[2024-01-24 13:50:10,501] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:50:10,503] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:50:10,503] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb82b218-f4d1-4611-b1e3-dcf4e6a2db7c/dqc_reference
[2024-01-24 13:50:11,789] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:50:11,790] [INFO] Task started: Prodigal
[2024-01-24 13:50:11,790] [INFO] Running command: gunzip -c /var/lib/cwl/stg91ee77cc-692b-4059-8a96-c2d83ae4c518/GCF_004342245.1_ASM434224v1_genomic.fna.gz | prodigal -d GCF_004342245.1_ASM434224v1_genomic.fna/cds.fna -a GCF_004342245.1_ASM434224v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:29,202] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:29,202] [INFO] Task started: HMMsearch
[2024-01-24 13:50:29,203] [INFO] Running command: hmmsearch --tblout GCF_004342245.1_ASM434224v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb82b218-f4d1-4611-b1e3-dcf4e6a2db7c/dqc_reference/reference_markers.hmm GCF_004342245.1_ASM434224v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:29,491] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:29,492] [INFO] Found 6/6 markers.
[2024-01-24 13:50:29,547] [INFO] Query marker FASTA was written to GCF_004342245.1_ASM434224v1_genomic.fna/markers.fasta
[2024-01-24 13:50:29,548] [INFO] Task started: Blastn
[2024-01-24 13:50:29,548] [INFO] Running command: blastn -query GCF_004342245.1_ASM434224v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb82b218-f4d1-4611-b1e3-dcf4e6a2db7c/dqc_reference/reference_markers.fasta -out GCF_004342245.1_ASM434224v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:30,481] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:30,484] [INFO] Selected 16 target genomes.
[2024-01-24 13:50:30,484] [INFO] Target genome list was writen to GCF_004342245.1_ASM434224v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:30,489] [INFO] Task started: fastANI
[2024-01-24 13:50:30,489] [INFO] Running command: fastANI --query /var/lib/cwl/stg91ee77cc-692b-4059-8a96-c2d83ae4c518/GCF_004342245.1_ASM434224v1_genomic.fna.gz --refList GCF_004342245.1_ASM434224v1_genomic.fna/target_genomes.txt --output GCF_004342245.1_ASM434224v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:47,677] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:47,678] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb82b218-f4d1-4611-b1e3-dcf4e6a2db7c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:47,678] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb82b218-f4d1-4611-b1e3-dcf4e6a2db7c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:47,690] [INFO] Found 16 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:50:47,690] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:47,691] [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
Gibbsiella quercinecans	strain=DSM 25889	GCA_004342245.1	929813	929813	type	True	100.0	1805	1807	95	conclusive
Gibbsiella quercinecans	strain=FRB97	GCA_002291425.1	929813	929813	type	True	99.9999	1807	1807	95	conclusive
Gibbsiella quercinecans	strain=FRB97	GCA_003666185.1	929813	929813	type	True	99.9896	1779	1807	95	conclusive
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	82.5551	931	1807	95	below_threshold
Serratia surfactantfaciens	strain=YD25	GCA_001642805.2	2741499	2741499	type	True	82.4824	886	1807	95	below_threshold
Serratia marcescens	strain=ATCC 13880	GCA_017654245.1	615	615	suspected-type	True	82.4642	916	1807	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	82.4566	924	1807	95	below_threshold
Serratia marcescens	strain=ATCC 13880 substr. Sm_S65_jyu2015	GCA_017298975.1	615	615	suspected-type	True	82.3985	928	1807	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	82.354	884	1807	95	below_threshold
Serratia rubidaea	strain=FDAARGOS_926	GCA_016026735.1	61652	61652	type	True	82.2447	859	1807	95	below_threshold
Serratia rubidaea	strain=CIP 103234	GCA_001304675.1	61652	61652	type	True	82.1207	812	1807	95	below_threshold
Serratia rhizosphaerae	strain=KUDC3025	GCA_009817885.1	2597702	2597702	type	True	81.9492	858	1807	95	below_threshold
Serratia odorifera	strain=DSM 4582	GCA_000163595.1	618	618	type	True	81.7821	837	1807	95	below_threshold
Serratia odorifera	strain=NCTC11214	GCA_900635445.1	618	618	type	True	81.6612	859	1807	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	78.508	518	1807	95	below_threshold
Rahnella perminowiae	strain=SL6	GCA_019049755.1	2816244	2816244	type	True	78.4349	455	1807	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:47,692] [INFO] DFAST Taxonomy check result was written to GCF_004342245.1_ASM434224v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:47,693] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:47,693] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:47,693] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb82b218-f4d1-4611-b1e3-dcf4e6a2db7c/dqc_reference/checkm_data
[2024-01-24 13:50:47,694] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:47,743] [INFO] Task started: CheckM
[2024-01-24 13:50:47,743] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004342245.1_ASM434224v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004342245.1_ASM434224v1_genomic.fna/checkm_input GCF_004342245.1_ASM434224v1_genomic.fna/checkm_result
[2024-01-24 13:51:34,303] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:34,304] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:34,324] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:34,324] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:34,324] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004342245.1_ASM434224v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:34,325] [INFO] Task started: Blastn
[2024-01-24 13:51:34,325] [INFO] Running command: blastn -query GCF_004342245.1_ASM434224v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb82b218-f4d1-4611-b1e3-dcf4e6a2db7c/dqc_reference/reference_markers_gtdb.fasta -out GCF_004342245.1_ASM434224v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:35,717] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:35,722] [INFO] Selected 18 target genomes.
