[2023-06-17 11:48:58,639] [INFO] DFAST_QC pipeline started.
[2023-06-17 11:48:58,644] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 11:48:58,645] [INFO] DQC Reference Directory: /var/lib/cwl/stgc376f0f4-d7a8-4542-9a57-12b946aa94d4/dqc_reference
[2023-06-17 11:49:00,942] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 11:49:00,943] [INFO] Task started: Prodigal
[2023-06-17 11:49:00,943] [INFO] Running command: gunzip -c /var/lib/cwl/stg64a48616-bcee-4592-973a-fbe8b266ba97/GCA_013393545.1_ASM1339354v1_genomic.fna.gz | prodigal -d GCA_013393545.1_ASM1339354v1_genomic.fna/cds.fna -a GCA_013393545.1_ASM1339354v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 11:49:13,293] [INFO] Task succeeded: Prodigal
[2023-06-17 11:49:13,293] [INFO] Task started: HMMsearch
[2023-06-17 11:49:13,293] [INFO] Running command: hmmsearch --tblout GCA_013393545.1_ASM1339354v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc376f0f4-d7a8-4542-9a57-12b946aa94d4/dqc_reference/reference_markers.hmm GCA_013393545.1_ASM1339354v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 11:49:13,617] [INFO] Task succeeded: HMMsearch
[2023-06-17 11:49:13,618] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg64a48616-bcee-4592-973a-fbe8b266ba97/GCA_013393545.1_ASM1339354v1_genomic.fna.gz]
[2023-06-17 11:49:13,669] [INFO] Query marker FASTA was written to GCA_013393545.1_ASM1339354v1_genomic.fna/markers.fasta
[2023-06-17 11:49:13,670] [INFO] Task started: Blastn
[2023-06-17 11:49:13,670] [INFO] Running command: blastn -query GCA_013393545.1_ASM1339354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc376f0f4-d7a8-4542-9a57-12b946aa94d4/dqc_reference/reference_markers.fasta -out GCA_013393545.1_ASM1339354v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:49:14,371] [INFO] Task succeeded: Blastn
[2023-06-17 11:49:14,376] [INFO] Selected 16 target genomes.
[2023-06-17 11:49:14,377] [INFO] Target genome list was writen to GCA_013393545.1_ASM1339354v1_genomic.fna/target_genomes.txt
[2023-06-17 11:49:14,383] [INFO] Task started: fastANI
[2023-06-17 11:49:14,383] [INFO] Running command: fastANI --query /var/lib/cwl/stg64a48616-bcee-4592-973a-fbe8b266ba97/GCA_013393545.1_ASM1339354v1_genomic.fna.gz --refList GCA_013393545.1_ASM1339354v1_genomic.fna/target_genomes.txt --output GCA_013393545.1_ASM1339354v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 11:49:25,937] [INFO] Task succeeded: fastANI
[2023-06-17 11:49:25,937] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc376f0f4-d7a8-4542-9a57-12b946aa94d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 11:49:25,938] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc376f0f4-d7a8-4542-9a57-12b946aa94d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 11:49:25,956] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 11:49:25,956] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 11:49:25,956] [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 persicus	strain=KCTC 23561	GCA_014652295.1	930118	930118	type	True	87.7087	681	1216	95	below_threshold
Marinobacter persicus	strain=IBRC-M 10445	GCA_900114155.1	930118	930118	type	True	87.6418	688	1216	95	below_threshold
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	80.1846	486	1216	95	below_threshold
Marinobacter oulmenensis	strain=DSM 22359	GCA_014201735.1	643747	643747	type	True	79.8435	448	1216	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	79.4279	408	1216	95	below_threshold
Marinobacter nauticus	strain=DSM 50418	GCA_003634635.1	2743	2743	type	True	79.0018	425	1216	95	below_threshold
Marinobacter fuscus	strain=NH169-3	GCA_003007675.1	2109942	2109942	type	True	78.9823	402	1216	95	below_threshold
Marinobacter halophilus	strain=JCM 30472	GCA_003007685.1	1323740	1323740	type	True	78.8046	395	1216	95	below_threshold
Marinobacter halophilus	strain=CGMCC 1.12481	GCA_014637865.1	1323740	1323740	type	True	78.8032	396	1216	95	below_threshold
Marinobacter gudaonensis	strain=CGMCC 1.6294	GCA_900115175.1	375760	375760	type	True	78.6067	384	1216	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	78.225	334	1216	95	below_threshold
Marinobacter bryozoorum	strain=DSM 15401	GCA_023156245.1	256324	256324	type	True	78.2097	294	1216	95	below_threshold
Marinobacter koreensis	strain=DSM 17924	GCA_023156285.1	335974	335974	type	True	78.155	300	1216	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	77.7943	309	1216	95	below_threshold
