[2024-01-24 13:17:11,575] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:11,578] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:11,578] [INFO] DQC Reference Directory: /var/lib/cwl/stga645c21f-5983-40ea-8230-ec29503f4aff/dqc_reference
[2024-01-24 13:17:12,767] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:12,768] [INFO] Task started: Prodigal
[2024-01-24 13:17:12,768] [INFO] Running command: gunzip -c /var/lib/cwl/stg00d0279c-e91b-464a-8bf1-1b97d3021129/GCF_008801455.1_ASM880145v1_genomic.fna.gz | prodigal -d GCF_008801455.1_ASM880145v1_genomic.fna/cds.fna -a GCF_008801455.1_ASM880145v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:33,399] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:33,399] [INFO] Task started: HMMsearch
[2024-01-24 13:17:33,400] [INFO] Running command: hmmsearch --tblout GCF_008801455.1_ASM880145v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga645c21f-5983-40ea-8230-ec29503f4aff/dqc_reference/reference_markers.hmm GCF_008801455.1_ASM880145v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:33,709] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:33,710] [INFO] Found 6/6 markers.
[2024-01-24 13:17:33,763] [INFO] Query marker FASTA was written to GCF_008801455.1_ASM880145v1_genomic.fna/markers.fasta
[2024-01-24 13:17:33,763] [INFO] Task started: Blastn
[2024-01-24 13:17:33,763] [INFO] Running command: blastn -query GCF_008801455.1_ASM880145v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga645c21f-5983-40ea-8230-ec29503f4aff/dqc_reference/reference_markers.fasta -out GCF_008801455.1_ASM880145v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:34,713] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:34,717] [INFO] Selected 16 target genomes.
[2024-01-24 13:17:34,717] [INFO] Target genome list was writen to GCF_008801455.1_ASM880145v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:34,899] [INFO] Task started: fastANI
[2024-01-24 13:17:34,899] [INFO] Running command: fastANI --query /var/lib/cwl/stg00d0279c-e91b-464a-8bf1-1b97d3021129/GCF_008801455.1_ASM880145v1_genomic.fna.gz --refList GCF_008801455.1_ASM880145v1_genomic.fna/target_genomes.txt --output GCF_008801455.1_ASM880145v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:59,382] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:59,382] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga645c21f-5983-40ea-8230-ec29503f4aff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:59,383] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga645c21f-5983-40ea-8230-ec29503f4aff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:59,397] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:17:59,397] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:59,397] [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
Pseudomonas reinekei	strain=CCUG 53116	GCA_008801455.1	395598	395598	type	True	100.0	2051	2055	95	conclusive
Pseudomonas reinekei	strain=MT1	GCA_001945365.1	395598	395598	type	True	99.9947	2045	2055	95	conclusive
Pseudomonas azerbaijanoccidens	strain=SWRI74	GCA_019145495.1	2842347	2842347	type	True	90.9159	1664	2055	95	below_threshold
Pseudomonas moorei	strain=CCUG 53114	GCA_008801475.1	395599	395599	type	True	87.8976	1529	2055	95	below_threshold
Pseudomonas izuensis	strain=IzPS43_3003	GCA_009861505.1	2684212	2684212	type	True	87.8191	1504	2055	95	below_threshold
Pseudomonas jessenii	strain=DSM 17150	GCA_002236115.1	77298	77298	suspected-type	True	87.788	1502	2055	95	below_threshold
Pseudomonas mohnii	strain=DSM 18327	GCA_900105115.1	395600	395600	type	True	87.5008	1511	2055	95	below_threshold
Pseudomonas laurylsulfatiphila	strain=AP3_16	GCA_002934665.1	2011015	2011015	type	True	87.488	1512	2055	95	below_threshold
Pseudomonas azerbaijanoriens	strain=SWRI123	GCA_019139795.1	2842350	2842350	type	True	87.3919	1479	2055	95	below_threshold
Pseudomonas umsongensis	strain=DSM 16611	GCA_002236105.1	198618	198618	type	True	87.3195	1514	2055	95	below_threshold
Pseudomonas lini	strain=CCUG 51522	GCA_008801525.1	163011	163011	type	True	86.6259	1395	2055	95	below_threshold
Pseudomonas farris	strain=SWRI79	GCA_019145235.1	2841207	2841207	type	True	86.5601	1398	2055	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	86.2056	1405	2055	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	86.0199	1372	2055	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	85.4944	1408	2055	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	83.2465	1185	2055	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:59,399] [INFO] DFAST Taxonomy check result was written to GCF_008801455.1_ASM880145v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:59,400] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:59,400] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:59,401] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga645c21f-5983-40ea-8230-ec29503f4aff/dqc_reference/checkm_data
[2024-01-24 13:17:59,402] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:59,461] [INFO] Task started: CheckM
[2024-01-24 13:17:59,462] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008801455.1_ASM880145v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008801455.1_ASM880145v1_genomic.fna/checkm_input GCF_008801455.1_ASM880145v1_genomic.fna/checkm_result
[2024-01-24 13:18:59,467] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:59,468] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:59,491] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:59,491] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:59,492] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008801455.1_ASM880145v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:59,492] [INFO] Task started: Blastn
[2024-01-24 13:18:59,492] [INFO] Running command: blastn -query GCF_008801455.1_ASM880145v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga645c21f-5983-40ea-8230-ec29503f4aff/dqc_reference/reference_markers_gtdb.fasta -out GCF_008801455.1_ASM880145v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:01,131] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:01,134] [INFO] Selected 18 target genomes.