[2024-01-24 13:51:35,722] [INFO] Target genome list was writen to GCF_004342245.1_ASM434224v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:35,784] [INFO] Task started: fastANI
[2024-01-24 13:51:35,784] [INFO] Running command: fastANI --query /var/lib/cwl/stg91ee77cc-692b-4059-8a96-c2d83ae4c518/GCF_004342245.1_ASM434224v1_genomic.fna.gz --refList GCF_004342245.1_ASM434224v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004342245.1_ASM434224v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:54,635] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:54,649] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:54,650] [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_002291425.1	s__Gibbsiella quercinecans	99.9999	1807	1807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gibbsiella	95.0	99.45	98.17	0.96	0.87	5	conclusive
GCF_900187015.1	s__Serratia ficaria	82.7396	970	1807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	99.70	99.56	0.95	0.92	5	-
GCF_013375155.1	s__Serratia ureilytica	82.5779	904	1807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.3985	98.73	97.62	0.94	0.88	142	-
GCF_016742975.1	s__Serratia nevei	82.519	812	1807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.1913	97.82	96.26	0.83	0.75	139	-
GCF_006715005.1	s__Serratia marcescens_J	82.5026	896	1807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.1913	98.92	98.92	0.95	0.95	2	-
GCF_001642805.2	s__Serratia surfactantfaciens	82.4769	886	1807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	98.81	97.95	0.93	0.91	10	-
GCF_002220655.1	s__Serratia marcescens_K	82.4756	917	1807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.0833	98.79	98.10	0.94	0.88	411	-
GCF_000738675.1	s__Serratia nematodiphila	82.4408	916	1807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.8494	98.32	97.66	0.93	0.88	85	-
GCF_017299535.1	s__Serratia marcescens	82.4089	927	1807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.8494	99.42	98.47	0.97	0.85	72	-
GCF_001902635.1	s__Serratia marcescens_F	82.398	867	1807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003812745.1	s__Serratia sp003812745	82.3797	901	1807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.8367	N/A	N/A	N/A	N/A	1	-
GCF_000513215.1	s__Serratia bockelmannii	82.3719	911	1807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.0065	98.98	98.60	0.94	0.92	42	-
GCA_901472405.1	s__Serratia_B rubidaea	82.1282	861	1807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_B	95.0	98.79	97.55	0.96	0.91	11	-
GCF_009817885.1	s__Serratia_B rhizosphaerae	81.9619	857	1807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_B	95.0	97.16	97.09	0.90	0.89	7	-
GCF_900635445.1	s__Serratia_F odorifera	81.6675	859	1807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_F	95.0	99.83	99.53	0.98	0.94	5	-
GCF_001006005.1	s__Serratia_A fonticola	81.0816	798	1807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_A	95.0	96.10	95.03	0.87	0.81	45	-
GCF_006715025.1	s__Serratia_A fonticola_A	80.9269	731	1807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_A	95.0	100.00	100.00	1.00	1.00	4	-
GCF_000633355.1	s__Serratia_A sp000633355	80.8021	788	1807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_A	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:54,651] [INFO] GTDB search result was written to GCF_004342245.1_ASM434224v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:54,652] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:54,656] [INFO] DFAST_QC result json was written to GCF_004342245.1_ASM434224v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:54,656] [INFO] DFAST_QC completed!
[2024-01-24 13:51:54,656] [INFO] Total running time: 0h1m44s