[2024-01-24 15:02:18,655] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:18,656] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:18,656] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e6a5976-62d7-4123-8a41-6f54c7434575/dqc_reference
[2024-01-24 15:02:22,118] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:22,119] [INFO] Task started: Prodigal
[2024-01-24 15:02:22,119] [INFO] Running command: gunzip -c /var/lib/cwl/stg044fb462-0c88-43b8-9c73-9399f6b4375b/GCF_003054775.1_ASM305477v1_genomic.fna.gz | prodigal -d GCF_003054775.1_ASM305477v1_genomic.fna/cds.fna -a GCF_003054775.1_ASM305477v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:33,687] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:33,688] [INFO] Task started: HMMsearch
[2024-01-24 15:02:33,688] [INFO] Running command: hmmsearch --tblout GCF_003054775.1_ASM305477v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e6a5976-62d7-4123-8a41-6f54c7434575/dqc_reference/reference_markers.hmm GCF_003054775.1_ASM305477v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:33,942] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:33,943] [INFO] Found 6/6 markers.
[2024-01-24 15:02:33,975] [INFO] Query marker FASTA was written to GCF_003054775.1_ASM305477v1_genomic.fna/markers.fasta
[2024-01-24 15:02:33,976] [INFO] Task started: Blastn
[2024-01-24 15:02:33,976] [INFO] Running command: blastn -query GCF_003054775.1_ASM305477v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e6a5976-62d7-4123-8a41-6f54c7434575/dqc_reference/reference_markers.fasta -out GCF_003054775.1_ASM305477v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:34,809] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:34,814] [INFO] Selected 17 target genomes.
[2024-01-24 15:02:34,814] [INFO] Target genome list was writen to GCF_003054775.1_ASM305477v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:34,894] [INFO] Task started: fastANI
[2024-01-24 15:02:34,895] [INFO] Running command: fastANI --query /var/lib/cwl/stg044fb462-0c88-43b8-9c73-9399f6b4375b/GCF_003054775.1_ASM305477v1_genomic.fna.gz --refList GCF_003054775.1_ASM305477v1_genomic.fna/target_genomes.txt --output GCF_003054775.1_ASM305477v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:49,500] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:49,501] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e6a5976-62d7-4123-8a41-6f54c7434575/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:49,501] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e6a5976-62d7-4123-8a41-6f54c7434575/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:49,516] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:02:49,517] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:49,517] [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
Saccharospirillum mangrovi	strain=HK-33	GCA_003054775.1	2161747	2161747	type	True	100.0	1209	1210	95	conclusive
Saccharospirillum mangrovi	strain=HK-33	GCA_003367315.1	2161747	2161747	type	True	99.9975	1209	1210	95	conclusive
Saccharospirillum salsuginis	strain=KCTC 22169	GCA_014651855.1	418750	418750	type	True	78.397	418	1210	95	below_threshold
Saccharospirillum alexandrii	strain=LZ-5	GCA_004000275.1	2448477	2448477	type	True	77.8805	323	1210	95	below_threshold
Saccharospirillum impatiens	strain=DSM 12546	GCA_000423605.1	169438	169438	type	True	77.4943	270	1210	95	below_threshold
Reinekea blandensis	strain=MED297	GCA_000153185.1	374838	374838	type	True	76.6629	98	1210	95	below_threshold
Reinekea forsetii	strain=Hel1_31_D35	GCA_002795845.1	1336806	1336806	type	True	76.6085	69	1210	95	below_threshold
Pseudomonas cavernicola	strain=K1S02-6	GCA_003596405.1	2320866	2320866	type	True	76.4479	97	1210	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	76.3694	126	1210	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	76.1979	72	1210	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	76.196	107	1210	95	below_threshold
Pseudomonas baetica	strain=LMG 25716	GCA_002813455.1	674054	674054	type	True	76.1444	90	1210	95	below_threshold
Pseudomonas borbori	strain=DSM 17834	GCA_900115555.1	289003	289003	type	True	76.0892	113	1210	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	76.0769	88	1210	95	below_threshold
Pseudomonas bharatica	strain=CSV86	GCA_000319305.2	2692112	2692112	type	True	75.9452	105	1210	95	below_threshold
Pseudomonas graminis	strain=DSM 11363	GCA_900111735.1	158627	158627	suspected-type	True	75.7574	83	1210	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:49,518] [INFO] DFAST Taxonomy check result was written to GCF_003054775.1_ASM305477v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:49,519] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:49,519] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:49,519] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e6a5976-62d7-4123-8a41-6f54c7434575/dqc_reference/checkm_data