[2024-01-24 13:19:01,134] [INFO] Target genome list was writen to GCF_008801455.1_ASM880145v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:01,196] [INFO] Task started: fastANI
[2024-01-24 13:19:01,196] [INFO] Running command: fastANI --query /var/lib/cwl/stg00d0279c-e91b-464a-8bf1-1b97d3021129/GCF_008801455.1_ASM880145v1_genomic.fna.gz --refList GCF_008801455.1_ASM880145v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008801455.1_ASM880145v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:28,010] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:28,029] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:28,029] [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_001945365.1	s__Pseudomonas_E reinekei	99.9947	2045	2055	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.76	95.43	0.93	0.85	5	conclusive
GCF_902497845.1	s__Pseudomonas_E fluorescens_BN	91.0245	1665	2055	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.81	98.81	0.91	0.91	2	-
GCF_001427125.1	s__Pseudomonas_E sp001427125	90.5017	1619	2055	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.98	98.83	0.91	0.89	5	-
GCF_000802965.1	s__Pseudomonas_E fluorescens_A	88.7746	1566	2055	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282475.1	s__Pseudomonas_E sp000282475	87.8093	1471	2055	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.45	95.45	0.83	0.83	2	-
GCF_000282455.1	s__Pseudomonas_E sp000282455	87.7952	1401	2055	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002236115.1	s__Pseudomonas_E jessenii	87.7849	1502	2055	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.88	96.89	0.89	0.84	18	-
GCF_000967965.1	s__Pseudomonas_E fluorescens_O	87.7637	1482	2055	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.01	99.01	0.96	0.96	2	-
GCF_902498135.1	s__Pseudomonas_E fluorescens_BH	87.7449	1493	2055	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.39	98.07	0.87	0.86	3	-
GCF_002303925.1	s__Pseudomonas_E sp002303925	87.6992	1438	2055	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.04	99.04	0.91	0.91	2	-
GCF_001429045.1	s__Pseudomonas_E sp001429045	87.6985	1479	2055	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900187615.1	s__Pseudomonas_E sp900187615	87.5594	1411	2055	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.27	99.27	0.93	0.93	2	-
GCF_003053605.1	s__Pseudomonas_E sp003053605	87.4945	1441	2055	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.75	96.54	0.88	0.80	4	-
GCF_002236105.1	s__Pseudomonas_E umsongensis	87.3263	1513	2055	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.47	96.72	0.91	0.86	9	-
GCF_000968015.1	s__Pseudomonas_E fluorescens_W	87.0965	1423	2055	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.19	96.19	0.86	0.86	2	-
GCF_001269805.1	s__Pseudomonas_E sp001269805	87.0407	1464	2055	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282495.1	s__Pseudomonas_E sp000282495	86.5806	1358	2055	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.86	95.96	0.87	0.86	6	-
GCF_000512695.2	s__Pseudomonas_E sp000512695	86.4945	1339	2055	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:28,031] [INFO] GTDB search result was written to GCF_008801455.1_ASM880145v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:28,031] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:28,037] [INFO] DFAST_QC result json was written to GCF_008801455.1_ASM880145v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:28,037] [INFO] DFAST_QC completed!
[2024-01-24 13:19:28,037] [INFO] Total running time: 0h2m16s