[2024-01-24 13:03:20,695] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:03:20,698] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:03:20,698] [INFO] DQC Reference Directory: /var/lib/cwl/stg4953714b-4b8b-41e6-8258-e356dfbeb281/dqc_reference
[2024-01-24 13:03:21,925] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:03:21,926] [INFO] Task started: Prodigal
[2024-01-24 13:03:21,926] [INFO] Running command: gunzip -c /var/lib/cwl/stg5dcc958f-d68c-403a-a7b0-c30090e10d6e/GCF_005877905.1_ASM587790v1_genomic.fna.gz | prodigal -d GCF_005877905.1_ASM587790v1_genomic.fna/cds.fna -a GCF_005877905.1_ASM587790v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:03:41,552] [INFO] Task succeeded: Prodigal
[2024-01-24 13:03:41,553] [INFO] Task started: HMMsearch
[2024-01-24 13:03:41,553] [INFO] Running command: hmmsearch --tblout GCF_005877905.1_ASM587790v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4953714b-4b8b-41e6-8258-e356dfbeb281/dqc_reference/reference_markers.hmm GCF_005877905.1_ASM587790v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:03:41,910] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:03:41,912] [INFO] Found 6/6 markers.
[2024-01-24 13:03:41,972] [INFO] Query marker FASTA was written to GCF_005877905.1_ASM587790v1_genomic.fna/markers.fasta
[2024-01-24 13:03:41,972] [INFO] Task started: Blastn
[2024-01-24 13:03:41,973] [INFO] Running command: blastn -query GCF_005877905.1_ASM587790v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4953714b-4b8b-41e6-8258-e356dfbeb281/dqc_reference/reference_markers.fasta -out GCF_005877905.1_ASM587790v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:43,029] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:43,034] [INFO] Selected 15 target genomes.
[2024-01-24 13:03:43,035] [INFO] Target genome list was writen to GCF_005877905.1_ASM587790v1_genomic.fna/target_genomes.txt
[2024-01-24 13:03:43,043] [INFO] Task started: fastANI
[2024-01-24 13:03:43,044] [INFO] Running command: fastANI --query /var/lib/cwl/stg5dcc958f-d68c-403a-a7b0-c30090e10d6e/GCF_005877905.1_ASM587790v1_genomic.fna.gz --refList GCF_005877905.1_ASM587790v1_genomic.fna/target_genomes.txt --output GCF_005877905.1_ASM587790v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:04:05,876] [INFO] Task succeeded: fastANI
[2024-01-24 13:04:05,876] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4953714b-4b8b-41e6-8258-e356dfbeb281/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:04:05,877] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4953714b-4b8b-41e6-8258-e356dfbeb281/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:04:05,894] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:04:05,894] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:04:05,894] [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 nicosulfuronedens	strain=LAM1902	GCA_005877905.1	2571105	2571105	type	True	100.0	2148	2156	95	conclusive
Pseudomonas nitroreducens	strain=DSM 14399	GCA_012986245.1	46680	46680	suspected-type	True	91.7528	1806	2156	95	below_threshold
Pseudomonas nitroreducens	strain=NBRC 12694	GCA_002091755.1	46680	46680	suspected-type	True	91.7238	1795	2156	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	86.2804	1520	2156	95	below_threshold
Pseudomonas citronellolis	strain=LMG 18378	GCA_900112375.1	53408	53408	type	True	86.2698	1550	2156	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	86.2485	1508	2156	95	below_threshold
Pseudomonas delhiensis	strain=RLD-1	GCA_900187975.1	366289	366289	type	True	86.1849	1521	2156	95	below_threshold
Pseudomonas knackmussii	strain=B13	GCA_000689415.1	65741	65741	type	True	85.6912	1418	2156	95	below_threshold
Pseudomonas jinjuensis	strain=NBRC 103047	GCA_002091655.1	198616	198616	type	True	85.429	1230	2156	95	below_threshold
Pseudomonas jinjuensis	strain=JCM 21621	GCA_900103845.1	198616	198616	type	True	85.4009	1238	2156	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	82.1512	913	2156	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	82.1074	1050	2156	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	81.9726	1011	2156	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	81.8101	982	2156	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	81.3087	932	2156	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:04:05,896] [INFO] DFAST Taxonomy check result was written to GCF_005877905.1_ASM587790v1_genomic.fna/tc_result.tsv
