[2024-01-25 20:01:35,493] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:01:35,494] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:01:35,494] [INFO] DQC Reference Directory: /var/lib/cwl/stg67e118ae-b1e7-44c7-a58b-89ce61cd98a7/dqc_reference
[2024-01-25 20:01:36,661] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:01:36,662] [INFO] Task started: Prodigal
[2024-01-25 20:01:36,662] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ea194fc-6eb1-4309-aef4-c42366970470/GCF_001042915.1_G8690_genomic.fna.gz | prodigal -d GCF_001042915.1_G8690_genomic.fna/cds.fna -a GCF_001042915.1_G8690_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:01:50,634] [INFO] Task succeeded: Prodigal
[2024-01-25 20:01:50,635] [INFO] Task started: HMMsearch
[2024-01-25 20:01:50,635] [INFO] Running command: hmmsearch --tblout GCF_001042915.1_G8690_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67e118ae-b1e7-44c7-a58b-89ce61cd98a7/dqc_reference/reference_markers.hmm GCF_001042915.1_G8690_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:01:50,983] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:01:50,984] [INFO] Found 6/6 markers.
[2024-01-25 20:01:51,032] [INFO] Query marker FASTA was written to GCF_001042915.1_G8690_genomic.fna/markers.fasta
[2024-01-25 20:01:51,032] [INFO] Task started: Blastn
[2024-01-25 20:01:51,032] [INFO] Running command: blastn -query GCF_001042915.1_G8690_genomic.fna/markers.fasta -db /var/lib/cwl/stg67e118ae-b1e7-44c7-a58b-89ce61cd98a7/dqc_reference/reference_markers.fasta -out GCF_001042915.1_G8690_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:01:51,915] [INFO] Task succeeded: Blastn
[2024-01-25 20:01:51,918] [INFO] Selected 15 target genomes.
[2024-01-25 20:01:51,918] [INFO] Target genome list was writen to GCF_001042915.1_G8690_genomic.fna/target_genomes.txt
[2024-01-25 20:01:51,934] [INFO] Task started: fastANI
[2024-01-25 20:01:51,934] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ea194fc-6eb1-4309-aef4-c42366970470/GCF_001042915.1_G8690_genomic.fna.gz --refList GCF_001042915.1_G8690_genomic.fna/target_genomes.txt --output GCF_001042915.1_G8690_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:02:09,310] [INFO] Task succeeded: fastANI
[2024-01-25 20:02:09,310] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67e118ae-b1e7-44c7-a58b-89ce61cd98a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:02:09,311] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67e118ae-b1e7-44c7-a58b-89ce61cd98a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:02:09,321] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:02:09,321] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:02:09,321] [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 taetrolens	strain=DSM 21104	GCA_001042915.1	47884	47884	type	True	100.0	1627	1628	95	conclusive
Pseudomonas taetrolens	strain=NCTC10697	GCA_900475285.1	47884	47884	type	True	99.9624	1594	1628	95	conclusive
Pseudomonas deceptionensis	strain=LMG 25555	GCA_900106095.1	882211	882211	type	True	85.3695	1174	1628	95	below_threshold
Pseudomonas deceptionensis	strain=DSM 26521	GCA_001042895.1	882211	882211	type	True	85.3278	1183	1628	95	below_threshold
Pseudomonas fragi	strain=NRRL B-727	GCA_900105835.1	296	296	type	True	84.9405	1140	1628	95	below_threshold
Pseudomonas fragi	strain=NBRC 3458	GCA_002091615.1	296	296	type	True	84.8985	1128	1628	95	below_threshold
Pseudomonas helleri	strain=DSM 29165	GCA_001043025.1	1608996	1608996	type	True	83.9722	1064	1628	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	81.55	879	1628	95	below_threshold
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	81.4382	894	1628	95	below_threshold
Pseudomonas jessenii	strain=DSM 17150	GCA_002236115.1	77298	77298	suspected-type	True	81.4192	889	1628	95	below_threshold
Pseudomonas reinekei	strain=MT1	GCA_001945365.1	395598	395598	type	True	81.4181	882	1628	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	81.4165	858	1628	95	below_threshold
Pseudomonas reinekei	strain=CCUG 53116	GCA_008801455.1	395598	395598	type	True	81.3957	886	1628	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	81.2334	878	1628	95	below_threshold
Pseudomonas amygdali	strain=DSM 105780	GCA_022828345.1	47877	47877	pathovar	True	80.1411	615	1628	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:02:09,323] [INFO] DFAST Taxonomy check result was written to GCF_001042915.1_G8690_genomic.fna/tc_result.tsv
[2024-01-25 20:02:09,323] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:02:09,323] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:02:09,323] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67e118ae-b1e7-44c7-a58b-89ce61cd98a7/dqc_reference/checkm_data
