[2024-01-24 11:26:54,312] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:54,316] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:54,316] [INFO] DQC Reference Directory: /var/lib/cwl/stge1bbfd21-d8db-44b7-bd8d-7dee75fb482b/dqc_reference
[2024-01-24 11:26:58,221] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:58,223] [INFO] Task started: Prodigal
[2024-01-24 11:26:58,224] [INFO] Running command: gunzip -c /var/lib/cwl/stg7e9e81a5-7e72-4911-90fc-224868f1159a/GCF_014863585.1_ASM1486358v1_genomic.fna.gz | prodigal -d GCF_014863585.1_ASM1486358v1_genomic.fna/cds.fna -a GCF_014863585.1_ASM1486358v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:22,212] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:22,212] [INFO] Task started: HMMsearch
[2024-01-24 11:27:22,212] [INFO] Running command: hmmsearch --tblout GCF_014863585.1_ASM1486358v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1bbfd21-d8db-44b7-bd8d-7dee75fb482b/dqc_reference/reference_markers.hmm GCF_014863585.1_ASM1486358v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:22,543] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:22,545] [INFO] Found 6/6 markers.
[2024-01-24 11:27:22,599] [INFO] Query marker FASTA was written to GCF_014863585.1_ASM1486358v1_genomic.fna/markers.fasta
[2024-01-24 11:27:22,600] [INFO] Task started: Blastn
[2024-01-24 11:27:22,600] [INFO] Running command: blastn -query GCF_014863585.1_ASM1486358v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1bbfd21-d8db-44b7-bd8d-7dee75fb482b/dqc_reference/reference_markers.fasta -out GCF_014863585.1_ASM1486358v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:23,642] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:23,646] [INFO] Selected 15 target genomes.
[2024-01-24 11:27:23,646] [INFO] Target genome list was writen to GCF_014863585.1_ASM1486358v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:23,655] [INFO] Task started: fastANI
[2024-01-24 11:27:23,655] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e9e81a5-7e72-4911-90fc-224868f1159a/GCF_014863585.1_ASM1486358v1_genomic.fna.gz --refList GCF_014863585.1_ASM1486358v1_genomic.fna/target_genomes.txt --output GCF_014863585.1_ASM1486358v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:48,532] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:48,532] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1bbfd21-d8db-44b7-bd8d-7dee75fb482b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:48,533] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1bbfd21-d8db-44b7-bd8d-7dee75fb482b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:48,544] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:27:48,545] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:27:48,545] [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 pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	93.8184	1835	2187	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	93.5671	1785	2187	95	below_threshold
Pseudomonas allokribbensis	strain=IzPS23	GCA_014863605.1	2774460	2774460	type	True	91.9829	1854	2187	95	below_threshold
Pseudomonas kribbensis	strain=46-2	GCA_003352185.1	1628086	1628086	type	True	91.8141	1818	2187	95	below_threshold
Pseudomonas bananamidigenes	strain=BW11P2	GCA_001679645.1	2843610	2843610	type	True	90.3808	1680	2187	95	below_threshold
Pseudomonas koreensis	strain=DSM 16610	GCA_012986595.1	198620	198620	suspected-type	True	88.8228	1714	2187	95	below_threshold
Pseudomonas koreensis	strain=JCM 14769	GCA_014646955.1	198620	198620	suspected-type	True	88.7872	1723	2187	95	below_threshold
Pseudomonas monsensis	strain=PGSB 8459	GCA_014268495.2	2745509	2745509	type	True	88.3854	1735	2187	95	below_threshold
Pseudomonas neuropathica	strain=P155	GCA_015461835.1	2730425	2730425	type	True	88.1363	1741	2187	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	88.1065	1737	2187	95	below_threshold
Pseudomonas crudilactis	strain=UCMA 17988	GCA_013433315.1	2697028	2697028	type	True	88.0731	1740	2187	95	below_threshold
Pseudomonas atacamensis	strain=M7D1	GCA_004801935.1	2565368	2565368	type	True	87.6573	1575	2187	95	below_threshold
Pseudomonas moorei	strain=CCUG 53114	GCA_008801475.1	395599	395599	type	True	85.974	1425	2187	95	below_threshold
