[2024-01-24 12:14:33,696] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:33,698] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:33,698] [INFO] DQC Reference Directory: /var/lib/cwl/stg16416004-6d47-4d1b-9257-26d261823a15/dqc_reference
[2024-01-24 12:14:34,948] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:34,949] [INFO] Task started: Prodigal
[2024-01-24 12:14:34,949] [INFO] Running command: gunzip -c /var/lib/cwl/stgab699cab-3eec-43cb-b478-6e6037232c7d/GCF_019145435.1_ASM1914543v1_genomic.fna.gz | prodigal -d GCF_019145435.1_ASM1914543v1_genomic.fna/cds.fna -a GCF_019145435.1_ASM1914543v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:57,912] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:57,912] [INFO] Task started: HMMsearch
[2024-01-24 12:14:57,912] [INFO] Running command: hmmsearch --tblout GCF_019145435.1_ASM1914543v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg16416004-6d47-4d1b-9257-26d261823a15/dqc_reference/reference_markers.hmm GCF_019145435.1_ASM1914543v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:58,237] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:58,239] [INFO] Found 6/6 markers.
[2024-01-24 12:14:58,291] [INFO] Query marker FASTA was written to GCF_019145435.1_ASM1914543v1_genomic.fna/markers.fasta
[2024-01-24 12:14:58,291] [INFO] Task started: Blastn
[2024-01-24 12:14:58,291] [INFO] Running command: blastn -query GCF_019145435.1_ASM1914543v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16416004-6d47-4d1b-9257-26d261823a15/dqc_reference/reference_markers.fasta -out GCF_019145435.1_ASM1914543v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:59,341] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:59,344] [INFO] Selected 23 target genomes.
[2024-01-24 12:14:59,344] [INFO] Target genome list was writen to GCF_019145435.1_ASM1914543v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:59,357] [INFO] Task started: fastANI
[2024-01-24 12:14:59,357] [INFO] Running command: fastANI --query /var/lib/cwl/stgab699cab-3eec-43cb-b478-6e6037232c7d/GCF_019145435.1_ASM1914543v1_genomic.fna.gz --refList GCF_019145435.1_ASM1914543v1_genomic.fna/target_genomes.txt --output GCF_019145435.1_ASM1914543v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:35,616] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:35,616] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg16416004-6d47-4d1b-9257-26d261823a15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:35,617] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg16416004-6d47-4d1b-9257-26d261823a15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:35,640] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:35,640] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:35,640] [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 ekonensis	strain=COR58	GCA_019145435.1	2842353	2842353	type	True	100.0	2041	2041	95	conclusive
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	88.3449	1594	2041	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	88.3417	1630	2041	95	below_threshold
Pseudomonas kribbensis	strain=46-2	GCA_003352185.1	1628086	1628086	type	True	88.3182	1673	2041	95	below_threshold
Pseudomonas allokribbensis	strain=IzPS23	GCA_014863605.1	2774460	2774460	type	True	88.2392	1694	2041	95	below_threshold
Pseudomonas bananamidigenes	strain=BW11P2	GCA_001679645.1	2843610	2843610	type	True	87.7979	1584	2041	95	below_threshold
Pseudomonas iranensis	strain=SWRI54	GCA_014268585.2	2745503	2745503	type	True	86.4348	1498	2041	95	below_threshold
Pseudomonas siliginis	strain=SWRI31	GCA_019145195.1	2842346	2842346	type	True	86.3382	1413	2041	95	below_threshold
Pseudomonas granadensis	strain=LMG 27940	GCA_900105485.1	1421430	1421430	suspected-type	True	86.2374	1549	2041	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	86.1915	1625	2041	95	below_threshold
Pseudomonas crudilactis	strain=UCMA 17988	GCA_013433315.1	2697028	2697028	type	True	86.1018	1612	2041	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=LMG 1245	GCA_001269575.1	587851	587753	type	True	85.8781	1493	2041	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=NBRC 3521	GCA_000813225.1	587851	587753	type	True	85.8752	1481	2041	95	below_threshold
Pseudomonas azerbaijanoriens	strain=SWRI123	GCA_019139795.1	2842350	2842350	type	True	85.8736	1429	2041	95	below_threshold
Pseudomonas laurylsulfatiphila	strain=AP3_16	GCA_002934665.1	2011015	2011015	type	True	85.8601	1444	2041	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=CCUG 712	GCA_008801625.1	587851	587753	type	True	85.8377	1491	2041	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=DSM 6698	GCA_003851905.1	587851	587753	type	True	85.7674	1514	2041	95	below_threshold
Pseudomonas jessenii	strain=DSM 17150	GCA_002236115.1	77298	77298	suspected-type	True	85.7164	1455	2041	95	below_threshold
Pseudomonas laurylsulfativorans	strain=AP3_22	GCA_002906155.1	1943631	1943631	type	True	85.4909	1437	2041	95	below_threshold
Pseudomonas thivervalensis	strain=DSM 13194	GCA_001269655.1	86265	86265	type	True	85.1502	1325	2041	95	below_threshold
Pseudomonas umsongensis	strain=DSM 16611	GCA_002236105.1	198618	198618	type	True	85.1192	1358	2041	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	83.6951	1299	2041	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	83.4899	924	2041	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:35,642] [INFO] DFAST Taxonomy check result was written to GCF_019145435.1_ASM1914543v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:35,642] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:35,642] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:35,643] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg16416004-6d47-4d1b-9257-26d261823a15/dqc_reference/checkm_data
[2024-01-24 12:15:35,643] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:35,703] [INFO] Task started: CheckM
[2024-01-24 12:15:35,703] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019145435.1_ASM1914543v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019145435.1_ASM1914543v1_genomic.fna/checkm_input GCF_019145435.1_ASM1914543v1_genomic.fna/checkm_result
[2024-01-24 12:16:50,543] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:50,544] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:50,567] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:50,567] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:50,567] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019145435.1_ASM1914543v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:50,568] [INFO] Task started: Blastn
[2024-01-24 12:16:50,568] [INFO] Running command: blastn -query GCF_019145435.1_ASM1914543v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16416004-6d47-4d1b-9257-26d261823a15/dqc_reference/reference_markers_gtdb.fasta -out GCF_019145435.1_ASM1914543v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:52,357] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:52,361] [INFO] Selected 25 target genomes.
