[2024-01-25 18:39:50,771] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:39:50,772] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:39:50,772] [INFO] DQC Reference Directory: /var/lib/cwl/stgf687c662-bcf4-4cde-86c1-c6a179e21777/dqc_reference
[2024-01-25 18:39:51,908] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:39:51,909] [INFO] Task started: Prodigal
[2024-01-25 18:39:51,909] [INFO] Running command: gunzip -c /var/lib/cwl/stg351b9de2-b18b-4bbd-bf1e-03d5194382bd/GCF_000422085.1_ASM42208v1_genomic.fna.gz | prodigal -d GCF_000422085.1_ASM42208v1_genomic.fna/cds.fna -a GCF_000422085.1_ASM42208v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:40:05,910] [INFO] Task succeeded: Prodigal
[2024-01-25 18:40:05,910] [INFO] Task started: HMMsearch
[2024-01-25 18:40:05,910] [INFO] Running command: hmmsearch --tblout GCF_000422085.1_ASM42208v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf687c662-bcf4-4cde-86c1-c6a179e21777/dqc_reference/reference_markers.hmm GCF_000422085.1_ASM42208v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:40:06,230] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:40:06,231] [INFO] Found 6/6 markers.
[2024-01-25 18:40:06,272] [INFO] Query marker FASTA was written to GCF_000422085.1_ASM42208v1_genomic.fna/markers.fasta
[2024-01-25 18:40:06,272] [INFO] Task started: Blastn
[2024-01-25 18:40:06,273] [INFO] Running command: blastn -query GCF_000422085.1_ASM42208v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf687c662-bcf4-4cde-86c1-c6a179e21777/dqc_reference/reference_markers.fasta -out GCF_000422085.1_ASM42208v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:07,074] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:07,077] [INFO] Selected 14 target genomes.
[2024-01-25 18:40:07,078] [INFO] Target genome list was writen to GCF_000422085.1_ASM42208v1_genomic.fna/target_genomes.txt
[2024-01-25 18:40:07,083] [INFO] Task started: fastANI
[2024-01-25 18:40:07,083] [INFO] Running command: fastANI --query /var/lib/cwl/stg351b9de2-b18b-4bbd-bf1e-03d5194382bd/GCF_000422085.1_ASM42208v1_genomic.fna.gz --refList GCF_000422085.1_ASM42208v1_genomic.fna/target_genomes.txt --output GCF_000422085.1_ASM42208v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:40:24,018] [INFO] Task succeeded: fastANI
[2024-01-25 18:40:24,019] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf687c662-bcf4-4cde-86c1-c6a179e21777/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:40:24,019] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf687c662-bcf4-4cde-86c1-c6a179e21777/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:40:24,028] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:40:24,029] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:40:24,029] [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 liquefaciens	strain=ATCC 27592	GCA_000422085.1	614	614	type	True	100.0	1758	1760	95	conclusive
Serratia quinivorans	strain=NCTC11544	GCA_900457075.1	137545	137545	suspected-type	True	88.2988	1479	1760	95	below_threshold
Serratia proteamaculans	strain=CCUG 14510	GCA_008830365.1	28151	28151	type	True	88.2451	1438	1760	95	below_threshold
Serratia plymuthica	strain=FDAARGOS_895	GCA_016027675.1	82996	82996	type	True	87.0625	1389	1760	95	below_threshold
Serratia inhibens	strain=S40	GCA_003591175.1	2338073	2338073	type	True	86.931	1351	1760	95	below_threshold
Serratia plymuthica	strain=NBRC 102599	GCA_001590925.1	82996	82996	type	True	86.8822	1360	1760	95	below_threshold
Serratia grimesii	strain=NCTC11543	GCA_900456935.1	82995	82995	type	True	86.8511	1433	1760	95	below_threshold
Serratia grimesii	strain=NBRC 13537	GCA_001590905.1	82995	82995	type	True	86.7177	1399	1760	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	85.4403	1287	1760	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	84.6742	1231	1760	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	84.4405	1235	1760	95	below_threshold
Serratia fonticola	strain=LMG 7882	GCA_000469035.1	47917	47917	suspected-type	True	82.5128	953	1760	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	79.3615	596	1760	95	below_threshold
Rahnella perminowiae	strain=SL6	GCA_019049755.1	2816244	2816244	type	True	79.0099	513	1760	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:40:24,030] [INFO] DFAST Taxonomy check result was written to GCF_000422085.1_ASM42208v1_genomic.fna/tc_result.tsv
