[2024-01-24 13:10:19,395] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:10:19,397] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:10:19,397] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2a4dcd3-4957-4ee6-947e-52bb62a1e12e/dqc_reference
[2024-01-24 13:10:20,691] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:10:20,692] [INFO] Task started: Prodigal
[2024-01-24 13:10:20,692] [INFO] Running command: gunzip -c /var/lib/cwl/stgf56b4b01-efdf-44d8-b48d-8d6611e19e5f/GCF_021602155.1_ASM2160215v1_genomic.fna.gz | prodigal -d GCF_021602155.1_ASM2160215v1_genomic.fna/cds.fna -a GCF_021602155.1_ASM2160215v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:44,164] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:44,165] [INFO] Task started: HMMsearch
[2024-01-24 13:10:44,165] [INFO] Running command: hmmsearch --tblout GCF_021602155.1_ASM2160215v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2a4dcd3-4957-4ee6-947e-52bb62a1e12e/dqc_reference/reference_markers.hmm GCF_021602155.1_ASM2160215v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:44,495] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:44,497] [INFO] Found 6/6 markers.
[2024-01-24 13:10:44,554] [INFO] Query marker FASTA was written to GCF_021602155.1_ASM2160215v1_genomic.fna/markers.fasta
[2024-01-24 13:10:44,554] [INFO] Task started: Blastn
[2024-01-24 13:10:44,554] [INFO] Running command: blastn -query GCF_021602155.1_ASM2160215v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2a4dcd3-4957-4ee6-947e-52bb62a1e12e/dqc_reference/reference_markers.fasta -out GCF_021602155.1_ASM2160215v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:45,692] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:45,696] [INFO] Selected 19 target genomes.
[2024-01-24 13:10:45,697] [INFO] Target genome list was writen to GCF_021602155.1_ASM2160215v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:45,711] [INFO] Task started: fastANI
[2024-01-24 13:10:45,711] [INFO] Running command: fastANI --query /var/lib/cwl/stgf56b4b01-efdf-44d8-b48d-8d6611e19e5f/GCF_021602155.1_ASM2160215v1_genomic.fna.gz --refList GCF_021602155.1_ASM2160215v1_genomic.fna/target_genomes.txt --output GCF_021602155.1_ASM2160215v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:11:14,623] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:14,624] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2a4dcd3-4957-4ee6-947e-52bb62a1e12e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:11:14,625] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2a4dcd3-4957-4ee6-947e-52bb62a1e12e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:11:14,651] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:11:14,651] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:11:14,651] [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 koreensis	strain=CCUG 51519	GCA_008801535.1	198620	198620	suspected-type	True	91.7684	1726	2041	95	below_threshold
Pseudomonas koreensis	strain=DSM 16610	GCA_012986595.1	198620	198620	suspected-type	True	91.7654	1725	2041	95	below_threshold
Pseudomonas koreensis	strain=JCM 14769	GCA_014646955.1	198620	198620	suspected-type	True	91.7189	1747	2041	95	below_threshold
Pseudomonas monsensis	strain=PGSB 8459	GCA_014268495.2	2745509	2745509	type	True	89.6799	1673	2041	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	88.7672	1695	2041	95	below_threshold
Pseudomonas kribbensis	strain=46-2	GCA_003352185.1	1628086	1628086	type	True	88.7453	1650	2041	95	below_threshold
Pseudomonas allokribbensis	strain=IzPS23	GCA_014863605.1	2774460	2774460	type	True	88.7058	1662	2041	95	below_threshold
Pseudomonas crudilactis	strain=UCMA 17988	GCA_013433315.1	2697028	2697028	type	True	88.6924	1679	2041	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	88.6816	1648	2041	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	88.6136	1598	2041	95	below_threshold
Pseudomonas iranensis	strain=SWRI54	GCA_014268585.2	2745503	2745503	type	True	87.9263	1559	2041	95	below_threshold
Pseudomonas atacamensis	strain=M7D1	GCA_004801935.1	2565368	2565368	type	True	87.9263	1570	2041	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	83.3797	1266	2041	95	below_threshold
Pseudomonas karstica	strain=CCM 7891	GCA_009707515.1	1055468	1055468	type	True	82.6371	1126	2041	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	82.1805	870	2041	95	below_threshold
Pseudomonas mosselii	strain=DSM 17497	GCA_019823065.1	78327	78327	type	True	81.7374	1050	2041	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_021602025.1	2740516	2740516	type	True	81.1383	912	2041	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_013373895.1	2740516	2740516	type	True	81.0801	912	2041	95	below_threshold