[2024-01-24 13:04:05,897] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:04:05,897] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:04:05,897] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4953714b-4b8b-41e6-8258-e356dfbeb281/dqc_reference/checkm_data
[2024-01-24 13:04:05,898] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:04:05,964] [INFO] Task started: CheckM
[2024-01-24 13:04:05,965] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005877905.1_ASM587790v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005877905.1_ASM587790v1_genomic.fna/checkm_input GCF_005877905.1_ASM587790v1_genomic.fna/checkm_result
[2024-01-24 13:05:03,410] [INFO] Task succeeded: CheckM
[2024-01-24 13:05:03,412] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:05:03,435] [INFO] ===== Completeness check finished =====
[2024-01-24 13:05:03,436] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:05:03,436] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005877905.1_ASM587790v1_genomic.fna/markers.fasta)
[2024-01-24 13:05:03,437] [INFO] Task started: Blastn
[2024-01-24 13:05:03,437] [INFO] Running command: blastn -query GCF_005877905.1_ASM587790v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4953714b-4b8b-41e6-8258-e356dfbeb281/dqc_reference/reference_markers_gtdb.fasta -out GCF_005877905.1_ASM587790v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:05:05,422] [INFO] Task succeeded: Blastn
[2024-01-24 13:05:05,425] [INFO] Selected 11 target genomes.
[2024-01-24 13:05:05,425] [INFO] Target genome list was writen to GCF_005877905.1_ASM587790v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:05:05,433] [INFO] Task started: fastANI
[2024-01-24 13:05:05,433] [INFO] Running command: fastANI --query /var/lib/cwl/stg5dcc958f-d68c-403a-a7b0-c30090e10d6e/GCF_005877905.1_ASM587790v1_genomic.fna.gz --refList GCF_005877905.1_ASM587790v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005877905.1_ASM587790v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:05:24,734] [INFO] Task succeeded: fastANI
[2024-01-24 13:05:24,751] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:05:24,751] [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_005877905.1	s__Pseudomonas nicosulfuronedens	100.0	2148	2156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000955805.1	s__Pseudomonas sp000955805	93.1105	1862	2156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.94	99.94	0.99	0.99	2	-
GCF_008807415.1	s__Pseudomonas sp002079985	92.8911	1873	2156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	97.48	95.53	0.92	0.91	9	-
GCF_014852585.1	s__Pseudomonas sp014852585	92.2696	1810	2156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000313755.1	s__Pseudomonas nitroreducens_A	92.1684	1699	2156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	96.60	96.60	0.86	0.86	2	-
GCF_002091755.1	s__Pseudomonas nitroreducens	91.7295	1794	2156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	98.47	95.19	0.93	0.83	16	-
GCA_002452115.1	s__Pseudomonas nitroreducens_B	91.393	1504	2156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204515.1	s__Pseudomonas nitritireducens_A	91.3274	1787	2156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016919445.1	s__Pseudomonas sp016919445	90.8424	1778	2156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000349845.1	s__Pseudomonas sp000349845	89.7076	1511	2156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017491605.1	s__Pseudomonas sp017491605	89.5233	1538	2156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:05:24,753] [INFO] GTDB search result was written to GCF_005877905.1_ASM587790v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:05:24,753] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:05:24,757] [INFO] DFAST_QC result json was written to GCF_005877905.1_ASM587790v1_genomic.fna/dqc_result.json
[2024-01-24 13:05:24,757] [INFO] DFAST_QC completed!
[2024-01-24 13:05:24,757] [INFO] Total running time: 0h2m4s