[2024-01-25 20:02:09,324] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:02:09,370] [INFO] Task started: CheckM
[2024-01-25 20:02:09,370] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001042915.1_G8690_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001042915.1_G8690_genomic.fna/checkm_input GCF_001042915.1_G8690_genomic.fna/checkm_result
[2024-01-25 20:02:51,644] [INFO] Task succeeded: CheckM
[2024-01-25 20:02:51,645] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:02:51,669] [INFO] ===== Completeness check finished =====
[2024-01-25 20:02:51,669] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:02:51,669] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001042915.1_G8690_genomic.fna/markers.fasta)
[2024-01-25 20:02:51,670] [INFO] Task started: Blastn
[2024-01-25 20:02:51,670] [INFO] Running command: blastn -query GCF_001042915.1_G8690_genomic.fna/markers.fasta -db /var/lib/cwl/stg67e118ae-b1e7-44c7-a58b-89ce61cd98a7/dqc_reference/reference_markers_gtdb.fasta -out GCF_001042915.1_G8690_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:02:53,287] [INFO] Task succeeded: Blastn
[2024-01-25 20:02:53,290] [INFO] Selected 18 target genomes.
[2024-01-25 20:02:53,290] [INFO] Target genome list was writen to GCF_001042915.1_G8690_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:02:53,322] [INFO] Task started: fastANI
[2024-01-25 20:02:53,322] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ea194fc-6eb1-4309-aef4-c42366970470/GCF_001042915.1_G8690_genomic.fna.gz --refList GCF_001042915.1_G8690_genomic.fna/target_genomes_gtdb.txt --output GCF_001042915.1_G8690_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:03:15,254] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:15,265] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:03:15,265] [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_900475285.1	s__Pseudomonas_E taetrolens	99.9624	1594	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.98	0.99	0.99	4	conclusive
GCF_900106095.1	s__Pseudomonas_E deceptionensis	85.375	1173	1628	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_900105835.1	s__Pseudomonas_E fragi	84.9332	1141	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.76	96.96	0.94	0.89	28	-
GCF_904063065.1	s__Pseudomonas_E paraversuta	84.8768	1165	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.24	99.22	0.95	0.95	9	-
GCF_002269505.1	s__Pseudomonas_E fragi_D	84.8518	1114	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.09	96.09	0.88	0.88	2	-
GCF_900618535.1	s__Pseudomonas_E bubulae	84.712	1125	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.12	98.96	0.92	0.87	18	-
GCF_000282975.1	s__Pseudomonas_E psychrophila_A	83.7298	1036	1628	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_001043055.1	s__Pseudomonas_E weihenstephanensis	83.7089	1026	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.02	97.13	0.92	0.88	6	-
GCF_009600315.1	s__Pseudomonas_E helleri_A	83.3441	1048	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.82	99.80	0.94	0.93	4	-
GCF_007858365.1	s__Pseudomonas_E saxonica	83.2387	1066	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.82	98.82	0.90	0.90	2	-
GCF_000282415.1	s__Pseudomonas_E sp000282415	81.6753	862	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.45	97.21	0.89	0.87	6	-
GCF_000802965.1	s__Pseudomonas_E fluorescens_A	81.6098	849	1628	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_002303925.1	s__Pseudomonas_E sp002303925	81.5378	875	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.04	99.04	0.91	0.91	2	-
GCF_018502625.1	s__Pseudomonas_E fluorescens_BW	81.4973	887	1628	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_002091715.1	s__Pseudomonas_E migulae	81.4473	874	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.54	99.09	0.95	0.90	3	-
GCF_016650695.1	s__Pseudomonas_E sp016650695	81.4363	869	1628	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_002236115.1	s__Pseudomonas_E jessenii	81.4321	888	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.88	96.89	0.89	0.84	18	-
GCF_016909445.1	s__Pseudomonas_E stutzeri_A	81.3789	867	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.88	96.88	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:03:15,266] [INFO] GTDB search result was written to GCF_001042915.1_G8690_genomic.fna/result_gtdb.tsv
[2024-01-25 20:03:15,267] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:03:15,270] [INFO] DFAST_QC result json was written to GCF_001042915.1_G8690_genomic.fna/dqc_result.json
[2024-01-25 20:03:15,270] [INFO] DFAST_QC completed!
[2024-01-25 20:03:15,270] [INFO] Total running time: 0h1m40s