[2024-01-25 19:50:35,427] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:50:35,428] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:50:35,428] [INFO] DQC Reference Directory: /var/lib/cwl/stgea5e0de3-02a7-403c-a636-9e985afa682c/dqc_reference
[2024-01-25 19:50:36,607] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:50:36,608] [INFO] Task started: Prodigal
[2024-01-25 19:50:36,608] [INFO] Running command: gunzip -c /var/lib/cwl/stg8c7c5826-2638-4909-92c1-5c14cb791547/GCF_021147825.1_ASM2114782v1_genomic.fna.gz | prodigal -d GCF_021147825.1_ASM2114782v1_genomic.fna/cds.fna -a GCF_021147825.1_ASM2114782v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:50:53,416] [INFO] Task succeeded: Prodigal
[2024-01-25 19:50:53,417] [INFO] Task started: HMMsearch
[2024-01-25 19:50:53,417] [INFO] Running command: hmmsearch --tblout GCF_021147825.1_ASM2114782v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea5e0de3-02a7-403c-a636-9e985afa682c/dqc_reference/reference_markers.hmm GCF_021147825.1_ASM2114782v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:50:53,691] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:50:53,692] [INFO] Found 6/6 markers.
[2024-01-25 19:50:53,740] [INFO] Query marker FASTA was written to GCF_021147825.1_ASM2114782v1_genomic.fna/markers.fasta
[2024-01-25 19:50:53,740] [INFO] Task started: Blastn
[2024-01-25 19:50:53,741] [INFO] Running command: blastn -query GCF_021147825.1_ASM2114782v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea5e0de3-02a7-403c-a636-9e985afa682c/dqc_reference/reference_markers.fasta -out GCF_021147825.1_ASM2114782v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:50:54,559] [INFO] Task succeeded: Blastn
[2024-01-25 19:50:54,562] [INFO] Selected 35 target genomes.
[2024-01-25 19:50:54,563] [INFO] Target genome list was writen to GCF_021147825.1_ASM2114782v1_genomic.fna/target_genomes.txt
[2024-01-25 19:50:54,592] [INFO] Task started: fastANI
[2024-01-25 19:50:54,592] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c7c5826-2638-4909-92c1-5c14cb791547/GCF_021147825.1_ASM2114782v1_genomic.fna.gz --refList GCF_021147825.1_ASM2114782v1_genomic.fna/target_genomes.txt --output GCF_021147825.1_ASM2114782v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:51:36,321] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:36,321] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea5e0de3-02a7-403c-a636-9e985afa682c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:51:36,322] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea5e0de3-02a7-403c-a636-9e985afa682c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:51:36,340] [INFO] Found 35 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:51:36,340] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:51:36,340] [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 cichorii	strain=ATCC 10857	GCA_900104015.1	36746	36746	suspected-type	True	81.6158	1011	2102	95	below_threshold
Pseudomonas cichorii	strain=LMG 2162	GCA_015471425.1	36746	36746	suspected-type	True	81.6112	1009	2102	95	below_threshold
Pseudomonas cichorii	strain=DSM 50259	GCA_018343775.1	36746	36746	suspected-type	True	81.609	1019	2102	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP3956	GCA_001400635.1	251701	251701	pathovar	True	81.4634	990	2102	95	below_threshold
Pseudomonas avellanae	strain=JCM 11937	GCA_014646595.1	46257	46257	type	True	81.3633	972	2102	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP529	GCA_001400335.1	251701	251701	pathovar	True	81.3623	958	2102	95	below_threshold
Pseudomonas syringae	strain=ICMP 9617	GCA_000658965.1	317	317	pathovar	True	81.3408	1006	2102	95	below_threshold
Pseudomonas avellanae	strain=BPIC 631	GCA_000302915.1	46257	46257	type	True	81.2994	1020	2102	95	below_threshold
Pseudomonas syringae pv. coryli	strain=NCPPB 4273	GCA_000972175.1	317659	317659	pathovar	True	81.2839	989	2102	95	below_threshold
Pseudomonas syringae pv. coryli	strain=ICMP17001	GCA_001400235.1	317659	317659	pathovar	True	81.2746	785	2102	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=DC3000	GCA_000007805.1	251701	251701	type	True	81.2703	1022	2102	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP2814	GCA_001401385.1	251701	251701	pathovar	True	81.27	985	2102	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP4116	GCA_001401405.1	251701	251701	pathovar	True	81.2647	1008	2102	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP8903	GCA_001400595.1	251701	251701	pathovar	True	81.2565	997	2102	95	below_threshold
Pseudomonas syringae	strain=ICMP3023	GCA_001401075.1	317	317	suspected-type	True	81.2341	983	2102	95	below_threshold
Pseudomonas syringae	strain=KCTC 12500	GCA_000507185.2	317	317	suspected-type	True	81.2285	978	2102	95	below_threshold
Pseudomonas abietaniphila	strain=ATCC 700689	GCA_900100795.1	89065	89065	type	True	80.928	988	2102	95	below_threshold
Pseudomonas farris	strain=SWRI79	GCA_019145235.1	2841207	2841207	type	True	80.8109	878	2102	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	80.8108	879	2102	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	80.7471	866	2102	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	80.7227	861	2102	95	below_threshold
Pseudomonas izuensis	strain=IzPS43_3003	GCA_009861505.1	2684212	2684212	type	True	80.6613	774	2102	95	below_threshold