[2024-01-25 18:40:24,031] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:40:24,031] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:40:24,031] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf687c662-bcf4-4cde-86c1-c6a179e21777/dqc_reference/checkm_data
[2024-01-25 18:40:24,032] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:40:24,084] [INFO] Task started: CheckM
[2024-01-25 18:40:24,084] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000422085.1_ASM42208v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000422085.1_ASM42208v1_genomic.fna/checkm_input GCF_000422085.1_ASM42208v1_genomic.fna/checkm_result
[2024-01-25 18:41:06,497] [INFO] Task succeeded: CheckM
[2024-01-25 18:41:06,498] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:41:06,526] [INFO] ===== Completeness check finished =====
[2024-01-25 18:41:06,526] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:41:06,527] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000422085.1_ASM42208v1_genomic.fna/markers.fasta)
[2024-01-25 18:41:06,527] [INFO] Task started: Blastn
[2024-01-25 18:41:06,527] [INFO] Running command: blastn -query GCF_000422085.1_ASM42208v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf687c662-bcf4-4cde-86c1-c6a179e21777/dqc_reference/reference_markers_gtdb.fasta -out GCF_000422085.1_ASM42208v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:41:07,684] [INFO] Task succeeded: Blastn
[2024-01-25 18:41:07,689] [INFO] Selected 12 target genomes.
[2024-01-25 18:41:07,689] [INFO] Target genome list was writen to GCF_000422085.1_ASM42208v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:41:07,698] [INFO] Task started: fastANI
[2024-01-25 18:41:07,699] [INFO] Running command: fastANI --query /var/lib/cwl/stg351b9de2-b18b-4bbd-bf1e-03d5194382bd/GCF_000422085.1_ASM42208v1_genomic.fna.gz --refList GCF_000422085.1_ASM42208v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000422085.1_ASM42208v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:41:24,467] [INFO] Task succeeded: fastANI
[2024-01-25 18:41:24,475] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:41:24,476] [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_000422085.1	s__Serratia liquefaciens	100.0	1760	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	98.63	98.20	0.94	0.91	25	conclusive
GCA_012719855.1	s__Serratia liquefaciens_A	94.9825	1566	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	97.92	97.90	0.90	0.89	3	-
GCF_900457075.1	s__Serratia quinivorans	88.2986	1479	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	98.38	95.64	0.93	0.85	9	-
GCF_008830365.1	s__Serratia proteamaculans	88.2433	1438	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	97.96	95.51	0.92	0.86	11	-
GCF_013337185.1	s__Serratia proteamaculans_D	88.0944	1445	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	97.78	95.57	0.96	0.91	3	-
GCF_018336935.1	s__Serratia plymuthica_B	87.1048	1374	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003591175.1	s__Serratia inhibens	86.931	1351	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	96.90	95.73	0.88	0.85	4	-
GCF_001590925.1	s__Serratia plymuthica	86.8822	1360	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	97.90	96.52	0.93	0.88	29	-
GCF_017832355.1	s__Serratia sp017832355	86.8256	1428	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001590905.1	s__Serratia grimesii	86.7177	1399	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	99.09	98.89	0.96	0.93	7	-
GCF_016742975.1	s__Serratia nevei	84.5931	1100	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.1913	97.82	96.26	0.83	0.75	139	-
GCF_007680145.1	s__Pseudescherichia sp002298805	78.5101	479	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pseudescherichia	95.0	98.55	96.56	0.95	0.92	13	-
--------------------------------------------------------------------------------
[2024-01-25 18:41:24,477] [INFO] GTDB search result was written to GCF_000422085.1_ASM42208v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:41:24,477] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:41:24,480] [INFO] DFAST_QC result json was written to GCF_000422085.1_ASM42208v1_genomic.fna/dqc_result.json
[2024-01-25 18:41:24,481] [INFO] DFAST_QC completed!
[2024-01-25 18:41:24,481] [INFO] Total running time: 0h1m34s