[2024-01-25 19:47:20,679] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:47:20,681] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:47:20,681] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf7a14e4-8c0e-4f8b-b3f2-e0299e86774e/dqc_reference
[2024-01-25 19:47:21,843] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:47:21,844] [INFO] Task started: Prodigal
[2024-01-25 19:47:21,844] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9427beb-f287-4e5f-9122-f4807d2f059a/GCF_031451645.1_ASM3145164v1_genomic.fna.gz | prodigal -d GCF_031451645.1_ASM3145164v1_genomic.fna/cds.fna -a GCF_031451645.1_ASM3145164v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:47:32,009] [INFO] Task succeeded: Prodigal
[2024-01-25 19:47:32,010] [INFO] Task started: HMMsearch
[2024-01-25 19:47:32,010] [INFO] Running command: hmmsearch --tblout GCF_031451645.1_ASM3145164v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf7a14e4-8c0e-4f8b-b3f2-e0299e86774e/dqc_reference/reference_markers.hmm GCF_031451645.1_ASM3145164v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:47:32,235] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:47:32,236] [INFO] Found 6/6 markers.
[2024-01-25 19:47:32,266] [INFO] Query marker FASTA was written to GCF_031451645.1_ASM3145164v1_genomic.fna/markers.fasta
[2024-01-25 19:47:32,266] [INFO] Task started: Blastn
[2024-01-25 19:47:32,266] [INFO] Running command: blastn -query GCF_031451645.1_ASM3145164v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf7a14e4-8c0e-4f8b-b3f2-e0299e86774e/dqc_reference/reference_markers.fasta -out GCF_031451645.1_ASM3145164v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:32,990] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:32,993] [INFO] Selected 28 target genomes.
[2024-01-25 19:47:32,994] [INFO] Target genome list was writen to GCF_031451645.1_ASM3145164v1_genomic.fna/target_genomes.txt
[2024-01-25 19:47:33,030] [INFO] Task started: fastANI
[2024-01-25 19:47:33,031] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9427beb-f287-4e5f-9122-f4807d2f059a/GCF_031451645.1_ASM3145164v1_genomic.fna.gz --refList GCF_031451645.1_ASM3145164v1_genomic.fna/target_genomes.txt --output GCF_031451645.1_ASM3145164v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:47:52,482] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:52,483] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf7a14e4-8c0e-4f8b-b3f2-e0299e86774e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:47:52,483] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf7a14e4-8c0e-4f8b-b3f2-e0299e86774e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:47:52,498] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:47:52,498] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:47:52,498] [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 arcis	strain=CGMCC 1.6494	GCA_900103865.1	416873	416873	type	True	82.9913	839	1228	95	below_threshold
Halomonas stevensii	strain=S18214	GCA_000275725.1	502821	502821	type	True	80.337	561	1228	95	below_threshold
Halomonas johnsoniae	strain=KCTC 22157	GCA_014651795.1	502832	502832	type	True	80.2671	561	1228	95	below_threshold
Halomonas hamiltonii	strain=KCTC 22154	GCA_014651775.1	502829	502829	type	True	80.189	606	1228	95	below_threshold
Halomonas songnenensis	strain=CGMCC 1.12152	GCA_003002925.1	1176243	1176243	type	True	79.9784	559	1228	95	below_threshold
Halomonas aquamarina	strain=558	GCA_900110265.1	77097	77097	type	True	79.7939	485	1228	95	below_threshold
Halomonas meridiana	strain=NBRC 15608	GCA_006540125.1	29570	29570	type	True	79.7668	473	1228	95	below_threshold
Halomonas meridiana	strain=ACAM 246	GCA_900129255.1	29570	29570	type	True	79.6615	492	1228	95	below_threshold
Halomonas lionensis	strain=RHS90	GCA_002087295.1	1144478	1144478	type	True	79.5065	462	1228	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	79.1764	449	1228	95	below_threshold
Halomonas zhanjiangensis	strain=DSM 21076	GCA_000377665.1	1121960	1121960	type	True	79.1648	441	1228	95	below_threshold
Halomonas subglaciescola	strain=ACAM 12	GCA_900142895.1	29571	29571	type	True	79.1305	417	1228	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	79.1103	469	1228	95	below_threshold
Halomonas populi	strain=MC	GCA_003989825.1	2498858	2498858	type	True	79.0799	459	1228	95	below_threshold
Halomonas massiliensis	strain=Marseille-P2426	GCA_900155385.1	1816686	1816686	type	True	79.0609	414	1228	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019504685.1	2852117	2852117	type	True	78.9335	397	1228	95	below_threshold
Halomonas halophila	strain=NBRC 102604	GCA_007989465.1	29573	29573	type	True	78.925	463	1228	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019722725.1	2852117	2852117	type	True	78.9136	407	1228	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	78.906	471	1228	95	below_threshold
