[2024-01-24 13:37:05,198] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:05,201] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:05,201] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d5d5ee3-6439-4dee-b3da-afd44c1a3d49/dqc_reference
[2024-01-24 13:37:06,574] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:06,575] [INFO] Task started: Prodigal
[2024-01-24 13:37:06,575] [INFO] Running command: gunzip -c /var/lib/cwl/stg551aeb04-ce93-40a1-a580-27873c7ae44d/GCF_000177235.2_ASM17723v2_genomic.fna.gz | prodigal -d GCF_000177235.2_ASM17723v2_genomic.fna/cds.fna -a GCF_000177235.2_ASM17723v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:16,424] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:16,424] [INFO] Task started: HMMsearch
[2024-01-24 13:37:16,425] [INFO] Running command: hmmsearch --tblout GCF_000177235.2_ASM17723v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d5d5ee3-6439-4dee-b3da-afd44c1a3d49/dqc_reference/reference_markers.hmm GCF_000177235.2_ASM17723v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:16,881] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:16,883] [INFO] Found 6/6 markers.
[2024-01-24 13:37:16,921] [INFO] Query marker FASTA was written to GCF_000177235.2_ASM17723v2_genomic.fna/markers.fasta
[2024-01-24 13:37:16,922] [INFO] Task started: Blastn
[2024-01-24 13:37:16,922] [INFO] Running command: blastn -query GCF_000177235.2_ASM17723v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d5d5ee3-6439-4dee-b3da-afd44c1a3d49/dqc_reference/reference_markers.fasta -out GCF_000177235.2_ASM17723v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:17,613] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:17,616] [INFO] Selected 25 target genomes.
[2024-01-24 13:37:17,616] [INFO] Target genome list was writen to GCF_000177235.2_ASM17723v2_genomic.fna/target_genomes.txt
[2024-01-24 13:37:17,623] [INFO] Task started: fastANI
[2024-01-24 13:37:17,623] [INFO] Running command: fastANI --query /var/lib/cwl/stg551aeb04-ce93-40a1-a580-27873c7ae44d/GCF_000177235.2_ASM17723v2_genomic.fna.gz --refList GCF_000177235.2_ASM17723v2_genomic.fna/target_genomes.txt --output GCF_000177235.2_ASM17723v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:36,668] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:36,669] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d5d5ee3-6439-4dee-b3da-afd44c1a3d49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:36,669] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d5d5ee3-6439-4dee-b3da-afd44c1a3d49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:36,684] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:36,684] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:36,684] [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
Evansella cellulosilytica	strain=DSM 2522	GCA_000177235.2	1413	1413	type	True	100.0	1559	1560	95	conclusive
Evansella clarkii	strain=DSM 8720	GCA_002019695.1	79879	79879	type	True	79.686	134	1560	95	below_threshold
Bacillus alkalicellulosilyticus	strain=FJAT-44921	GCA_002019795.1	1912214	1912214	type	True	79.2051	85	1560	95	below_threshold
Bacillus shivajii	strain=JCM 32183	GCA_020519665.1	1983719	1983719	type	True	78.6645	170	1560	95	below_threshold
Alkalihalobacterium alkalinitrilicum	strain=DSM 22532	GCA_002019605.1	427920	427920	type	True	78.5887	103	1560	95	below_threshold
Bacillus toyonensis	strain=BCT-7112	GCA_000496285.1	155322	155322	type	True	78.4276	71	1560	95	below_threshold
Alteribacter aurantiacus	strain=DSM 18675	GCA_000429705.1	254410	254410	type	True	77.3743	70	1560	95	below_threshold
Bacillus yapensis	strain=XXST-01	GCA_003966255.1	2492960	2492960	type	True	77.307	54	1560	95	below_threshold
Bacillus yapensis	strain=XXST-01	GCA_005280205.1	2492960	2492960	type	True	77.2787	54	1560	95	below_threshold
Anaerobacillus alkalilacustris	strain=DSM 18345	GCA_001866005.1	393763	393763	type	True	77.1762	80	1560	95	below_threshold
Alkalihalobacillus bogoriensis	strain=ATCC BAA-922	GCA_000621445.1	246272	246272	type	True	77.0714	92	1560	95	below_threshold
Bacillus gaemokensis	strain=KCTC 13318	GCA_001590835.1	574375	574375	type	True	76.8216	57	1560	95	below_threshold
Bacillus suaedae	strain=YZJH907-2	GCA_017939705.1	2822140	2822140	type	True	76.8205	63	1560	95	below_threshold
Bacillus suaedaesalsae	strain=RD4P76	GCA_016890225.1	2810349	2810349	type	True	76.7365	53	1560	95	below_threshold
Bacillus gaemokensis	strain=JCM 15801	GCA_000712615.1	574375	574375	type	True	76.2821	53	1560	95	below_threshold
Bacillus tropicus	strain=N24	GCA_001884035.1	2026188	2026188	type	True	76.2691	57	1560	95	below_threshold
Gottfriedia endophyticus	strain=RG28	GCA_017814275.1	2820819	2820819	type	True	76.0543	50	1560	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:36,686] [INFO] DFAST Taxonomy check result was written to GCF_000177235.2_ASM17723v2_genomic.fna/tc_result.tsv
[2024-01-24 13:37:36,686] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:36,686] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:36,687] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d5d5ee3-6439-4dee-b3da-afd44c1a3d49/dqc_reference/checkm_data