[2024-01-24 12:16:52,361] [INFO] Target genome list was writen to GCF_019145435.1_ASM1914543v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:52,379] [INFO] Task started: fastANI
[2024-01-24 12:16:52,379] [INFO] Running command: fastANI --query /var/lib/cwl/stgab699cab-3eec-43cb-b478-6e6037232c7d/GCF_019145435.1_ASM1914543v1_genomic.fna.gz --refList GCF_019145435.1_ASM1914543v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019145435.1_ASM1914543v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:17:30,413] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:30,439] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:17:30,439] [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_002113595.1	s__Pseudomonas_E sp002113595	96.4195	1889	2041	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.23	96.42	0.97	0.93	16	conclusive
GCF_004006335.1	s__Pseudomonas_E sp002112885	88.4761	1672	2041	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.01	95.48	0.92	0.90	14	-
GCF_019145475.1	s__Pseudomonas_E sp019145475	88.3931	1669	2041	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_010448615.1	s__Pseudomonas_E sp001655595	88.3779	1669	2041	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.61	96.24	0.94	0.90	22	-
GCF_014863585.1	s__Pseudomonas_E gozinkensis	88.3349	1698	2041	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_003352185.1	s__Pseudomonas_E kribbensis	88.3055	1674	2041	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.22	95.68	0.92	0.89	10	-
GCF_001594225.2	s__Pseudomonas_E glycinae	88.2284	1653	2041	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.56	95.98	0.93	0.88	9	-
GCF_002113125.1	s__Pseudomonas_E sp002113125	88.1917	1656	2041	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_001679645.1	s__Pseudomonas_E fluorescens_K	87.7881	1585	2041	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_003999415.1	s__Pseudomonas_E koreensis_E	87.4134	1603	2041	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.57	98.57	0.92	0.92	2	-
GCF_000282275.2	s__Pseudomonas_E sp000282275	87.3803	1597	2041	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_004683905.1	s__Pseudomonas_E putida_A	87.2723	1650	2041	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.80	95.08	0.93	0.90	22	-
GCF_002287825.1	s__Pseudomonas_E koreensis_B	87.2354	1627	2041	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.58	96.55	0.92	0.86	13	-
GCF_000292795.1	s__Pseudomonas_E fluorescens_H	87.2096	1648	2041	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.99	97.99	0.94	0.93	3	-
GCF_014472415.1	s__Pseudomonas_E sp014472415	86.3002	1529	2041	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_000931465.1	s__Pseudomonas_E sp000931465	85.8988	1493	2041	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.57	98.57	0.96	0.96	2	-
GCF_000967965.1	s__Pseudomonas_E fluorescens_O	85.8369	1419	2041	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_001921865.1	s__Pseudomonas_E chlororaphis_D	85.792	1515	2041	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_001976065.1	s__Pseudomonas_E putida_G	85.5742	1385	2041	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.27	99.27	0.91	0.91	2	-
GCF_900636825.1	s__Pseudomonas_E fluorescens_BG	85.3567	1484	2041	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_006094435.1	s__Pseudomonas_E sp002029345	85.3048	1375	2041	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.75	98.73	0.83	0.83	3	-
GCF_902497855.1	s__Pseudomonas_E fluorescens_BI	85.1958	1379	2041	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.52	95.78	0.88	0.82	3	-
GCF_902497995.1	s__Pseudomonas_E fluorescens_BK	85.1591	1297	2041	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.06	99.06	0.89	0.89	2	-
GCF_001547895.1	s__Pseudomonas_E sp001547895	85.1269	1429	2041	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.12	98.88	0.95	0.94	4	-
GCF_900105185.1	s__Pseudomonas_E saponiphila	84.9844	1385	2041	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.25	98.25	0.89	0.89	5	-
--------------------------------------------------------------------------------
[2024-01-24 12:17:30,441] [INFO] GTDB search result was written to GCF_019145435.1_ASM1914543v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:17:30,442] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:17:30,448] [INFO] DFAST_QC result json was written to GCF_019145435.1_ASM1914543v1_genomic.fna/dqc_result.json
[2024-01-24 12:17:30,448] [INFO] DFAST_QC completed!
[2024-01-24 12:17:30,448] [INFO] Total running time: 0h2m57s