[2024-01-24 12:53:36,051] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:36,053] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:36,054] [INFO] DQC Reference Directory: /var/lib/cwl/stgeb0513c5-61d0-454c-8be1-6b9c6b422345/dqc_reference
[2024-01-24 12:53:37,349] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:37,350] [INFO] Task started: Prodigal
[2024-01-24 12:53:37,351] [INFO] Running command: gunzip -c /var/lib/cwl/stgd2a62ce7-ebc4-4013-af01-90ab1984c5aa/GCF_003007685.1_ASM300768v1_genomic.fna.gz | prodigal -d GCF_003007685.1_ASM300768v1_genomic.fna/cds.fna -a GCF_003007685.1_ASM300768v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:49,069] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:49,070] [INFO] Task started: HMMsearch
[2024-01-24 12:53:49,070] [INFO] Running command: hmmsearch --tblout GCF_003007685.1_ASM300768v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeb0513c5-61d0-454c-8be1-6b9c6b422345/dqc_reference/reference_markers.hmm GCF_003007685.1_ASM300768v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:49,355] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:49,356] [INFO] Found 6/6 markers.
[2024-01-24 12:53:49,399] [INFO] Query marker FASTA was written to GCF_003007685.1_ASM300768v1_genomic.fna/markers.fasta
[2024-01-24 12:53:49,399] [INFO] Task started: Blastn
[2024-01-24 12:53:49,399] [INFO] Running command: blastn -query GCF_003007685.1_ASM300768v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb0513c5-61d0-454c-8be1-6b9c6b422345/dqc_reference/reference_markers.fasta -out GCF_003007685.1_ASM300768v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:50,256] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:50,259] [INFO] Selected 17 target genomes.
[2024-01-24 12:53:50,260] [INFO] Target genome list was writen to GCF_003007685.1_ASM300768v1_genomic.fna/target_genomes.txt
[2024-01-24 12:53:50,273] [INFO] Task started: fastANI
[2024-01-24 12:53:50,273] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2a62ce7-ebc4-4013-af01-90ab1984c5aa/GCF_003007685.1_ASM300768v1_genomic.fna.gz --refList GCF_003007685.1_ASM300768v1_genomic.fna/target_genomes.txt --output GCF_003007685.1_ASM300768v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:02,683] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:02,684] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeb0513c5-61d0-454c-8be1-6b9c6b422345/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:02,685] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeb0513c5-61d0-454c-8be1-6b9c6b422345/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:02,699] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:54:02,699] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:02,699] [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
Marinobacter halophilus	strain=JCM 30472	GCA_003007685.1	1323740	1323740	type	True	100.0	1294	1297	95	conclusive
Marinobacter halophilus	strain=CGMCC 1.12481	GCA_014637865.1	1323740	1323740	type	True	99.9958	1289	1297	95	conclusive
Marinobacter shengliensis	strain=SL013A34A2	GCA_003007715.1	1389223	1389223	type	True	81.7782	877	1297	95	below_threshold
Marinobacter shengliensis subsp. alexandrii	strain=LZ-6	GCA_005871095.1	2570350	1389223	type	True	81.6654	865	1297	95	below_threshold
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	81.4402	700	1297	95	below_threshold
Marinobacter nauticus	strain=DSM 50418	GCA_003634635.1	2743	2743	type	True	80.5929	671	1297	95	below_threshold
Marinobacter flavimaris	strain=LMG 23834	GCA_002933295.1	262076	262076	type	True	79.4438	541	1297	95	below_threshold
Marinobacter flavimaris	strain=KCTC 12185	GCA_003363485.1	262076	262076	type	True	79.3905	547	1297	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	79.1345	498	1297	95	below_threshold
Marinobacter bryozoorum	strain=DSM 15401	GCA_023156245.1	256324	256324	type	True	78.664	336	1297	95	below_threshold
Marinobacter caseinilyticus	strain=M3-13	GCA_011074955.1	2692195	2692195	type	True	78.2011	256	1297	95	below_threshold
Marinobacter changyiensis	strain=CLL7-20	GCA_009193265.1	2604091	2604091	type	True	78.1879	338	1297	95	below_threshold
Marinobacter gelidimuriae	strain=BF04_CF-4	GCA_000372805.1	2739064	2739064	type	True	78.1402	302	1297	95	below_threshold
Stutzerimonas chloritidismutans	strain=AW-1	GCA_000495915.1	203192	203192	type	True	76.2893	107	1297	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	76.0539	95	1297	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_900114065.1	1211807	1211807	type	True	75.9649	94	1297	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:02,702] [INFO] DFAST Taxonomy check result was written to GCF_003007685.1_ASM300768v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:02,702] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:02,702] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:02,702] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeb0513c5-61d0-454c-8be1-6b9c6b422345/dqc_reference/checkm_data
[2024-01-24 12:54:02,703] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:02,744] [INFO] Task started: CheckM
[2024-01-24 12:54:02,745] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003007685.1_ASM300768v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003007685.1_ASM300768v1_genomic.fna/checkm_input GCF_003007685.1_ASM300768v1_genomic.fna/checkm_result
[2024-01-24 12:54:40,511] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:40,512] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:40,536] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:40,536] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:40,537] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003007685.1_ASM300768v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:40,537] [INFO] Task started: Blastn
[2024-01-24 12:54:40,537] [INFO] Running command: blastn -query GCF_003007685.1_ASM300768v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb0513c5-61d0-454c-8be1-6b9c6b422345/dqc_reference/reference_markers_gtdb.fasta -out GCF_003007685.1_ASM300768v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:41,996] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:42,001] [INFO] Selected 11 target genomes.
[2024-01-24 12:54:42,001] [INFO] Target genome list was writen to GCF_003007685.1_ASM300768v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:42,013] [INFO] Task started: fastANI
[2024-01-24 12:54:42,014] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2a62ce7-ebc4-4013-af01-90ab1984c5aa/GCF_003007685.1_ASM300768v1_genomic.fna.gz --refList GCF_003007685.1_ASM300768v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003007685.1_ASM300768v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:51,297] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:51,313] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:51,313] [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_003007685.1	s__Marinobacter halophilus	100.0	1295	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_018402255.1	s__Marinobacter sp018402255	83.9725	891	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.33	99.33	0.88	0.88	2	-
GCF_000934705.1	s__Marinobacter excellens	83.8246	957	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_014859525.1	s__Marinobacter sp014859525	83.4412	797	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003007715.1	s__Marinobacter shengliensis	81.8102	876	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	95.96	95.10	0.86	0.82	7	-
GCF_002258215.1	s__Marinobacter vinifirmus	81.4734	700	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	96.96	96.78	0.87	0.84	7	-
GCF_000284615.1	s__Marinobacter hydrocarbonoclasticus	80.6812	674	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.10	96.48	0.88	0.81	26	-
GCF_002933295.1	s__Marinobacter flavimaris	79.4347	542	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.6719	97.80	96.90	0.89	0.83	14	-
GCF_009193265.1	s__Marinobacter changyiensis	78.1837	339	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000372805.1	s__Marinobacter gelidimuriae	78.1286	303	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011074955.1	s__Marinobacter caseinilyticus	78.11	257	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:54:51,315] [INFO] GTDB search result was written to GCF_003007685.1_ASM300768v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:51,315] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:51,319] [INFO] DFAST_QC result json was written to GCF_003007685.1_ASM300768v1_genomic.fna/dqc_result.json
[2024-01-24 12:54:51,319] [INFO] DFAST_QC completed!
[2024-01-24 12:54:51,319] [INFO] Total running time: 0h1m15s