[2024-01-24 13:46:26,082] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:26,085] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:26,085] [INFO] DQC Reference Directory: /var/lib/cwl/stgc4afe9b8-b929-4c0f-82aa-fa1b9273073a/dqc_reference
[2024-01-24 13:46:27,734] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:27,735] [INFO] Task started: Prodigal
[2024-01-24 13:46:27,735] [INFO] Running command: gunzip -c /var/lib/cwl/stg295adbfe-c954-407f-999f-bc8363fac1df/GCF_007858155.1_ASM785815v1_genomic.fna.gz | prodigal -d GCF_007858155.1_ASM785815v1_genomic.fna/cds.fna -a GCF_007858155.1_ASM785815v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:48,844] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:48,844] [INFO] Task started: HMMsearch
[2024-01-24 13:46:48,844] [INFO] Running command: hmmsearch --tblout GCF_007858155.1_ASM785815v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc4afe9b8-b929-4c0f-82aa-fa1b9273073a/dqc_reference/reference_markers.hmm GCF_007858155.1_ASM785815v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:49,255] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:49,256] [INFO] Found 6/6 markers.
[2024-01-24 13:46:49,325] [INFO] Query marker FASTA was written to GCF_007858155.1_ASM785815v1_genomic.fna/markers.fasta
[2024-01-24 13:46:49,325] [INFO] Task started: Blastn
[2024-01-24 13:46:49,325] [INFO] Running command: blastn -query GCF_007858155.1_ASM785815v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4afe9b8-b929-4c0f-82aa-fa1b9273073a/dqc_reference/reference_markers.fasta -out GCF_007858155.1_ASM785815v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:50,186] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:50,189] [INFO] Selected 24 target genomes.
[2024-01-24 13:46:50,190] [INFO] Target genome list was writen to GCF_007858155.1_ASM785815v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:50,207] [INFO] Task started: fastANI
[2024-01-24 13:46:50,207] [INFO] Running command: fastANI --query /var/lib/cwl/stg295adbfe-c954-407f-999f-bc8363fac1df/GCF_007858155.1_ASM785815v1_genomic.fna.gz --refList GCF_007858155.1_ASM785815v1_genomic.fna/target_genomes.txt --output GCF_007858155.1_ASM785815v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:26,514] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:26,515] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc4afe9b8-b929-4c0f-82aa-fa1b9273073a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:26,515] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc4afe9b8-b929-4c0f-82aa-fa1b9273073a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:26,528] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:26,528] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:26,528] [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 marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	100.0	2348	2356	95	conclusive
Pseudomonas marginalis	strain=ICMP 3553	GCA_003700725.1	298	298	suspected-type	True	89.4756	1639	2356	95	below_threshold
Pseudomonas marginalis	strain=ICMP 3553	GCA_001645105.1	298	298	suspected-type	True	89.4044	1730	2356	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	89.1172	1688	2356	95	below_threshold
Pseudomonas asgharzadehiana	strain=SWRI132	GCA_019139815.1	2842349	2842349	type	True	89.0183	1650	2356	95	below_threshold
Pseudomonas lactucae	strain=MAFF 301380	GCA_016937615.1	2813360	2813360	type	True	88.9792	1533	2356	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	88.8129	1646	2356	95	below_threshold
Pseudomonas canadensis	strain=2-92	GCA_000503215.1	915099	915099	type	True	88.8119	1655	2356	95	below_threshold
Pseudomonas simiae	strain=CCUG 50988	GCA_001730615.1	321846	321846	type	True	88.7958	1639	2356	95	below_threshold
Pseudomonas simiae	strain=CCUG 50988	GCA_900111895.1	321846	321846	type	True	88.7549	1644	2356	95	below_threshold
Pseudomonas nabeulensis	strain=E10B	GCA_004682045.1	2293833	2293833	type	True	88.5891	1596	2356	95	below_threshold
Pseudomonas kairouanensis	strain=KC12	GCA_004682055.1	2293832	2293832	type	True	88.5489	1625	2356	95	below_threshold
Pseudomonas salomonii	strain=LMG 22120	GCA_001730645.1	191391	191391	type	True	88.3567	1659	2356	95	below_threshold
Pseudomonas cremoris	strain=WS 5106	GCA_014230465.1	2724178	2724178	type	True	88.337	1652	2356	95	below_threshold
Pseudomonas salomonii	strain=ICMP 14252	GCA_900107155.1	191391	191391	type	True	88.3087	1641	2356	95	below_threshold
Pseudomonas fluorescens	strain=DSM 50090	GCA_001269845.1	294	294	suspected-type	True	88.2565	1601	2356	95	below_threshold
Pseudomonas fluorescens	strain=DSM 50090	GCA_007858165.1	294	294	suspected-type	True	88.2431	1594	2356	95	below_threshold
Pseudomonas fluorescens	strain=NBRC 14160	GCA_002091595.1	294	294	suspected-type	True	88.2423	1579	2356	95	below_threshold
Pseudomonas fluorescens	strain=NCTC10038	GCA_900475215.1	294	294	suspected-type	True	88.1505	1619	2356	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	86.1839	1480	2356	95	below_threshold