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	77.7612	311	1216	95	below_threshold
Marinobacter confluentis	strain=KCTC 42705	GCA_008795935.1	1697557	1697557	type	True	77.6103	288	1216	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 11:49:25,958] [INFO] DFAST Taxonomy check result was written to GCA_013393545.1_ASM1339354v1_genomic.fna/tc_result.tsv
[2023-06-17 11:49:25,959] [INFO] ===== Taxonomy check completed =====
[2023-06-17 11:49:25,959] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 11:49:25,959] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc376f0f4-d7a8-4542-9a57-12b946aa94d4/dqc_reference/checkm_data
[2023-06-17 11:49:25,960] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 11:49:26,006] [INFO] Task started: CheckM
[2023-06-17 11:49:26,006] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013393545.1_ASM1339354v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013393545.1_ASM1339354v1_genomic.fna/checkm_input GCA_013393545.1_ASM1339354v1_genomic.fna/checkm_result
[2023-06-17 11:50:06,953] [INFO] Task succeeded: CheckM
[2023-06-17 11:50:06,954] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.24%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 11:50:06,981] [INFO] ===== Completeness check finished =====
[2023-06-17 11:50:06,981] [INFO] ===== Start GTDB Search =====
[2023-06-17 11:50:06,982] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013393545.1_ASM1339354v1_genomic.fna/markers.fasta)
[2023-06-17 11:50:06,982] [INFO] Task started: Blastn
[2023-06-17 11:50:06,982] [INFO] Running command: blastn -query GCA_013393545.1_ASM1339354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc376f0f4-d7a8-4542-9a57-12b946aa94d4/dqc_reference/reference_markers_gtdb.fasta -out GCA_013393545.1_ASM1339354v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:50:08,090] [INFO] Task succeeded: Blastn
[2023-06-17 11:50:08,094] [INFO] Selected 11 target genomes.
[2023-06-17 11:50:08,095] [INFO] Target genome list was writen to GCA_013393545.1_ASM1339354v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 11:50:08,100] [INFO] Task started: fastANI
[2023-06-17 11:50:08,101] [INFO] Running command: fastANI --query /var/lib/cwl/stg64a48616-bcee-4592-973a-fbe8b266ba97/GCA_013393545.1_ASM1339354v1_genomic.fna.gz --refList GCA_013393545.1_ASM1339354v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013393545.1_ASM1339354v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 11:50:16,784] [INFO] Task succeeded: fastANI
[2023-06-17 11:50:16,794] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 11:50:16,795] [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
GCA_013393545.1	s__Marinobacter sp013393545	100.0	1202	1216	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900114155.1	s__Marinobacter persicus	87.6552	687	1216	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002934325.1	s__Marinobacter persicus_A	82.4081	596	1216	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.99	99.99	0.99	0.99	3	-
GCF_002258215.1	s__Marinobacter vinifirmus	80.1916	485	1216	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	96.96	96.78	0.87	0.84	7	-
GCF_900114925.1	s__Marinobacter pelagius	79.4279	408	1216	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315345.1	s__Marinobacter pelagius_A	79.4091	402	1216	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623515.1	s__Marinobacter sp018623515	79.3548	350	1216	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762755.1	s__Marinobacter sp014762755	79.0102	295	1216	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284615.1	s__Marinobacter hydrocarbonoclasticus	78.8841	430	1216	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.10	96.48	0.88	0.81	26	-
GCF_003007685.1	s__Marinobacter halophilus	78.8152	394	1216	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	78.2518	309	1216	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 11:50:16,797] [INFO] GTDB search result was written to GCA_013393545.1_ASM1339354v1_genomic.fna/result_gtdb.tsv
[2023-06-17 11:50:16,797] [INFO] ===== GTDB Search completed =====
[2023-06-17 11:50:16,811] [INFO] DFAST_QC result json was written to GCA_013393545.1_ASM1339354v1_genomic.fna/dqc_result.json
[2023-06-17 11:50:16,812] [INFO] DFAST_QC completed!
[2023-06-17 11:50:16,812] [INFO] Total running time: 0h1m18s