[2024-01-24 14:22:17,497] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:17,503] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:17,504] [INFO] DQC Reference Directory: /var/lib/cwl/stgbbc841fc-3468-4e78-b55b-b7c58ccea1d3/dqc_reference
[2024-01-24 14:22:18,769] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:18,770] [INFO] Task started: Prodigal
[2024-01-24 14:22:18,770] [INFO] Running command: gunzip -c /var/lib/cwl/stgf1e038d6-bb49-478f-a3a0-d93f9d2c1d51/GCF_016937615.1_ASM1693761v1_genomic.fna.gz | prodigal -d GCF_016937615.1_ASM1693761v1_genomic.fna/cds.fna -a GCF_016937615.1_ASM1693761v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:38,093] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:38,093] [INFO] Task started: HMMsearch
[2024-01-24 14:22:38,094] [INFO] Running command: hmmsearch --tblout GCF_016937615.1_ASM1693761v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbbc841fc-3468-4e78-b55b-b7c58ccea1d3/dqc_reference/reference_markers.hmm GCF_016937615.1_ASM1693761v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:38,429] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:38,431] [INFO] Found 6/6 markers.
[2024-01-24 14:22:38,489] [INFO] Query marker FASTA was written to GCF_016937615.1_ASM1693761v1_genomic.fna/markers.fasta
[2024-01-24 14:22:38,490] [INFO] Task started: Blastn
[2024-01-24 14:22:38,490] [INFO] Running command: blastn -query GCF_016937615.1_ASM1693761v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbc841fc-3468-4e78-b55b-b7c58ccea1d3/dqc_reference/reference_markers.fasta -out GCF_016937615.1_ASM1693761v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:39,448] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:39,453] [INFO] Selected 21 target genomes.
[2024-01-24 14:22:39,454] [INFO] Target genome list was writen to GCF_016937615.1_ASM1693761v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:39,471] [INFO] Task started: fastANI
[2024-01-24 14:22:39,472] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1e038d6-bb49-478f-a3a0-d93f9d2c1d51/GCF_016937615.1_ASM1693761v1_genomic.fna.gz --refList GCF_016937615.1_ASM1693761v1_genomic.fna/target_genomes.txt --output GCF_016937615.1_ASM1693761v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:08,651] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:08,652] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbbc841fc-3468-4e78-b55b-b7c58ccea1d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:08,652] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbbc841fc-3468-4e78-b55b-b7c58ccea1d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:08,671] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:23:08,671] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:08,672] [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 lactucae	strain=MAFF 301380	GCA_016937615.1	2813360	2813360	type	True	100.0	1942	1959	95	conclusive
Pseudomonas asgharzadehiana	strain=SWRI132	GCA_019139815.1	2842349	2842349	type	True	90.7652	1548	1959	95	below_threshold
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	88.9866	1553	1959	95	below_threshold
Pseudomonas azotoformans	strain=NBRC 12693	GCA_002091515.1	47878	47878	suspected-type	True	88.4408	1462	1959	95	below_threshold
Pseudomonas extremorientalis		GCA_900625005.1	169669	169669	type	True	88.4303	1430	1959	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	88.3878	1453	1959	95	below_threshold
Pseudomonas marginalis	strain=ICMP 3553	GCA_001645105.1	298	298	suspected-type	True	88.3784	1486	1959	95	below_threshold
Pseudomonas marginalis	strain=ICMP 3553	GCA_003700725.1	298	298	suspected-type	True	88.367	1403	1959	95	below_threshold
Pseudomonas simiae	strain=CCUG 50988	GCA_001730615.1	321846	321846	type	True	88.1299	1427	1959	95	below_threshold
Pseudomonas simiae	strain=CCUG 50988	GCA_900111895.1	321846	321846	type	True	88.1029	1424	1959	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	88.082	1415	1959	95	below_threshold
Pseudomonas extremaustralis	strain=DSM 17835	GCA_007858235.1	359110	359110	type	True	88.0658	1385	1959	95	below_threshold
Pseudomonas lactis	strain=DSM 29167	GCA_001439845.1	1615674	1615674	type	True	87.6987	1429	1959	95	below_threshold
Pseudomonas salmasensis	strain=SWRI126	GCA_014268375.2	2745514	2745514	type	True	87.655	1421	1959	95	below_threshold
Pseudomonas paracarnis	strain=V5/DAB/2/5	GCA_904063055.1	2750625	2750625	type	True	87.6301	1403	1959	95	below_threshold
Pseudomonas fluorescens	strain=NBRC 14160	GCA_002091595.1	294	294	suspected-type	True	87.6163	1394	1959	95	below_threshold
Pseudomonas fluorescens	strain=DSM 50090	GCA_007858165.1	294	294	suspected-type	True	87.573	1406	1959	95	below_threshold
Pseudomonas fluorescens	strain=NCTC10038	GCA_900475215.1	294	294	suspected-type	True	87.5077	1423	1959	95	below_threshold
Pseudomonas paralactis	strain=DSM 29164	GCA_001439735.1	1615673	1615673	type	True	87.4015	1373	1959	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	85.8301	1290	1959	95	below_threshold
Pseudomonas karstica	strain=CCM 7891	GCA_009707515.1	1055468	1055468	type	True	85.0894	1188	1959	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:08,676] [INFO] DFAST Taxonomy check result was written to GCF_016937615.1_ASM1693761v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:08,677] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:08,677] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:08,677] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbbc841fc-3468-4e78-b55b-b7c58ccea1d3/dqc_reference/checkm_data
[2024-01-24 14:23:08,679] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:08,744] [INFO] Task started: CheckM
[2024-01-24 14:23:08,745] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016937615.1_ASM1693761v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016937615.1_ASM1693761v1_genomic.fna/checkm_input GCF_016937615.1_ASM1693761v1_genomic.fna/checkm_result
[2024-01-24 14:24:04,564] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:04,565] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:04,589] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:04,590] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:04,590] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016937615.1_ASM1693761v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:04,591] [INFO] Task started: Blastn
[2024-01-24 14:24:04,591] [INFO] Running command: blastn -query GCF_016937615.1_ASM1693761v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbc841fc-3468-4e78-b55b-b7c58ccea1d3/dqc_reference/reference_markers_gtdb.fasta -out GCF_016937615.1_ASM1693761v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:06,283] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:06,287] [INFO] Selected 22 target genomes.
