[2024-01-24 11:05:49,404] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:49,419] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:49,419] [INFO] DQC Reference Directory: /var/lib/cwl/stg34383575-b72a-43ca-97b1-f03881158425/dqc_reference
[2024-01-24 11:05:51,286] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:51,287] [INFO] Task started: Prodigal
[2024-01-24 11:05:51,287] [INFO] Running command: gunzip -c /var/lib/cwl/stgbcac3046-a1c0-4d13-8f7b-004ca3b9cce5/GCF_009932375.1_ASM993237v1_genomic.fna.gz | prodigal -d GCF_009932375.1_ASM993237v1_genomic.fna/cds.fna -a GCF_009932375.1_ASM993237v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:06:08,709] [INFO] Task succeeded: Prodigal
[2024-01-24 11:06:08,710] [INFO] Task started: HMMsearch
[2024-01-24 11:06:08,710] [INFO] Running command: hmmsearch --tblout GCF_009932375.1_ASM993237v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34383575-b72a-43ca-97b1-f03881158425/dqc_reference/reference_markers.hmm GCF_009932375.1_ASM993237v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:06:08,955] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:06:08,956] [INFO] Found 6/6 markers.
[2024-01-24 11:06:09,001] [INFO] Query marker FASTA was written to GCF_009932375.1_ASM993237v1_genomic.fna/markers.fasta
[2024-01-24 11:06:09,001] [INFO] Task started: Blastn
[2024-01-24 11:06:09,001] [INFO] Running command: blastn -query GCF_009932375.1_ASM993237v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34383575-b72a-43ca-97b1-f03881158425/dqc_reference/reference_markers.fasta -out GCF_009932375.1_ASM993237v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:09,906] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:09,909] [INFO] Selected 18 target genomes.
[2024-01-24 11:06:09,909] [INFO] Target genome list was writen to GCF_009932375.1_ASM993237v1_genomic.fna/target_genomes.txt
[2024-01-24 11:06:09,915] [INFO] Task started: fastANI
[2024-01-24 11:06:09,915] [INFO] Running command: fastANI --query /var/lib/cwl/stgbcac3046-a1c0-4d13-8f7b-004ca3b9cce5/GCF_009932375.1_ASM993237v1_genomic.fna.gz --refList GCF_009932375.1_ASM993237v1_genomic.fna/target_genomes.txt --output GCF_009932375.1_ASM993237v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:31,576] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:31,577] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34383575-b72a-43ca-97b1-f03881158425/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:31,577] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34383575-b72a-43ca-97b1-f03881158425/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:31,590] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:06:31,590] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:31,591] [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 juntendi	strain=BML3	GCA_009932375.1	2666183	2666183	type	True	100.0	1702	1716	95	conclusive
Pseudomonas inefficax	strain=JV551A3	GCA_900277125.1	2078786	2078786	type	True	88.2363	1253	1716	95	below_threshold
Pseudomonas putida	strain=IPO3752	GCA_013387005.1	303	303	suspected-type	True	88.1864	1254	1716	95	below_threshold
Pseudomonas putida	strain=NBRC 14164	GCA_000412675.1	303	303	suspected-type	True	88.1606	1267	1716	95	below_threshold
Pseudomonas putida	strain=NCTC10936	GCA_900455645.1	303	303	suspected-type	True	88.1589	1278	1716	95	below_threshold
Pseudomonas putida	strain=ATCC 12633	GCA_024508115.1	303	303	suspected-type	True	88.1302	1267	1716	95	below_threshold
Pseudomonas monteilii	strain=NBRC 103158	GCA_000730605.1	76759	76759	type	True	88.0682	1280	1716	95	below_threshold
Pseudomonas monteilii	strain=DSM 14164	GCA_000621245.1	76759	76759	type	True	88.0445	1290	1716	95	below_threshold
Pseudomonas anuradhapurensis	strain=RD8MR3	GCA_014269225.2	485870	485870	type	True	87.8617	1216	1716	95	below_threshold
Pseudomonas oryzicola	strain=RD9SR1	GCA_014269185.2	485876	485876	type	True	87.6129	1204	1716	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	87.1315	1180	1716	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	87.1001	1122	1716	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	86.4833	1233	1716	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	86.4239	1159	1716	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	86.4167	1206	1716	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_013373895.1	2740516	2740516	type	True	85.9064	1211	1716	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_021602025.1	2740516	2740516	type	True	85.8578	1229	1716	95	below_threshold
Pseudomonas defluvii	strain=WCHP16	GCA_001695625.1	1876757	1876757	type	True	81.9928	804	1716	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:31,592] [INFO] DFAST Taxonomy check result was written to GCF_009932375.1_ASM993237v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:31,593] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:31,593] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:31,593] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34383575-b72a-43ca-97b1-f03881158425/dqc_reference/checkm_data
[2024-01-24 11:06:31,594] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:31,645] [INFO] Task started: CheckM
[2024-01-24 11:06:31,645] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009932375.1_ASM993237v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009932375.1_ASM993237v1_genomic.fna/checkm_input GCF_009932375.1_ASM993237v1_genomic.fna/checkm_result
[2024-01-24 11:07:21,461] [INFO] Task succeeded: CheckM
[2024-01-24 11:07:21,462] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:07:21,480] [INFO] ===== Completeness check finished =====
[2024-01-24 11:07:21,480] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:07:21,481] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009932375.1_ASM993237v1_genomic.fna/markers.fasta)
[2024-01-24 11:07:21,481] [INFO] Task started: Blastn
[2024-01-24 11:07:21,481] [INFO] Running command: blastn -query GCF_009932375.1_ASM993237v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34383575-b72a-43ca-97b1-f03881158425/dqc_reference/reference_markers_gtdb.fasta -out GCF_009932375.1_ASM993237v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:07:23,060] [INFO] Task succeeded: Blastn
[2024-01-24 11:07:23,063] [INFO] Selected 23 target genomes.