Pseudomonas rhizophila	strain=S211	GCA_003033885.1	2045200	2045200	type	True	84.2551	1281	2187	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	83.7621	1294	2187	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:48,546] [INFO] DFAST Taxonomy check result was written to GCF_014863585.1_ASM1486358v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:48,547] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:48,547] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:48,547] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1bbfd21-d8db-44b7-bd8d-7dee75fb482b/dqc_reference/checkm_data
[2024-01-24 11:27:48,548] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:48,605] [INFO] Task started: CheckM
[2024-01-24 11:27:48,605] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014863585.1_ASM1486358v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014863585.1_ASM1486358v1_genomic.fna/checkm_input GCF_014863585.1_ASM1486358v1_genomic.fna/checkm_result
[2024-01-24 11:29:01,526] [INFO] Task succeeded: CheckM
[2024-01-24 11:29:01,528] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:29:01,552] [INFO] ===== Completeness check finished =====
[2024-01-24 11:29:01,553] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:29:01,553] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014863585.1_ASM1486358v1_genomic.fna/markers.fasta)
[2024-01-24 11:29:01,553] [INFO] Task started: Blastn
[2024-01-24 11:29:01,553] [INFO] Running command: blastn -query GCF_014863585.1_ASM1486358v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1bbfd21-d8db-44b7-bd8d-7dee75fb482b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014863585.1_ASM1486358v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:29:03,502] [INFO] Task succeeded: Blastn
[2024-01-24 11:29:03,506] [INFO] Selected 9 target genomes.
[2024-01-24 11:29:03,507] [INFO] Target genome list was writen to GCF_014863585.1_ASM1486358v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:29:03,514] [INFO] Task started: fastANI
[2024-01-24 11:29:03,515] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e9e81a5-7e72-4911-90fc-224868f1159a/GCF_014863585.1_ASM1486358v1_genomic.fna.gz --refList GCF_014863585.1_ASM1486358v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014863585.1_ASM1486358v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:29:19,721] [INFO] Task succeeded: fastANI
[2024-01-24 11:29:19,732] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:29:19,732] [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_014863585.1	s__Pseudomonas_E gozinkensis	100.0	2183	2187	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004006335.1	s__Pseudomonas_E sp002112885	94.7503	1910	2187	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.01	95.48	0.92	0.90	14	-
GCF_003352875.1	s__Pseudomonas_E fluorescens_BF	94.2702	1901	2187	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_010448615.1	s__Pseudomonas_E sp001655595	94.0342	1885	2187	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.61	96.24	0.94	0.90	22	-
GCF_001594225.2	s__Pseudomonas_E glycinae	93.8096	1834	2187	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.56	95.98	0.93	0.88	9	-
GCF_002113125.1	s__Pseudomonas_E sp002113125	93.7473	1831	2187	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_002113045.1	s__Pseudomonas_E sp002113045	93.4699	1797	2187	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.93	98.93	0.93	0.93	2	-
GCF_014863605.1	s__Pseudomonas_E allokribbensis	91.9894	1854	2187	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.79	97.76	0.93	0.92	10	-
GCF_003352185.1	s__Pseudomonas_E kribbensis	91.8123	1817	2187	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.22	95.68	0.92	0.89	10	-
--------------------------------------------------------------------------------
[2024-01-24 11:29:19,734] [INFO] GTDB search result was written to GCF_014863585.1_ASM1486358v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:29:19,734] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:29:19,738] [INFO] DFAST_QC result json was written to GCF_014863585.1_ASM1486358v1_genomic.fna/dqc_result.json
[2024-01-24 11:29:19,738] [INFO] DFAST_QC completed!
[2024-01-24 11:29:19,738] [INFO] Total running time: 0h2m25s