[2024-01-24 14:03:08,186] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:03:08,188] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:03:08,189] [INFO] DQC Reference Directory: /var/lib/cwl/stgf83b53b7-61a6-4e15-a5ff-d0ddc828f070/dqc_reference
[2024-01-24 14:03:09,561] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:03:09,563] [INFO] Task started: Prodigal
[2024-01-24 14:03:09,563] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d979c4b-166a-4f17-81be-32fab0e9d79e/GCF_021728295.1_ASM2172829v1_genomic.fna.gz | prodigal -d GCF_021728295.1_ASM2172829v1_genomic.fna/cds.fna -a GCF_021728295.1_ASM2172829v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:27,730] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:27,731] [INFO] Task started: HMMsearch
[2024-01-24 14:03:27,731] [INFO] Running command: hmmsearch --tblout GCF_021728295.1_ASM2172829v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf83b53b7-61a6-4e15-a5ff-d0ddc828f070/dqc_reference/reference_markers.hmm GCF_021728295.1_ASM2172829v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:28,073] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:28,074] [INFO] Found 6/6 markers.
[2024-01-24 14:03:28,130] [INFO] Query marker FASTA was written to GCF_021728295.1_ASM2172829v1_genomic.fna/markers.fasta
[2024-01-24 14:03:28,131] [INFO] Task started: Blastn
[2024-01-24 14:03:28,131] [INFO] Running command: blastn -query GCF_021728295.1_ASM2172829v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf83b53b7-61a6-4e15-a5ff-d0ddc828f070/dqc_reference/reference_markers.fasta -out GCF_021728295.1_ASM2172829v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:29,007] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:29,010] [INFO] Selected 31 target genomes.
[2024-01-24 14:03:29,011] [INFO] Target genome list was writen to GCF_021728295.1_ASM2172829v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:29,031] [INFO] Task started: fastANI
[2024-01-24 14:03:29,031] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d979c4b-166a-4f17-81be-32fab0e9d79e/GCF_021728295.1_ASM2172829v1_genomic.fna.gz --refList GCF_021728295.1_ASM2172829v1_genomic.fna/target_genomes.txt --output GCF_021728295.1_ASM2172829v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:04:09,499] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:09,499] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf83b53b7-61a6-4e15-a5ff-d0ddc828f070/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:04:09,500] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf83b53b7-61a6-4e15-a5ff-d0ddc828f070/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:04:09,521] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:04:09,521] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:04:09,521] [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 graminis	strain=DSM 11363	GCA_900111735.1	158627	158627	suspected-type	True	92.3932	1601	1933	95	below_threshold
Pseudomonas bohemica	strain=IA19	GCA_002934685.1	2044872	2044872	type	True	83.7674	1284	1933	95	below_threshold
Pseudomonas abietaniphila	strain=ATCC 700689	GCA_900100795.1	89065	89065	type	True	83.7202	1377	1933	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	81.3173	985	1933	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP4116	GCA_001401405.1	251701	251701	pathovar	True	81.3084	947	1933	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP3963	GCA_001401175.1	251701	251701	pathovar	True	81.2886	934	1933	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	81.2845	962	1933	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP8903	GCA_001400595.1	251701	251701	pathovar	True	81.2092	950	1933	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=CCUG 712	GCA_008801625.1	587851	587753	type	True	81.2028	993	1933	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=DSM 6698	GCA_003851905.1	587851	587753	type	True	81.1744	996	1933	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=LMG 1245	GCA_001269575.1	587851	587753	type	True	81.1566	1007	1933	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=NBRC 3521	GCA_000813225.1	587851	587753	type	True	81.1426	1002	1933	95	below_threshold
Pseudomonas izuensis	strain=IzPS43_3003	GCA_009861505.1	2684212	2684212	type	True	80.9924	906	1933	95	below_threshold
Pseudomonas extremorientalis	strain=LMG 19695	GCA_001870465.1	169669	169669	type	True	80.9807	953	1933	95	below_threshold
Pseudomonas extremorientalis		GCA_900625005.1	169669	169669	type	True	80.9793	948	1933	95	below_threshold
Pseudomonas meliae	strain=CFBP 3225	GCA_000935675.1	86176	86176	suspected-type	True	80.9502	859	1933	95	below_threshold
Pseudomonas meliae	strain=ICMP6289	GCA_001400515.1	86176	86176	suspected-type	True	80.9448	832	1933	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	80.8084	943	1933	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	80.7121	953	1933	95	below_threshold
Pseudomonas gessardii	strain=DSM 17152	GCA_009671285.1	78544	78544	type	True	80.6853	859	1933	95	below_threshold
