[2024-01-25 18:39:35,708] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:39:35,710] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:39:35,710] [INFO] DQC Reference Directory: /var/lib/cwl/stg36f81018-b82a-4174-9701-2e97f494909f/dqc_reference
[2024-01-25 18:39:36,806] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:39:36,807] [INFO] Task started: Prodigal
[2024-01-25 18:39:36,807] [INFO] Running command: gunzip -c /var/lib/cwl/stg1757ea5f-cc2f-4168-b27b-c23b88c217f1/GCF_000423605.1_ASM42360v1_genomic.fna.gz | prodigal -d GCF_000423605.1_ASM42360v1_genomic.fna/cds.fna -a GCF_000423605.1_ASM42360v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:39:48,802] [INFO] Task succeeded: Prodigal
[2024-01-25 18:39:48,803] [INFO] Task started: HMMsearch
[2024-01-25 18:39:48,803] [INFO] Running command: hmmsearch --tblout GCF_000423605.1_ASM42360v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36f81018-b82a-4174-9701-2e97f494909f/dqc_reference/reference_markers.hmm GCF_000423605.1_ASM42360v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:39:49,127] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:39:49,128] [INFO] Found 6/6 markers.
[2024-01-25 18:39:49,174] [INFO] Query marker FASTA was written to GCF_000423605.1_ASM42360v1_genomic.fna/markers.fasta
[2024-01-25 18:39:49,174] [INFO] Task started: Blastn
[2024-01-25 18:39:49,174] [INFO] Running command: blastn -query GCF_000423605.1_ASM42360v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36f81018-b82a-4174-9701-2e97f494909f/dqc_reference/reference_markers.fasta -out GCF_000423605.1_ASM42360v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:39:49,855] [INFO] Task succeeded: Blastn
[2024-01-25 18:39:49,859] [INFO] Selected 19 target genomes.
[2024-01-25 18:39:49,859] [INFO] Target genome list was writen to GCF_000423605.1_ASM42360v1_genomic.fna/target_genomes.txt
[2024-01-25 18:39:49,932] [INFO] Task started: fastANI
[2024-01-25 18:39:49,932] [INFO] Running command: fastANI --query /var/lib/cwl/stg1757ea5f-cc2f-4168-b27b-c23b88c217f1/GCF_000423605.1_ASM42360v1_genomic.fna.gz --refList GCF_000423605.1_ASM42360v1_genomic.fna/target_genomes.txt --output GCF_000423605.1_ASM42360v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:40:05,986] [INFO] Task succeeded: fastANI
[2024-01-25 18:40:05,986] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36f81018-b82a-4174-9701-2e97f494909f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:40:05,987] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36f81018-b82a-4174-9701-2e97f494909f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:40:05,995] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:40:05,995] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:40:05,995] [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 impatiens	strain=DSM 12546	GCA_000423605.1	169438	169438	type	True	100.0	1489	1502	95	conclusive
Saccharospirillum alexandrii	strain=LZ-5	GCA_004000275.1	2448477	2448477	type	True	82.4164	1008	1502	95	below_threshold
Saccharospirillum salsuginis	strain=KCTC 22169	GCA_014651855.1	418750	418750	type	True	77.6552	380	1502	95	below_threshold
Saccharospirillum mangrovi	strain=HK-33	GCA_003367315.1	2161747	2161747	type	True	77.6209	254	1502	95	below_threshold
Saccharospirillum mangrovi	strain=HK-33	GCA_003054775.1	2161747	2161747	type	True	77.5563	251	1502	95	below_threshold
Reinekea marinisedimentorum	strain=DSM 15388	GCA_004341165.1	230495	230495	type	True	76.444	95	1502	95	below_threshold
Marinobacter fuscus	strain=NH169-3	GCA_003007675.1	2109942	2109942	type	True	76.1308	69	1502	95	below_threshold
Pseudomonas cuatrocienegasensis	strain=CIP 109853	GCA_900110925.1	543360	543360	type	True	76.0781	68	1502	95	below_threshold
Marinobacter shengliensis	strain=SL013A34A2	GCA_003007715.1	1389223	1389223	type	True	75.9272	64	1502	95	below_threshold
Pseudomonas taeanensis	strain=MS-3	GCA_000498575.2	574962	574962	type	True	75.7992	57	1502	95	below_threshold
Pseudomonas bohemica	strain=IA19	GCA_002934685.1	2044872	2044872	type	True	75.6304	51	1502	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:40:05,997] [INFO] DFAST Taxonomy check result was written to GCF_000423605.1_ASM42360v1_genomic.fna/tc_result.tsv
[2024-01-25 18:40:05,997] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:40:05,997] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:40:05,998] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36f81018-b82a-4174-9701-2e97f494909f/dqc_reference/checkm_data
[2024-01-25 18:40:05,999] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:40:06,047] [INFO] Task started: CheckM
[2024-01-25 18:40:06,047] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000423605.1_ASM42360v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000423605.1_ASM42360v1_genomic.fna/checkm_input GCF_000423605.1_ASM42360v1_genomic.fna/checkm_result
[2024-01-25 18:40:43,806] [INFO] Task succeeded: CheckM
[2024-01-25 18:40:43,807] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:40:43,823] [INFO] ===== Completeness check finished =====
[2024-01-25 18:40:43,823] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:40:43,824] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000423605.1_ASM42360v1_genomic.fna/markers.fasta)
[2024-01-25 18:40:43,824] [INFO] Task started: Blastn
[2024-01-25 18:40:43,824] [INFO] Running command: blastn -query GCF_000423605.1_ASM42360v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36f81018-b82a-4174-9701-2e97f494909f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000423605.1_ASM42360v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:44,996] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:44,999] [INFO] Selected 12 target genomes.
[2024-01-25 18:40:44,999] [INFO] Target genome list was writen to GCF_000423605.1_ASM42360v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:40:45,024] [INFO] Task started: fastANI
[2024-01-25 18:40:45,024] [INFO] Running command: fastANI --query /var/lib/cwl/stg1757ea5f-cc2f-4168-b27b-c23b88c217f1/GCF_000423605.1_ASM42360v1_genomic.fna.gz --refList GCF_000423605.1_ASM42360v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000423605.1_ASM42360v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:40:56,643] [INFO] Task succeeded: fastANI
[2024-01-25 18:40:56,650] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:40:56,650] [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_000423605.1	s__Saccharospirillum impatiens	100.0	1488	1502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Saccharospirillum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018402545.1	s__Saccharospirillum sp018402545	82.5351	949	1502	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	82.4158	1008	1502	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	77.6947	376	1502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Saccharospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003367315.1	s__Saccharospirillum mangrovi	77.6295	254	1502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Saccharospirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003054965.1	s__Saccharospirillum sp003054965	77.4231	238	1502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Saccharospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341165.1	s__Reinekea marinisedimentorum	76.3523	99	1502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Reinekea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002795845.1	s__Reinekea forsetii	76.3114	72	1502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Reinekea	95.0	99.43	98.93	0.96	0.91	7	-
GCF_004364335.1	s__Pseudomonas_E graminis_D	75.6031	51	1502	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_014219065.1	s__Pseudomonas_D xiamenensis	75.5822	58	1502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:40:56,653] [INFO] GTDB search result was written to GCF_000423605.1_ASM42360v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:40:56,654] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:40:56,656] [INFO] DFAST_QC result json was written to GCF_000423605.1_ASM42360v1_genomic.fna/dqc_result.json
[2024-01-25 18:40:56,656] [INFO] DFAST_QC completed!
[2024-01-25 18:40:56,656] [INFO] Total running time: 0h1m21s