[2024-01-24 13:52:12,450] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:52:12,452] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:52:12,452] [INFO] DQC Reference Directory: /var/lib/cwl/stga22cbcb2-05c3-4936-9905-8b908e69bb90/dqc_reference
[2024-01-24 13:52:13,662] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:52:13,663] [INFO] Task started: Prodigal
[2024-01-24 13:52:13,663] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d46b7df-888a-4ca7-9585-3ca90ecf1965/GCF_002335815.1_ASM233581v1_genomic.fna.gz | prodigal -d GCF_002335815.1_ASM233581v1_genomic.fna/cds.fna -a GCF_002335815.1_ASM233581v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:52:25,880] [INFO] Task succeeded: Prodigal
[2024-01-24 13:52:25,881] [INFO] Task started: HMMsearch
[2024-01-24 13:52:25,881] [INFO] Running command: hmmsearch --tblout GCF_002335815.1_ASM233581v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga22cbcb2-05c3-4936-9905-8b908e69bb90/dqc_reference/reference_markers.hmm GCF_002335815.1_ASM233581v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:52:26,196] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:52:26,197] [INFO] Found 6/6 markers.
[2024-01-24 13:52:26,248] [INFO] Query marker FASTA was written to GCF_002335815.1_ASM233581v1_genomic.fna/markers.fasta
[2024-01-24 13:52:26,249] [INFO] Task started: Blastn
[2024-01-24 13:52:26,249] [INFO] Running command: blastn -query GCF_002335815.1_ASM233581v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga22cbcb2-05c3-4936-9905-8b908e69bb90/dqc_reference/reference_markers.fasta -out GCF_002335815.1_ASM233581v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:52:26,834] [INFO] Task succeeded: Blastn
[2024-01-24 13:52:26,838] [INFO] Selected 15 target genomes.
[2024-01-24 13:52:26,838] [INFO] Target genome list was writen to GCF_002335815.1_ASM233581v1_genomic.fna/target_genomes.txt
[2024-01-24 13:52:26,860] [INFO] Task started: fastANI
[2024-01-24 13:52:26,861] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d46b7df-888a-4ca7-9585-3ca90ecf1965/GCF_002335815.1_ASM233581v1_genomic.fna.gz --refList GCF_002335815.1_ASM233581v1_genomic.fna/target_genomes.txt --output GCF_002335815.1_ASM233581v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:52:42,210] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:42,211] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga22cbcb2-05c3-4936-9905-8b908e69bb90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:52:42,212] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga22cbcb2-05c3-4936-9905-8b908e69bb90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:52:42,229] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:52:42,229] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:52:42,229] [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 soli	strain=DSM 15604	GCA_002335815.1	220688	220688	type	True	99.998	1853	1859	95	conclusive
Neobacillus soli	strain=NBRC 102451	GCA_001591665.1	220688	220688	type	True	99.9422	1749	1859	95	conclusive
Neobacillus novalis	strain=FJAT-14227	GCA_001636395.1	220687	220687	type	True	83.0969	993	1859	95	below_threshold
Neobacillus novalis	strain=NBRC 102450	GCA_001591805.1	220687	220687	type	True	82.8169	984	1859	95	below_threshold
Neobacillus vireti	strain=DSM 15602	GCA_001026695.1	220686	220686	type	True	81.7795	902	1859	95	below_threshold
Neobacillus vireti	strain=LMG 21834	GCA_000508325.2	220686	220686	type	True	81.73	859	1859	95	below_threshold
Neobacillus bataviensis	strain=LMG 21833	GCA_000307875.1	220685	220685	type	True	80.6873	877	1859	95	below_threshold
Neobacillus drentensis	strain=FJAT-10044	GCA_001636415.1	220684	220684	type	True	80.4502	833	1859	95	below_threshold
Neobacillus drentensis	strain=NBRC 102427	GCA_001591445.1	220684	220684	type	True	80.1153	786	1859	95	below_threshold
Neobacillus rhizophilus	strain=FJAT-49825	GCA_018343535.1	2833579	2833579	type	True	78.69	508	1859	95	below_threshold
Sutcliffiella halmapala	strain=DSM 8723	GCA_002019665.1	79882	79882	type	True	78.557	102	1859	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	78.4268	196	1859	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	78.3384	441	1859	95	below_threshold
Neobacillus fumarioli	strain=NBRC 102428	GCA_001591485.1	105229	105229	type	True	77.7172	264	1859	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:52:42,231] [INFO] DFAST Taxonomy check result was written to GCF_002335815.1_ASM233581v1_genomic.fna/tc_result.tsv