[2024-01-24 14:24:06,287] [INFO] Target genome list was writen to GCF_016937615.1_ASM1693761v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:06,305] [INFO] Task started: fastANI
[2024-01-24 14:24:06,306] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1e038d6-bb49-478f-a3a0-d93f9d2c1d51/GCF_016937615.1_ASM1693761v1_genomic.fna.gz --refList GCF_016937615.1_ASM1693761v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016937615.1_ASM1693761v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:40,093] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:40,117] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:40,118] [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_002022265.1	s__Pseudomonas_E fluorescens_C	96.9955	1692	1959	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.28	96.98	0.88	0.86	8	conclusive
GCF_019139815.1	s__Pseudomonas_E sp900005815	90.7698	1548	1959	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.55	99.31	0.95	0.92	7	-
GCF_007858185.1	s__Pseudomonas_E grimontii	89.0227	1530	1959	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014207255.1	s__Pseudomonas_E sp014207255	88.9325	1543	1959	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.31	98.90	0.95	0.91	5	-
GCF_900105325.1	s__Pseudomonas_E marginalis	88.9244	1571	1959	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.53	96.47	0.90	0.85	19	-
GCF_002843605.1	s__Pseudomonas_E sp002843605	88.6986	1470	1959	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.70	97.45	0.92	0.91	7	-
GCF_001870465.1	s__Pseudomonas_E extremorientalis	88.4485	1418	1959	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.37	98.13	0.91	0.89	29	-
GCF_003612935.1	s__Pseudomonas_E sp003013355	88.2859	1448	1959	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.87	98.56	0.95	0.92	7	-
GCF_001186335.1	s__Pseudomonas_E trivialis_B	88.2524	1479	1959	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.34	95.31	0.86	0.86	8	-
GCF_001439695.1	s__Pseudomonas_E veronii	88.23	1451	1959	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.79	98.13	0.89	0.82	43	-
GCF_001983175.1	s__Pseudomonas_E cedrina	88.2225	1480	1959	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.10	97.30	0.97	0.92	4	-
GCF_013385825.1	s__Pseudomonas_E reactans	88.2093	1412	1959	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.45	96.30	0.89	0.87	7	-
GCF_900111895.1	s__Pseudomonas_E simiae	88.1166	1422	1959	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.45	99.32	0.95	0.92	20	-
GCF_012844475.1	s__Pseudomonas_E sp012844475	88.1052	1368	1959	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002563895.1	s__Pseudomonas_E lurida	88.0862	1414	1959	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.19	99.03	0.94	0.91	25	-
GCF_005938045.2	s__Pseudomonas_E sp005938045	87.8116	1400	1959	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.18	95.16	0.86	0.86	3	-
GCF_003851685.1	s__Pseudomonas_E sp003851685	87.7648	1382	1959	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_001902145.1	s__Pseudomonas_E fluorescens_BV	87.764	1384	1959	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.76	95.23	0.87	0.84	22	-
GCF_001439845.1	s__Pseudomonas_E lactis	87.7028	1428	1959	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.24	95.50	0.88	0.81	30	-
GCF_904063055.1	s__Pseudomonas_E paracarnis	87.6329	1403	1959	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.75	95.59	0.90	0.84	86	-
GCF_000263715.2	s__Pseudomonas_E synxantha_A	87.46	1405	1959	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.66	97.33	0.90	0.88	8	-
GCF_003851495.1	s__Pseudomonas_E fluorescens_BB	87.3135	1426	1959	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.3929	98.85	97.70	0.94	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:40,120] [INFO] GTDB search result was written to GCF_016937615.1_ASM1693761v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:40,120] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:40,125] [INFO] DFAST_QC result json was written to GCF_016937615.1_ASM1693761v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:40,126] [INFO] DFAST_QC completed!
[2024-01-24 14:24:40,126] [INFO] Total running time: 0h2m23s