------------------------------------------------
[2024-01-25 18:07:01,616] [INFO] GTDB search result was written to GCF_001866005.1_ASM186600v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:07:01,616] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:07:01,620] [INFO] DFAST_QC result json was written to GCF_001866005.1_ASM186600v1_genomic.fna/dqc_result.json
[2024-01-25 18:07:01,620] [INFO] DFAST_QC completed!
[2024-01-25 18:07:01,620] [INFO] Total running time: 0h1m11s