Pseudomonas yamanorum	strain=LMG 27247	GCA_900105735.1	515393	515393	suspected-type	True	80.6043	870	2102	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	80.5258	788	2102	95	below_threshold
Pseudomonas brenneri	strain=DSM 15294	GCA_007858285.1	129817	129817	type	True	80.4772	780	2102	95	below_threshold
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	80.4523	906	2102	95	below_threshold
Pseudomonas brenneri	strain=JCM 13307	GCA_014646715.1	129817	129817	type	True	80.4358	788	2102	95	below_threshold
Pseudomonas batumici	strain=UCM B-321	GCA_000820515.1	226910	226910	type	True	80.3903	791	2102	95	below_threshold
Pseudomonas gessardii	strain=DSM 17152	GCA_009671285.1	78544	78544	type	True	80.3639	803	2102	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	80.1864	608	2102	95	below_threshold
Pseudomonas farsensis	strain=SWRI107	GCA_014268805.2	2745492	2745492	type	True	79.6561	632	2102	95	below_threshold
Pseudomonas sichuanensis	strain=WCHPs060039	GCA_003231305.1	2213015	2213015	type	True	79.6475	635	2102	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_000731675.1	1495066	1495066	type	True	79.6044	645	2102	95	below_threshold
Pseudomonas oryziphila	strain=1257	GCA_003940825.1	2894079	2894079	type	True	79.5157	673	2102	95	below_threshold
Pseudomonas guariconensis	strain=LMG 27394	GCA_900102675.1	1288410	1288410	suspected-type	True	79.1664	583	2102	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:51:36,341] [INFO] DFAST Taxonomy check result was written to GCF_021147825.1_ASM2114782v1_genomic.fna/tc_result.tsv
[2024-01-25 19:51:36,342] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:51:36,342] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:51:36,342] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea5e0de3-02a7-403c-a636-9e985afa682c/dqc_reference/checkm_data
[2024-01-25 19:51:36,343] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:51:36,408] [INFO] Task started: CheckM
[2024-01-25 19:51:36,408] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021147825.1_ASM2114782v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021147825.1_ASM2114782v1_genomic.fna/checkm_input GCF_021147825.1_ASM2114782v1_genomic.fna/checkm_result
[2024-01-25 19:52:26,510] [INFO] Task succeeded: CheckM
[2024-01-25 19:52:26,511] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:52:26,534] [INFO] ===== Completeness check finished =====
[2024-01-25 19:52:26,534] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:52:26,536] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021147825.1_ASM2114782v1_genomic.fna/markers.fasta)
[2024-01-25 19:52:26,536] [INFO] Task started: Blastn
[2024-01-25 19:52:26,536] [INFO] Running command: blastn -query GCF_021147825.1_ASM2114782v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea5e0de3-02a7-403c-a636-9e985afa682c/dqc_reference/reference_markers_gtdb.fasta -out GCF_021147825.1_ASM2114782v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:52:27,882] [INFO] Task succeeded: Blastn
[2024-01-25 19:52:27,885] [INFO] Selected 11 target genomes.
[2024-01-25 19:52:27,885] [INFO] Target genome list was writen to GCF_021147825.1_ASM2114782v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:52:27,907] [INFO] Task started: fastANI
[2024-01-25 19:52:27,907] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c7c5826-2638-4909-92c1-5c14cb791547/GCF_021147825.1_ASM2114782v1_genomic.fna.gz --refList GCF_021147825.1_ASM2114782v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021147825.1_ASM2114782v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:52:46,516] [INFO] Task succeeded: fastANI
[2024-01-25 19:52:46,524] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:52:46,524] [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_002699985.1	s__Pseudomonas_E sp002699985	97.2827	1842	2102	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.02	96.43	0.89	0.87	4	conclusive
GCF_014357575.1	s__Pseudomonas_E foliumensis	91.9881	1581	2102	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.09	98.09	0.93	0.93	2	-
GCF_002158995.1	s__Pseudomonas_E caspiana	88.9	1589	2102	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_900602065.1	s__Pseudomonas_E sp900602065	88.0717	1597	2102	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_900590755.1	s__Pseudomonas_E sp900590755	84.2016	1323	2102	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900475325.1	s__Pseudomonas_E sp900475325	83.8777	1305	2102	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_000737245.1	s__Pseudomonas_E syringae_J	83.677	1245	2102	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003523465.1	s__Pseudomonas_E sp003523465	80.249	373	2102	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_003231305.1	s__Pseudomonas_E sichuanensis	79.603	641	2102	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.11	95.79	0.86	0.83	4	-
GCF_013523165.1	s__Pseudomonas_E entomophila_A	79.0931	544	2102	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_016518545.1	s__Pseudomonas_E sp016518545	78.975	583	2102	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:52:46,525] [INFO] GTDB search result was written to GCF_021147825.1_ASM2114782v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:52:46,526] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:52:46,529] [INFO] DFAST_QC result json was written to GCF_021147825.1_ASM2114782v1_genomic.fna/dqc_result.json
[2024-01-25 19:52:46,529] [INFO] DFAST_QC completed!
[2024-01-25 19:52:46,530] [INFO] Total running time: 0h2m11s