Pseudomonas gessardii		GCA_900625085.1	78544	78544	type	True	80.6317	865	1933	95	below_threshold
Pseudomonas brenneri	strain=DSM 15294	GCA_007858285.1	129817	129817	type	True	80.6237	863	1933	95	below_threshold
Pseudomonas brenneri	strain=JCM 13307	GCA_014646715.1	129817	129817	type	True	80.6231	865	1933	95	below_threshold
Oceanisphaera litoralis	strain=DSM 15406	GCA_016907015.1	225144	225144	type	True	75.9271	58	1933	95	below_threshold
Actinoplanes teichomyceticus	strain=ATCC 31121	GCA_003711105.1	1867	1867	type	True	74.8628	89	1933	95	below_threshold
Catellatospora citrea	strain=NBRC 14495	GCA_016862615.1	53366	53366	type	True	74.8172	68	1933	95	below_threshold
Catellatospora vulcania	strain=NEAU-JM1	GCA_009720385.1	1460450	1460450	type	True	74.7992	80	1933	95	below_threshold
Actinoplanes cyaneus	strain=NBRC 14990	GCA_016862095.1	52696	52696	type	True	74.7699	66	1933	95	below_threshold
Catellatospora paridis	strain=NEAU-CL2	GCA_009720365.1	1617086	1617086	type	True	74.7472	81	1933	95	below_threshold
Dactylosporangium siamense	strain=NBRC 106093	GCA_016862795.1	685454	685454	type	True	74.6389	94	1933	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:04:09,523] [INFO] DFAST Taxonomy check result was written to GCF_021728295.1_ASM2172829v1_genomic.fna/tc_result.tsv
[2024-01-24 14:04:09,523] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:04:09,523] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:04:09,524] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf83b53b7-61a6-4e15-a5ff-d0ddc828f070/dqc_reference/checkm_data
[2024-01-24 14:04:09,524] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:04:09,585] [INFO] Task started: CheckM
[2024-01-24 14:04:09,585] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021728295.1_ASM2172829v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021728295.1_ASM2172829v1_genomic.fna/checkm_input GCF_021728295.1_ASM2172829v1_genomic.fna/checkm_result
[2024-01-24 14:05:02,498] [INFO] Task succeeded: CheckM
[2024-01-24 14:05:02,500] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:05:02,529] [INFO] ===== Completeness check finished =====
[2024-01-24 14:05:02,530] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:05:02,530] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021728295.1_ASM2172829v1_genomic.fna/markers.fasta)
[2024-01-24 14:05:02,531] [INFO] Task started: Blastn
[2024-01-24 14:05:02,531] [INFO] Running command: blastn -query GCF_021728295.1_ASM2172829v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf83b53b7-61a6-4e15-a5ff-d0ddc828f070/dqc_reference/reference_markers_gtdb.fasta -out GCF_021728295.1_ASM2172829v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:03,930] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:03,934] [INFO] Selected 10 target genomes.
[2024-01-24 14:05:03,934] [INFO] Target genome list was writen to GCF_021728295.1_ASM2172829v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:05:03,960] [INFO] Task started: fastANI
[2024-01-24 14:05:03,960] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d979c4b-166a-4f17-81be-32fab0e9d79e/GCF_021728295.1_ASM2172829v1_genomic.fna.gz --refList GCF_021728295.1_ASM2172829v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021728295.1_ASM2172829v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:05:20,611] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:20,624] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:05:20,624] [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_014842265.1	s__Pseudomonas_E sp014842265	92.8452	1627	1933	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_004364335.1	s__Pseudomonas_E graminis_D	92.7625	1651	1933	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_001705435.1	s__Pseudomonas_E graminis_B	92.415	1594	1933	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.17	98.17	0.90	0.90	2	-
GCF_900111735.1	s__Pseudomonas_E graminis	92.3872	1602	1933	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.28	98.01	0.93	0.92	4	-
GCF_013201545.1	s__Pseudomonas_E sp900585815	92.0498	1616	1933	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.31	96.17	0.93	0.92	5	-
GCA_000759445.1	s__Pseudomonas_E lutea	86.7314	1510	1933	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.06	98.06	0.91	0.91	2	-
GCF_900108875.1	s__Pseudomonas_E sp900108875	83.6726	1366	1933	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_004339665.1	s__Azotobacter chroococcum	78.7612	484	1933	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	97.27	96.18	0.89	0.83	10	-
--------------------------------------------------------------------------------
[2024-01-24 14:05:20,626] [INFO] GTDB search result was written to GCF_021728295.1_ASM2172829v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:05:20,626] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:05:20,630] [INFO] DFAST_QC result json was written to GCF_021728295.1_ASM2172829v1_genomic.fna/dqc_result.json
[2024-01-24 14:05:20,631] [INFO] DFAST_QC completed!
[2024-01-24 14:05:20,631] [INFO] Total running time: 0h2m12s