[2024-01-24 11:07:23,064] [INFO] Target genome list was writen to GCF_009932375.1_ASM993237v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:07:23,077] [INFO] Task started: fastANI
[2024-01-24 11:07:23,077] [INFO] Running command: fastANI --query /var/lib/cwl/stgbcac3046-a1c0-4d13-8f7b-004ca3b9cce5/GCF_009932375.1_ASM993237v1_genomic.fna.gz --refList GCF_009932375.1_ASM993237v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009932375.1_ASM993237v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:54,336] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:54,353] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:07:54,353] [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_009932375.1	s__Pseudomonas_E juntendi	100.0	1702	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.06	97.13	0.84	0.79	41	conclusive
GCF_016658545.1	s__Pseudomonas_E sp016658545	89.457	1256	1716	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_000935045.1	s__Pseudomonas_E sp000935045	88.7657	1235	1716	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_001642705.1	s__Pseudomonas_E sp001642705	88.6768	1229	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.26	95.01	0.89	0.85	3	-
GCF_009932335.1	s__Pseudomonas_E asiatica	88.5282	1307	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0481	97.98	96.05	0.89	0.79	58	-
GCF_003331055.1	s__Pseudomonas_E sp003331055	88.4557	1196	1716	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_003205205.1	s__Pseudomonas_E sp003205205	88.4237	1256	1716	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_013393325.1	s__Pseudomonas_E putida_P	88.3087	1247	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.35	99.27	0.91	0.82	10	-
GCF_900277125.1	s__Pseudomonas_E inefficax	88.2562	1251	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.83	97.08	0.92	0.89	5	-
GCF_000708715.2	s__Pseudomonas_E putida_R	88.2416	1286	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.68	95.68	0.85	0.85	2	-
GCF_002113165.1	s__Pseudomonas_E sp002113165	88.2309	1226	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	3	-
GCF_002165135.1	s__Pseudomonas_E sp002165135	88.2296	1192	1716	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_015680405.1	s__Pseudomonas_E pudica	88.1564	1233	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0481	98.52	95.23	0.90	0.83	12	-
GCF_003671955.1	s__Pseudomonas_E hunanensis	87.8845	1274	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.33	95.26	0.86	0.79	88	-
GCF_002112505.1	s__Pseudomonas_E sp002112505	87.0617	1233	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	0.99	6	-
GCF_002906855.1	s__Pseudomonas_E putida_N	86.7092	1240	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	1.00	1.00	2	-
GCA_003428805.1	s__Pseudomonas_E sp003428805	86.5257	1245	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.29	96.05	0.90	0.83	9	-
GCF_000019445.1	s__Pseudomonas_E putida_E	85.6448	1213	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.71	96.19	0.87	0.82	12	-
GCF_002741075.1	s__Pseudomonas_E putida_T	84.8736	1141	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.21	95.06	0.91	0.90	4	-
GCF_007677725.1	s__Pseudomonas_E sp003445295	84.7644	1137	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.48	98.48	0.95	0.95	2	-
GCF_002806685.1	s__Pseudomonas_E qingdaonensis	83.6256	1051	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.05	98.91	0.93	0.89	13	-
GCF_004327355.1	s__Pseudomonas_E dryadis	80.6074	711	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.58	99.16	0.96	0.92	3	-
GCF_000452705.1	s__Pseudomonas_E syringae_F	79.6715	622	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.97	98.97	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:07:54,355] [INFO] GTDB search result was written to GCF_009932375.1_ASM993237v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:54,355] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:54,359] [INFO] DFAST_QC result json was written to GCF_009932375.1_ASM993237v1_genomic.fna/dqc_result.json
[2024-01-24 11:07:54,359] [INFO] DFAST_QC completed!
[2024-01-24 11:07:54,360] [INFO] Total running time: 0h2m5s