Halomonas ventosae	strain=CECT 5797	GCA_004363555.1	229007	229007	type	True	78.8974	461	1228	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	78.8143	451	1228	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	78.7992	468	1228	95	below_threshold
Halomonas pantelleriensis	strain=AAP	GCA_900102875.1	48727	48727	type	True	78.7729	433	1228	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	78.6846	434	1228	95	below_threshold
Halomonas taeanensis	strain=BH539	GCA_900100755.1	284577	284577	type	True	78.5524	376	1228	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	78.4895	410	1228	95	below_threshold
Halomonas zincidurans	strain=B6	GCA_000731955.1	1178777	1178777	type	True	78.2974	326	1228	95	below_threshold
Halomonas muralis	strain=DSM 14789	GCA_900102945.1	119000	119000	type	True	77.8687	319	1228	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:47:52,500] [INFO] DFAST Taxonomy check result was written to GCF_031451645.1_ASM3145164v1_genomic.fna/tc_result.tsv
[2024-01-25 19:47:52,501] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:47:52,501] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:47:52,501] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf7a14e4-8c0e-4f8b-b3f2-e0299e86774e/dqc_reference/checkm_data
[2024-01-25 19:47:52,502] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:47:52,553] [INFO] Task started: CheckM
[2024-01-25 19:47:52,554] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031451645.1_ASM3145164v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031451645.1_ASM3145164v1_genomic.fna/checkm_input GCF_031451645.1_ASM3145164v1_genomic.fna/checkm_result
[2024-01-25 19:48:23,973] [INFO] Task succeeded: CheckM
[2024-01-25 19:48:23,974] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:48:23,991] [INFO] ===== Completeness check finished =====
[2024-01-25 19:48:23,991] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:48:23,992] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031451645.1_ASM3145164v1_genomic.fna/markers.fasta)
[2024-01-25 19:48:23,993] [INFO] Task started: Blastn
[2024-01-25 19:48:23,993] [INFO] Running command: blastn -query GCF_031451645.1_ASM3145164v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf7a14e4-8c0e-4f8b-b3f2-e0299e86774e/dqc_reference/reference_markers_gtdb.fasta -out GCF_031451645.1_ASM3145164v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:48:25,182] [INFO] Task succeeded: Blastn
[2024-01-25 19:48:25,185] [INFO] Selected 12 target genomes.
[2024-01-25 19:48:25,185] [INFO] Target genome list was writen to GCF_031451645.1_ASM3145164v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:48:25,195] [INFO] Task started: fastANI
[2024-01-25 19:48:25,195] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9427beb-f287-4e5f-9122-f4807d2f059a/GCF_031451645.1_ASM3145164v1_genomic.fna.gz --refList GCF_031451645.1_ASM3145164v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031451645.1_ASM3145164v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:48:35,897] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:35,906] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:48:35,906] [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_000686925.1	s__Halomonas sp000686925	89.4472	966	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_015767635.1	s__Halomonas sp002119345	85.0748	918	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.32	98.32	0.86	0.86	2	-
GCF_900111305.1	s__Halomonas subterranea	84.9222	895	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.10	95.10	0.84	0.84	2	-
GCF_900086985.1	s__Halomonas sp900086985	83.5232	864	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.32	98.66	0.96	0.94	3	-
GCF_014263395.1	s__Halomonas sp014263395	83.1695	875	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103865.1	s__Halomonas arcis	82.9911	839	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651775.1	s__Halomonas hamiltonii	80.1706	608	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.843	98.09	97.51	0.90	0.88	5	-
GCA_001507855.1	s__Halomonas sp001507855	79.4837	454	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	0.98	0.98	2	-
GCF_000377665.1	s__Halomonas zhanjiangensis	79.1592	441	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155385.1	s__Halomonas massiliensis	79.0609	414	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.38	98.38	0.88	0.88	2	-
GCF_014897985.1	s__Halomonas sp014897985	79.0031	429	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.34	98.34	0.90	0.90	2	-
GCF_000731955.1	s__Halomonas_C zincidurans	78.2854	327	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:48:35,908] [INFO] GTDB search result was written to GCF_031451645.1_ASM3145164v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:48:35,909] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:48:35,925] [INFO] DFAST_QC result json was written to GCF_031451645.1_ASM3145164v1_genomic.fna/dqc_result.json
[2024-01-25 19:48:35,925] [INFO] DFAST_QC completed!
[2024-01-25 19:48:35,925] [INFO] Total running time: 0h1m15s