[2024-01-24 13:52:42,232] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:52:42,232] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:52:42,232] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga22cbcb2-05c3-4936-9905-8b908e69bb90/dqc_reference/checkm_data
[2024-01-24 13:52:42,233] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:52:42,305] [INFO] Task started: CheckM
[2024-01-24 13:52:42,306] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002335815.1_ASM233581v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002335815.1_ASM233581v1_genomic.fna/checkm_input GCF_002335815.1_ASM233581v1_genomic.fna/checkm_result
[2024-01-24 13:53:22,038] [INFO] Task succeeded: CheckM
[2024-01-24 13:53:22,039] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:53:22,063] [INFO] ===== Completeness check finished =====
[2024-01-24 13:53:22,064] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:53:22,064] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002335815.1_ASM233581v1_genomic.fna/markers.fasta)
[2024-01-24 13:53:22,065] [INFO] Task started: Blastn
[2024-01-24 13:53:22,065] [INFO] Running command: blastn -query GCF_002335815.1_ASM233581v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga22cbcb2-05c3-4936-9905-8b908e69bb90/dqc_reference/reference_markers_gtdb.fasta -out GCF_002335815.1_ASM233581v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:53:22,863] [INFO] Task succeeded: Blastn
[2024-01-24 13:53:22,868] [INFO] Selected 13 target genomes.
[2024-01-24 13:53:22,868] [INFO] Target genome list was writen to GCF_002335815.1_ASM233581v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:53:22,880] [INFO] Task started: fastANI
[2024-01-24 13:53:22,880] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d46b7df-888a-4ca7-9585-3ca90ecf1965/GCF_002335815.1_ASM233581v1_genomic.fna.gz --refList GCF_002335815.1_ASM233581v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002335815.1_ASM233581v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:53:38,710] [INFO] Task succeeded: fastANI
[2024-01-24 13:53:38,724] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:53:38,724] [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_001591665.1	s__Neobacillus soli	99.9422	1749	1859	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	conclusive
GCF_001591805.1	s__Neobacillus novalis	82.8104	987	1859	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_001026695.1	s__Neobacillus vireti	81.8007	900	1859	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_900177675.1	s__Neobacillus sp900177675	80.7347	882	1859	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	98.52	98.52	0.84	0.84	2	-
GCF_000307875.1	s__Neobacillus bataviensis	80.7	873	1859	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_018613065.1	s__Neobacillus sp018613065	80.5238	824	1859	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_005154805.1	s__Neobacillus sp005154805	80.3682	885	1859	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_001591445.1	s__Neobacillus drentensis	80.1113	787	1859	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_011250555.1	s__Neobacillus sp011250555	80.0007	712	1859	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	99.98	99.98	0.98	0.98	2	-
GCF_000686805.1	s__Neobacillus sp000686805	79.9238	762	1859	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_002559145.1	s__Neobacillus sp002559145	79.866	739	1859	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	95.43	95.43	0.81	0.81	2	-
GCA_019219025.1	s__Neobacillus sp019219025	79.8378	770	1859	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_007678255.1	s__Neobacillus sp007678255	79.5876	746	1859	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	-
--------------------------------------------------------------------------------
[2024-01-24 13:53:38,726] [INFO] GTDB search result was written to GCF_002335815.1_ASM233581v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:53:38,727] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:53:38,733] [INFO] DFAST_QC result json was written to GCF_002335815.1_ASM233581v1_genomic.fna/dqc_result.json
[2024-01-24 13:53:38,733] [INFO] DFAST_QC completed!
[2024-01-24 13:53:38,733] [INFO] Total running time: 0h1m26s