[2024-01-24 15:02:49,521] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:49,567] [INFO] Task started: CheckM
[2024-01-24 15:02:49,567] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003054775.1_ASM305477v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003054775.1_ASM305477v1_genomic.fna/checkm_input GCF_003054775.1_ASM305477v1_genomic.fna/checkm_result
[2024-01-24 15:03:31,321] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:31,322] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 14.99%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:31,390] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:31,391] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:31,391] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003054775.1_ASM305477v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:31,392] [INFO] Task started: Blastn
[2024-01-24 15:03:31,392] [INFO] Running command: blastn -query GCF_003054775.1_ASM305477v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e6a5976-62d7-4123-8a41-6f54c7434575/dqc_reference/reference_markers_gtdb.fasta -out GCF_003054775.1_ASM305477v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:33,107] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:33,111] [INFO] Selected 13 target genomes.
[2024-01-24 15:03:33,111] [INFO] Target genome list was writen to GCF_003054775.1_ASM305477v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:33,121] [INFO] Task started: fastANI
[2024-01-24 15:03:33,122] [INFO] Running command: fastANI --query /var/lib/cwl/stg044fb462-0c88-43b8-9c73-9399f6b4375b/GCF_003054775.1_ASM305477v1_genomic.fna.gz --refList GCF_003054775.1_ASM305477v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003054775.1_ASM305477v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:45,338] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:45,354] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:45,355] [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_003367315.1	s__Saccharospirillum mangrovi	99.9975	1209	1210	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Saccharospirillum	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003054965.1	s__Saccharospirillum sp003054965	81.5311	833	1210	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Saccharospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651855.1	s__Saccharospirillum salsuginis	78.379	419	1210	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Saccharospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402545.1	s__Saccharospirillum sp018402545	77.9662	303	1210	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Saccharospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004000275.1	s__Saccharospirillum alexandrii	77.879	322	1210	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Saccharospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423605.1	s__Saccharospirillum impatiens	77.5157	270	1210	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Saccharospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014490745.1	s__Pseudomonas_E alcaligenes_C	76.6306	110	1210	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_015265435.1	s__Alcanivorax profundimaris	76.5697	77	1210	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.49	97.23	0.85	0.77	11	-
GCF_000153185.1	s__Reinekea blandensis	76.5303	96	1210	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Reinekea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000292795.1	s__Pseudomonas_E fluorescens_H	76.1674	107	1210	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_001945445.1	s__Pseudomonas_E sp001945445	76.146	108	1210	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.66	98.66	0.91	0.91	2	-
GCF_002878485.1	s__Pseudomonas_E sp002878485	75.8947	106	1210	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_900111735.1	s__Pseudomonas_E graminis	75.7891	81	1210	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.28	98.01	0.93	0.92	4	-
--------------------------------------------------------------------------------
[2024-01-24 15:03:45,358] [INFO] GTDB search result was written to GCF_003054775.1_ASM305477v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:45,358] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:45,362] [INFO] DFAST_QC result json was written to GCF_003054775.1_ASM305477v1_genomic.fna/dqc_result.json
[2024-01-24 15:03:45,363] [INFO] DFAST_QC completed!
[2024-01-24 15:03:45,363] [INFO] Total running time: 0h1m27s