[2024-01-25 18:51:05,809] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:51:05,810] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:51:05,810] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c92b512-4353-4a69-bff3-3f63aa6e9b4f/dqc_reference
[2024-01-25 18:51:06,956] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:51:06,957] [INFO] Task started: Prodigal
[2024-01-25 18:51:06,957] [INFO] Running command: gunzip -c /var/lib/cwl/stgd9fdd266-e7a6-4b16-9859-03a31dc72dd1/GCF_013415115.1_ASM1341511v1_genomic.fna.gz | prodigal -d GCF_013415115.1_ASM1341511v1_genomic.fna/cds.fna -a GCF_013415115.1_ASM1341511v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:51:16,577] [INFO] Task succeeded: Prodigal
[2024-01-25 18:51:16,577] [INFO] Task started: HMMsearch
[2024-01-25 18:51:16,577] [INFO] Running command: hmmsearch --tblout GCF_013415115.1_ASM1341511v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c92b512-4353-4a69-bff3-3f63aa6e9b4f/dqc_reference/reference_markers.hmm GCF_013415115.1_ASM1341511v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:51:16,799] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:51:16,801] [INFO] Found 6/6 markers.
[2024-01-25 18:51:16,831] [INFO] Query marker FASTA was written to GCF_013415115.1_ASM1341511v1_genomic.fna/markers.fasta
[2024-01-25 18:51:16,831] [INFO] Task started: Blastn
[2024-01-25 18:51:16,832] [INFO] Running command: blastn -query GCF_013415115.1_ASM1341511v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c92b512-4353-4a69-bff3-3f63aa6e9b4f/dqc_reference/reference_markers.fasta -out GCF_013415115.1_ASM1341511v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:17,493] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:17,496] [INFO] Selected 14 target genomes.
[2024-01-25 18:51:17,497] [INFO] Target genome list was writen to GCF_013415115.1_ASM1341511v1_genomic.fna/target_genomes.txt
[2024-01-25 18:51:17,507] [INFO] Task started: fastANI
[2024-01-25 18:51:17,507] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9fdd266-e7a6-4b16-9859-03a31dc72dd1/GCF_013415115.1_ASM1341511v1_genomic.fna.gz --refList GCF_013415115.1_ASM1341511v1_genomic.fna/target_genomes.txt --output GCF_013415115.1_ASM1341511v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:51:28,294] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:28,295] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c92b512-4353-4a69-bff3-3f63aa6e9b4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:51:28,295] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c92b512-4353-4a69-bff3-3f63aa6e9b4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:51:28,304] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:51:28,304] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:51:28,304] [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
Halomonas zhaodongensis	strain=NEAU-ST10-25	GCA_013415115.1	1176240	1176240	type	True	100.0	1228	1229	95	conclusive
Halomonas humidisoli	strain=WN018	GCA_002286955.1	2032624	2032624	type	True	85.2735	924	1229	95	below_threshold
Halomonas alkaliphila	strain=DSM 16354	GCA_016107625.1	272774	272774	type	True	85.1492	911	1229	95	below_threshold
Halomonas venusta	strain=DSM 4743	GCA_016107635.1	44935	44935	type	True	84.1564	866	1229	95	below_threshold
Halomonas hydrothermalis	strain=Slthf2	GCA_011399095.1	115561	115561	type	True	84.0744	833	1229	95	below_threshold
Halomonas venusta	strain=NBRC 102221	GCA_007989605.1	44935	44935	type	True	84.0405	856	1229	95	below_threshold
Halomonas andesensis	strain=DSM 19434	GCA_003989795.1	447567	447567	type	True	83.1908	797	1229	95	below_threshold
Halomonas lutescens	strain=CGMCC 1.15122	GCA_014640815.1	1602943	1602943	type	True	80.3332	609	1229	95	below_threshold
Halomonas meridiana	strain=NBRC 15608	GCA_006540125.1	29570	29570	type	True	80.084	526	1229	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019504685.1	2852117	2852117	type	True	78.9169	396	1229	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019722725.1	2852117	2852117	type	True	78.8629	404	1229	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	77.7097	133	1229	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	77.6529	129	1229	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	77.2445	152	1229	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:51:28,306] [INFO] DFAST Taxonomy check result was written to GCF_013415115.1_ASM1341511v1_genomic.fna/tc_result.tsv
[2024-01-25 18:51:28,307] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:51:28,307] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:51:28,307] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c92b512-4353-4a69-bff3-3f63aa6e9b4f/dqc_reference/checkm_data
[2024-01-25 18:51:28,308] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:51:28,347] [INFO] Task started: CheckM
[2024-01-25 18:51:28,348] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013415115.1_ASM1341511v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013415115.1_ASM1341511v1_genomic.fna/checkm_input GCF_013415115.1_ASM1341511v1_genomic.fna/checkm_result
[2024-01-25 18:51:59,982] [INFO] Task succeeded: CheckM
[2024-01-25 18:51:59,983] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:51:59,998] [INFO] ===== Completeness check finished =====
[2024-01-25 18:51:59,998] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:51:59,998] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013415115.1_ASM1341511v1_genomic.fna/markers.fasta)
[2024-01-25 18:51:59,999] [INFO] Task started: Blastn
[2024-01-25 18:51:59,999] [INFO] Running command: blastn -query GCF_013415115.1_ASM1341511v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c92b512-4353-4a69-bff3-3f63aa6e9b4f/dqc_reference/reference_markers_gtdb.fasta -out GCF_013415115.1_ASM1341511v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:52:01,096] [INFO] Task succeeded: Blastn
[2024-01-25 18:52:01,099] [INFO] Selected 11 target genomes.
[2024-01-25 18:52:01,099] [INFO] Target genome list was writen to GCF_013415115.1_ASM1341511v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:52:01,123] [INFO] Task started: fastANI
[2024-01-25 18:52:01,123] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9fdd266-e7a6-4b16-9859-03a31dc72dd1/GCF_013415115.1_ASM1341511v1_genomic.fna.gz --refList GCF_013415115.1_ASM1341511v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013415115.1_ASM1341511v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:52:11,195] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:11,203] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:52:11,203] [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_013415115.1	s__Halomonas zhaodongensis	100.0	1228	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.15	99.15	0.93	0.93	2	conclusive
GCA_007116835.1	s__Halomonas sp007116835	87.4046	470	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.44	98.44	0.71	0.71	2	-
GCF_000219565.1	s__Halomonas sp000219565	86.7097	989	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002082565.1	s__Halomonas sp002082565	85.1551	933	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016107625.1	s__Halomonas alkaliphila	85.1492	911	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	96.32	95.46	0.84	0.80	12	-
GCF_000712975.1	s__Halomonas alkaliantarctica_A	84.2653	829	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007989605.1	s__Halomonas venusta	84.0292	857	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.80	96.64	0.92	0.83	8	-
GCF_003989795.1	s__Halomonas andesensis	83.1908	797	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003031405.1	s__Halomonas sp003031405	80.8607	715	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014640815.1	s__Halomonas lutescens	80.3462	607	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002366715.1	s__Halomonas sp002366715	79.0917	423	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:52:11,205] [INFO] GTDB search result was written to GCF_013415115.1_ASM1341511v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:52:11,205] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:52:11,208] [INFO] DFAST_QC result json was written to GCF_013415115.1_ASM1341511v1_genomic.fna/dqc_result.json
[2024-01-25 18:52:11,208] [INFO] DFAST_QC completed!
[2024-01-25 18:52:11,209] [INFO] Total running time: 0h1m5s