Halomonas cerina	strain=CECT 7282	GCA_014192215.1	447424	447424	type	True	76.1189	132	2041	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:11:14,653] [INFO] DFAST Taxonomy check result was written to GCF_021602155.1_ASM2160215v1_genomic.fna/tc_result.tsv
[2024-01-24 13:11:14,653] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:11:14,653] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:11:14,654] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2a4dcd3-4957-4ee6-947e-52bb62a1e12e/dqc_reference/checkm_data
[2024-01-24 13:11:14,655] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:11:14,715] [INFO] Task started: CheckM
[2024-01-24 13:11:14,715] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021602155.1_ASM2160215v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021602155.1_ASM2160215v1_genomic.fna/checkm_input GCF_021602155.1_ASM2160215v1_genomic.fna/checkm_result
[2024-01-24 13:12:23,474] [INFO] Task succeeded: CheckM
[2024-01-24 13:12:23,476] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:12:23,500] [INFO] ===== Completeness check finished =====
[2024-01-24 13:12:23,500] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:12:23,500] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021602155.1_ASM2160215v1_genomic.fna/markers.fasta)
[2024-01-24 13:12:23,501] [INFO] Task started: Blastn
[2024-01-24 13:12:23,501] [INFO] Running command: blastn -query GCF_021602155.1_ASM2160215v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2a4dcd3-4957-4ee6-947e-52bb62a1e12e/dqc_reference/reference_markers_gtdb.fasta -out GCF_021602155.1_ASM2160215v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:25,036] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:25,041] [INFO] Selected 16 target genomes.
[2024-01-24 13:12:25,041] [INFO] Target genome list was writen to GCF_021602155.1_ASM2160215v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:12:25,055] [INFO] Task started: fastANI
[2024-01-24 13:12:25,055] [INFO] Running command: fastANI --query /var/lib/cwl/stgf56b4b01-efdf-44d8-b48d-8d6611e19e5f/GCF_021602155.1_ASM2160215v1_genomic.fna.gz --refList GCF_021602155.1_ASM2160215v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021602155.1_ASM2160215v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:12:52,170] [INFO] Task succeeded: fastANI
[2024-01-24 13:12:52,187] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:12:52,187] [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_002287825.1	s__Pseudomonas_E koreensis_B	98.6261	1877	2041	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.58	96.55	0.92	0.86	13	conclusive
GCF_004683905.1	s__Pseudomonas_E putida_A	93.4002	1806	2041	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.80	95.08	0.93	0.90	22	-
GCF_000631985.1	s__Pseudomonas_E sp000631985	93.2522	1765	2041	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_000282275.2	s__Pseudomonas_E sp000282275	93.1562	1758	2041	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_000292795.1	s__Pseudomonas_E fluorescens_H	92.4064	1758	2041	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.99	97.99	0.94	0.93	3	-
GCF_003061005.1	s__Pseudomonas_E sp003061005	92.3004	1625	2041	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_012986595.1	s__Pseudomonas_E koreensis	91.7728	1723	2041	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.85	97.85	0.96	0.91	8	-
GCF_003999415.1	s__Pseudomonas_E koreensis_E	91.762	1716	2041	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.57	98.57	0.92	0.92	2	-
GCF_002878485.1	s__Pseudomonas_E sp002878485	91.4973	1679	2041	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_000633255.1	s__Pseudomonas_E sp000633255	91.168	1711	2041	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_014268495.2	s__Pseudomonas_E fluorescens_BC	89.6568	1676	2041	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.66	98.66	0.95	0.95	2	-
GCF_018326005.1	s__Pseudomonas_E sp002901475	88.9048	1690	2041	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.45	98.45	0.94	0.94	2	-
GCF_014472415.1	s__Pseudomonas_E sp014472415	88.818	1572	2041	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_900580865.1	s__Pseudomonas_E sp900580865	88.7552	1684	2041	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_009834515.1	s__Pseudomonas_E sp009834515	88.6606	1692	2041	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_900636825.1	s__Pseudomonas_E fluorescens_BG	87.2846	1532	2041	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:12:52,189] [INFO] GTDB search result was written to GCF_021602155.1_ASM2160215v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:12:52,189] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:12:52,196] [INFO] DFAST_QC result json was written to GCF_021602155.1_ASM2160215v1_genomic.fna/dqc_result.json
[2024-01-24 13:12:52,196] [INFO] DFAST_QC completed!
[2024-01-24 13:12:52,197] [INFO] Total running time: 0h2m33s