[2024-01-24 12:14:07,152] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:07,154] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:07,155] [INFO] DQC Reference Directory: /var/lib/cwl/stg036753f3-442e-4a3f-9f70-6648b2305e7a/dqc_reference
[2024-01-24 12:14:08,388] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:08,389] [INFO] Task started: Prodigal
[2024-01-24 12:14:08,390] [INFO] Running command: gunzip -c /var/lib/cwl/stgdad178bf-0011-49d3-a9c0-54ed381b08cb/GCF_008364245.1_ASM836424v1_genomic.fna.gz | prodigal -d GCF_008364245.1_ASM836424v1_genomic.fna/cds.fna -a GCF_008364245.1_ASM836424v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:24,423] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:24,424] [INFO] Task started: HMMsearch
[2024-01-24 12:14:24,424] [INFO] Running command: hmmsearch --tblout GCF_008364245.1_ASM836424v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg036753f3-442e-4a3f-9f70-6648b2305e7a/dqc_reference/reference_markers.hmm GCF_008364245.1_ASM836424v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:24,833] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:24,835] [INFO] Found 6/6 markers.
[2024-01-24 12:14:24,893] [INFO] Query marker FASTA was written to GCF_008364245.1_ASM836424v1_genomic.fna/markers.fasta
[2024-01-24 12:14:24,893] [INFO] Task started: Blastn
[2024-01-24 12:14:24,893] [INFO] Running command: blastn -query GCF_008364245.1_ASM836424v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg036753f3-442e-4a3f-9f70-6648b2305e7a/dqc_reference/reference_markers.fasta -out GCF_008364245.1_ASM836424v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:25,836] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:25,839] [INFO] Selected 15 target genomes.
[2024-01-24 12:14:25,839] [INFO] Target genome list was writen to GCF_008364245.1_ASM836424v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:25,846] [INFO] Task started: fastANI
[2024-01-24 12:14:25,846] [INFO] Running command: fastANI --query /var/lib/cwl/stgdad178bf-0011-49d3-a9c0-54ed381b08cb/GCF_008364245.1_ASM836424v1_genomic.fna.gz --refList GCF_008364245.1_ASM836424v1_genomic.fna/target_genomes.txt --output GCF_008364245.1_ASM836424v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:42,894] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:42,895] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg036753f3-442e-4a3f-9f70-6648b2305e7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:42,895] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg036753f3-442e-4a3f-9f70-6648b2305e7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:42,912] [INFO] Found 14 fastANI hits (6 hits with ANI > threshold)
[2024-01-24 12:14:42,912] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:14:42,913] [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
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	100.0	1789	1789	95	inconclusive
Serratia marcescens	strain=ATCC 13880	GCA_017654245.1	615	615	suspected-type	True	95.1252	1496	1789	95	inconclusive
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	95.1187	1502	1789	95	inconclusive
Serratia marcescens	strain=ATCC 13880 substr. Sm_S65_jyu2015	GCA_017298975.1	615	615	suspected-type	True	95.0836	1496	1789	95	inconclusive
Serratia marcescens	strain=ATCC 13880 substr. Sm_S37_jyu2015	GCA_017301315.1	615	615	suspected-type	True	95.0836	1496	1789	95	inconclusive
Serratia marcescens	strain=ATCC 13880 substr. Sm_S81_jyu2015	GCA_017298875.1	615	615	suspected-type	True	95.0836	1496	1789	95	inconclusive
Serratia nematodiphila	strain=DSM 21420	GCA_000738675.1	458197	458197	suspected-type	True	94.9371	1505	1789	95	below_threshold
Serratia nematodiphila	strain=CGMCC 1.6853	GCA_900101535.1	458197	458197	suspected-type	True	94.9235	1491	1789	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	88.3186	1346	1789	95	below_threshold
Serratia quinivorans	strain=NCTC11544	GCA_900457075.1	137545	137545	suspected-type	True	84.5156	1257	1789	95	below_threshold
Rahnella bonaserana	strain=H11b	GCA_019049675.1	2816248	2816248	type	True	79.1217	559	1789	95	below_threshold
Rahnella perminowiae	strain=SL6	GCA_019049755.1	2816244	2816244	type	True	78.799	491	1789	95	below_threshold
Salinivibrio sharmensis	strain=DSM 18182	GCA_001995985.1	390883	390883	type	True	76.6118	52	1789	95	below_threshold
