[2024-01-24 14:30:34,583] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:34,585] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:34,585] [INFO] DQC Reference Directory: /var/lib/cwl/stg35a476ed-b337-4d97-9fd0-300dd0d486c1/dqc_reference
[2024-01-24 14:30:35,946] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:35,947] [INFO] Task started: Prodigal
[2024-01-24 14:30:35,947] [INFO] Running command: gunzip -c /var/lib/cwl/stg569c0c65-94f6-49b1-bfc5-edaf2708fa99/GCF_003992625.1_ASM399262v1_genomic.fna.gz | prodigal -d GCF_003992625.1_ASM399262v1_genomic.fna/cds.fna -a GCF_003992625.1_ASM399262v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:49,670] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:49,671] [INFO] Task started: HMMsearch
[2024-01-24 14:30:49,671] [INFO] Running command: hmmsearch --tblout GCF_003992625.1_ASM399262v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35a476ed-b337-4d97-9fd0-300dd0d486c1/dqc_reference/reference_markers.hmm GCF_003992625.1_ASM399262v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:49,971] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:49,973] [INFO] Found 6/6 markers.
[2024-01-24 14:30:50,025] [INFO] Query marker FASTA was written to GCF_003992625.1_ASM399262v1_genomic.fna/markers.fasta
[2024-01-24 14:30:50,026] [INFO] Task started: Blastn
[2024-01-24 14:30:50,026] [INFO] Running command: blastn -query GCF_003992625.1_ASM399262v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35a476ed-b337-4d97-9fd0-300dd0d486c1/dqc_reference/reference_markers.fasta -out GCF_003992625.1_ASM399262v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:50,895] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:50,899] [INFO] Selected 12 target genomes.
[2024-01-24 14:30:50,900] [INFO] Target genome list was writen to GCF_003992625.1_ASM399262v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:50,904] [INFO] Task started: fastANI
[2024-01-24 14:30:50,904] [INFO] Running command: fastANI --query /var/lib/cwl/stg569c0c65-94f6-49b1-bfc5-edaf2708fa99/GCF_003992625.1_ASM399262v1_genomic.fna.gz --refList GCF_003992625.1_ASM399262v1_genomic.fna/target_genomes.txt --output GCF_003992625.1_ASM399262v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:02,420] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:02,421] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35a476ed-b337-4d97-9fd0-300dd0d486c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:02,421] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35a476ed-b337-4d97-9fd0-300dd0d486c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:02,432] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:31:02,432] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:02,433] [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
Pelagibacterium lentulum	strain=B2	GCA_003992625.1	2029865	2029865	type	True	100.0	1341	1346	95	conclusive
Pelagibacterium lentulum	strain=CGMCC 1.15896	GCA_014643755.1	2029865	2029865	type	True	99.979	1321	1346	95	conclusive
Pelagibacterium halotolerans	strain=B2	GCA_000230555.1	531813	531813	type	True	78.5841	405	1346	95	below_threshold
Pelagibacterium lacus	strain=XYN52	GCA_003345525.1	2282655	2282655	type	True	78.3845	334	1346	95	below_threshold
Pelagibacterium luteolum	strain=CGMCC 1.10267	GCA_900100665.1	440168	440168	type	True	78.3442	358	1346	95	below_threshold
Pelagibacterium sediminicola	strain=IMCC34151	GCA_003390885.1	2248761	2248761	type	True	78.3281	348	1346	95	below_threshold
Pelagibacterium montanilacus	strain=CCL18	GCA_003992665.1	2185280	2185280	type	True	78.1879	322	1346	95	below_threshold
Pelagibacterium xiamenense	strain=HS1C4-1	GCA_021166475.1	2901140	2901140	type	True	78.0096	330	1346	95	below_threshold
Aquamicrobium zhengzhouense	strain=cd-1	GCA_016124105.1	2781738	2781738	type	True	77.2916	72	1346	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	77.0901	176	1346	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	76.744	72	1346	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	76.3626	53	1346	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:02,434] [INFO] DFAST Taxonomy check result was written to GCF_003992625.1_ASM399262v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:02,435] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:02,435] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:02,435] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35a476ed-b337-4d97-9fd0-300dd0d486c1/dqc_reference/checkm_data
[2024-01-24 14:31:02,436] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:02,482] [INFO] Task started: CheckM
[2024-01-24 14:31:02,482] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003992625.1_ASM399262v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003992625.1_ASM399262v1_genomic.fna/checkm_input GCF_003992625.1_ASM399262v1_genomic.fna/checkm_result
[2024-01-24 14:31:46,545] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:46,546] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:46,566] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:46,566] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:46,567] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003992625.1_ASM399262v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:46,567] [INFO] Task started: Blastn
[2024-01-24 14:31:46,568] [INFO] Running command: blastn -query GCF_003992625.1_ASM399262v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35a476ed-b337-4d97-9fd0-300dd0d486c1/dqc_reference/reference_markers_gtdb.fasta -out GCF_003992625.1_ASM399262v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:48,087] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:48,090] [INFO] Selected 11 target genomes.
[2024-01-24 14:31:48,091] [INFO] Target genome list was writen to GCF_003992625.1_ASM399262v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:48,099] [INFO] Task started: fastANI
[2024-01-24 14:31:48,099] [INFO] Running command: fastANI --query /var/lib/cwl/stg569c0c65-94f6-49b1-bfc5-edaf2708fa99/GCF_003992625.1_ASM399262v1_genomic.fna.gz --refList GCF_003992625.1_ASM399262v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003992625.1_ASM399262v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:55,797] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:55,813] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:55,813] [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_003992625.1	s__Pelagibacterium lentulum	100.0	1340	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	99.98	99.98	0.99	0.99	2	conclusive
GCF_000230555.1	s__Pelagibacterium halotolerans	78.6046	403	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCA_002337455.1	s__Pelagibacterium sp002337455	78.4435	381	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	99.90	99.87	0.93	0.91	4	-
GCA_002375765.1	s__Pelagibacterium sp002375765	78.4063	409	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	99.84	99.84	0.95	0.95	2	-
GCA_002723255.1	s__Pelagibacterium sp002723255	78.392	340	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	98.69	98.23	0.81	0.73	4	-
GCF_003345525.1	s__Pelagibacterium lacus	78.3862	332	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100665.1	s__Pelagibacterium luteolum	78.3371	359	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390885.1	s__Pelagibacterium sp003390885	78.3281	348	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003992665.1	s__Pelagibacterium montanilacus	78.1243	322	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900470445.1	s__Devosia sp900470445	77.2375	195	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	95.41	95.41	0.81	0.81	2	-
GCF_016698645.1	s__Devosia sp016698645	77.105	175	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:31:55,815] [INFO] GTDB search result was written to GCF_003992625.1_ASM399262v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:55,815] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:55,818] [INFO] DFAST_QC result json was written to GCF_003992625.1_ASM399262v1_genomic.fna/dqc_result.json
[2024-01-24 14:31:55,819] [INFO] DFAST_QC completed!
[2024-01-24 14:31:55,819] [INFO] Total running time: 0h1m21s