[2024-01-24 13:37:36,688] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:36,735] [INFO] Task started: CheckM
[2024-01-24 13:37:36,735] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000177235.2_ASM17723v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000177235.2_ASM17723v2_genomic.fna/checkm_input GCF_000177235.2_ASM17723v2_genomic.fna/checkm_result
[2024-01-24 13:38:11,450] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:11,451] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:11,478] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:11,479] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:11,479] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000177235.2_ASM17723v2_genomic.fna/markers.fasta)
[2024-01-24 13:38:11,480] [INFO] Task started: Blastn
[2024-01-24 13:38:11,480] [INFO] Running command: blastn -query GCF_000177235.2_ASM17723v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d5d5ee3-6439-4dee-b3da-afd44c1a3d49/dqc_reference/reference_markers_gtdb.fasta -out GCF_000177235.2_ASM17723v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:12,276] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:12,279] [INFO] Selected 26 target genomes.
[2024-01-24 13:38:12,279] [INFO] Target genome list was writen to GCF_000177235.2_ASM17723v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:12,296] [INFO] Task started: fastANI
[2024-01-24 13:38:12,296] [INFO] Running command: fastANI --query /var/lib/cwl/stg551aeb04-ce93-40a1-a580-27873c7ae44d/GCF_000177235.2_ASM17723v2_genomic.fna.gz --refList GCF_000177235.2_ASM17723v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000177235.2_ASM17723v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:31,869] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:31,888] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:31,888] [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_000177235.2	s__Evansella cellulosilytica	100.0	1558	1560	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Evansella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002797325.1	s__Bacillus_S sp002797325	79.8649	71	1560	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_S	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002019695.1	s__Evansella clarkii	79.7523	134	1560	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Evansella	95.0	98.30	98.30	0.93	0.93	2	-
GCF_003586445.1	s__Robertmurraya sp003586445	79.3839	60	1560	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_002019795.1	s__Bacillus_AO alkalicellulosilyticus	79.1401	82	1560	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_AO	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002153425.1	s__Evansella alkalicola	78.7497	228	1560	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Evansella	95.0	99.98	99.98	0.99	0.99	2	-
GCF_002019605.1	s__Bacillus_BH alkalinitrilicus	78.3662	103	1560	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_BH	95.0	97.46	97.46	0.83	0.83	2	-
GCF_002335745.1	s__FJAT-44876 sp002335745	78.3469	175	1560	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__FJAT-44876	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000496285.1	s__Bacillus_A toyonensis	78.2459	69	1560	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.12	96.74	0.93	0.83	279	-
GCF_000429705.1	s__Alteribacter aurantiacus	77.3234	69	1560	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alteribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005280205.1	s__Robertmurraya yapensis	77.2805	53	1560	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_001866005.1	s__Anaerobacillus alkalilacustris	77.0794	78	1560	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_000621445.1	s__Bacillus_AO bogoriensis	77.0714	92	1560	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_AO	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001590835.1	s__Bacillus_A gaemokensis	76.9673	56	1560	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.98	99.98	1.00	1.00	2	-
GCF_017939705.1	s__Bacillus_L sp017939705	76.8205	63	1560	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830185.1	s__Bacillus_L nanhaiisediminis	76.6669	63	1560	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016890225.1	s__Bacillus_BS sp016890225	76.6659	51	1560	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__SA4;g__Bacillus_BS	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005116465.1	s__Robertmurraya kyonggiensis	76.1957	57	1560	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	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:31,890] [INFO] GTDB search result was written to GCF_000177235.2_ASM17723v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:31,891] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:31,895] [INFO] DFAST_QC result json was written to GCF_000177235.2_ASM17723v2_genomic.fna/dqc_result.json
[2024-01-24 13:38:31,895] [INFO] DFAST_QC completed!
[2024-01-24 13:38:31,895] [INFO] Total running time: 0h1m27s