Alcanivorax profundi	strain=MTEO17	GCA_003597125.1	2338368	2338368	type	True	75.9111	57	1789	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:42,921] [INFO] DFAST Taxonomy check result was written to GCF_008364245.1_ASM836424v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:42,922] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:42,922] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:42,922] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg036753f3-442e-4a3f-9f70-6648b2305e7a/dqc_reference/checkm_data
[2024-01-24 12:14:42,924] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:42,989] [INFO] Task started: CheckM
[2024-01-24 12:14:42,990] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008364245.1_ASM836424v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008364245.1_ASM836424v1_genomic.fna/checkm_input GCF_008364245.1_ASM836424v1_genomic.fna/checkm_result
[2024-01-24 12:15:29,477] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:29,478] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:29,500] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:29,501] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:29,501] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008364245.1_ASM836424v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:29,502] [INFO] Task started: Blastn
[2024-01-24 12:15:29,502] [INFO] Running command: blastn -query GCF_008364245.1_ASM836424v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg036753f3-442e-4a3f-9f70-6648b2305e7a/dqc_reference/reference_markers_gtdb.fasta -out GCF_008364245.1_ASM836424v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:30,856] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:30,867] [INFO] Selected 11 target genomes.
[2024-01-24 12:15:30,867] [INFO] Target genome list was writen to GCF_008364245.1_ASM836424v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:30,878] [INFO] Task started: fastANI
[2024-01-24 12:15:30,879] [INFO] Running command: fastANI --query /var/lib/cwl/stgdad178bf-0011-49d3-a9c0-54ed381b08cb/GCF_008364245.1_ASM836424v1_genomic.fna.gz --refList GCF_008364245.1_ASM836424v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008364245.1_ASM836424v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:44,881] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:44,896] [INFO] Found 11 fastANI hits (4 hits with ANI > circumscription radius)
[2024-01-24 12:15:44,896] [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_016742975.1	s__Serratia nevei	98.8254	1411	1789	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.1913	97.82	96.26	0.83	0.75	139	inconclusive
GCF_006715005.1	s__Serratia marcescens_J	96.2628	1599	1789	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.1913	98.92	98.92	0.95	0.95	2	inconclusive
GCF_002220655.1	s__Serratia marcescens_K	96.1775	1534	1789	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.0833	98.79	98.10	0.94	0.88	411	inconclusive
GCF_003812745.1	s__Serratia sp003812745	95.9038	1487	1789	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.8367	N/A	N/A	N/A	N/A	1	inconclusive
GCF_000513215.1	s__Serratia bockelmannii	95.1323	1497	1789	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.0065	98.98	98.60	0.94	0.92	42	-
GCF_017299535.1	s__Serratia marcescens	95.0856	1495	1789	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.8494	99.42	98.47	0.97	0.85	72	-
GCF_000738675.1	s__Serratia nematodiphila	94.9371	1505	1789	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.8494	98.32	97.66	0.93	0.88	85	-
GCF_013375155.1	s__Serratia ureilytica	94.5383	1543	1789	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.3985	98.73	97.62	0.94	0.88	142	-
GCF_001642805.2	s__Serratia surfactantfaciens	94.4379	1529	1789	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	98.81	97.95	0.93	0.91	10	-
GCF_001902635.1	s__Serratia marcescens_F	94.013	1411	1789	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012719855.1	s__Serratia liquefaciens_A	84.6553	1247	1789	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	97.92	97.90	0.90	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:44,900] [INFO] GTDB search result was written to GCF_008364245.1_ASM836424v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:44,900] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:44,904] [INFO] DFAST_QC result json was written to GCF_008364245.1_ASM836424v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:44,904] [INFO] DFAST_QC completed!
[2024-01-24 12:15:44,904] [INFO] Total running time: 0h1m38s