Pseudomonas karstica	strain=CCM 7891	GCA_009707515.1	1055468	1055468	type	True	85.4741	1327	2356	95	below_threshold
Marinobacter orientalis	strain=W62	GCA_012956055.1	1928859	1928859	type	True	76.3239	103	2356	95	below_threshold
Marinobacter orientalis	strain=W62	GCA_004792665.1	1928859	1928859	type	True	75.9061	98	2356	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:26,530] [INFO] DFAST Taxonomy check result was written to GCF_007858155.1_ASM785815v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:26,530] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:26,530] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:26,530] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc4afe9b8-b929-4c0f-82aa-fa1b9273073a/dqc_reference/checkm_data
[2024-01-24 13:47:26,531] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:26,593] [INFO] Task started: CheckM
[2024-01-24 13:47:26,594] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007858155.1_ASM785815v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007858155.1_ASM785815v1_genomic.fna/checkm_input GCF_007858155.1_ASM785815v1_genomic.fna/checkm_result
[2024-01-24 13:48:27,024] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:27,025] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:27,041] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:27,041] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:27,042] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007858155.1_ASM785815v1_genomic.fna/markers.fasta)
[2024-01-24 13:48:27,042] [INFO] Task started: Blastn
[2024-01-24 13:48:27,042] [INFO] Running command: blastn -query GCF_007858155.1_ASM785815v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4afe9b8-b929-4c0f-82aa-fa1b9273073a/dqc_reference/reference_markers_gtdb.fasta -out GCF_007858155.1_ASM785815v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:28,508] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:28,511] [INFO] Selected 14 target genomes.
[2024-01-24 13:48:28,511] [INFO] Target genome list was writen to GCF_007858155.1_ASM785815v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:28,522] [INFO] Task started: fastANI
[2024-01-24 13:48:28,522] [INFO] Running command: fastANI --query /var/lib/cwl/stg295adbfe-c954-407f-999f-bc8363fac1df/GCF_007858155.1_ASM785815v1_genomic.fna.gz --refList GCF_007858155.1_ASM785815v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007858155.1_ASM785815v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:54,303] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:54,312] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:54,313] [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_900105325.1	s__Pseudomonas_E marginalis	99.9979	2356	2356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.53	96.47	0.90	0.85	19	conclusive
GCF_014207255.1	s__Pseudomonas_E sp014207255	94.5268	1883	2356	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_007858185.1	s__Pseudomonas_E grimontii	93.9783	1854	2356	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_001269925.1	s__Pseudomonas_E sp001269925	93.747	1836	2356	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_009866765.1	s__Pseudomonas_E sp009866765	89.896	1754	2356	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_003097075.1	s__Pseudomonas_E sp003097075	89.7755	1667	2356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.77	98.77	0.94	0.94	2	-
GCF_002843605.1	s__Pseudomonas_E sp002843605	89.5622	1731	2356	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_001439695.1	s__Pseudomonas_E veronii	88.9413	1644	2356	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_001186335.1	s__Pseudomonas_E trivialis_B	88.9371	1739	2356	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_002563895.1	s__Pseudomonas_E lurida	88.8217	1645	2356	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_900111895.1	s__Pseudomonas_E simiae	88.7549	1644	2356	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_009659625.1	s__Pseudomonas_E haemolytica	88.219	1545	2356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.47	98.83	0.97	0.95	8	-
GCF_900215245.1	s__Pseudomonas_E fluorescens	88.1787	1615	2356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	99.25	0.98	0.92	14	-
GCF_001439815.1	s__Pseudomonas_E orientalis	87.9865	1576	2356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.01	96.05	0.91	0.89	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:48:54,314] [INFO] GTDB search result was written to GCF_007858155.1_ASM785815v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:54,314] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:54,318] [INFO] DFAST_QC result json was written to GCF_007858155.1_ASM785815v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:54,318] [INFO] DFAST_QC completed!
[2024-01-24 13:48:54,318] [INFO] Total running time: 0h2m28s