[2024-01-24 15:10:48,922] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:48,924] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:48,925] [INFO] DQC Reference Directory: /var/lib/cwl/stg10a0fa7e-520f-4459-945c-168f3585d930/dqc_reference
[2024-01-24 15:10:50,210] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:50,211] [INFO] Task started: Prodigal
[2024-01-24 15:10:50,211] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb190e96-d290-4236-a64e-ef76c5132f6d/GCF_004365635.1_ASM436563v1_genomic.fna.gz | prodigal -d GCF_004365635.1_ASM436563v1_genomic.fna/cds.fna -a GCF_004365635.1_ASM436563v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:02,719] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:02,719] [INFO] Task started: HMMsearch
[2024-01-24 15:11:02,719] [INFO] Running command: hmmsearch --tblout GCF_004365635.1_ASM436563v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10a0fa7e-520f-4459-945c-168f3585d930/dqc_reference/reference_markers.hmm GCF_004365635.1_ASM436563v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:03,051] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:03,053] [INFO] Found 6/6 markers.
[2024-01-24 15:11:03,176] [INFO] Query marker FASTA was written to GCF_004365635.1_ASM436563v1_genomic.fna/markers.fasta
[2024-01-24 15:11:03,176] [INFO] Task started: Blastn
[2024-01-24 15:11:03,177] [INFO] Running command: blastn -query GCF_004365635.1_ASM436563v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10a0fa7e-520f-4459-945c-168f3585d930/dqc_reference/reference_markers.fasta -out GCF_004365635.1_ASM436563v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:03,935] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:03,939] [INFO] Selected 12 target genomes.
[2024-01-24 15:11:03,940] [INFO] Target genome list was writen to GCF_004365635.1_ASM436563v1_genomic.fna/target_genomes.txt
[2024-01-24 15:11:03,946] [INFO] Task started: fastANI
[2024-01-24 15:11:03,946] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb190e96-d290-4236-a64e-ef76c5132f6d/GCF_004365635.1_ASM436563v1_genomic.fna.gz --refList GCF_004365635.1_ASM436563v1_genomic.fna/target_genomes.txt --output GCF_004365635.1_ASM436563v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:13,436] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:13,436] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10a0fa7e-520f-4459-945c-168f3585d930/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:13,436] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10a0fa7e-520f-4459-945c-168f3585d930/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:13,447] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:13,447] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:13,447] [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
Litoreibacter halocynthiae	strain=DSM 29467	GCA_004365635.1	1242689	1242689	type	True	100.0	1222	1222	95	conclusive
Litoreibacter ascidiaceicola	strain=DSM 100566	GCA_900129235.1	1486859	1486859	type	True	92.8435	1066	1222	95	below_threshold
Litoreibacter meonggei	strain=DSM 29466	GCA_003663885.1	1049199	1049199	type	True	86.4405	882	1222	95	below_threshold
Litoreibacter arenae	strain=DSM 19593	GCA_000442275.2	491388	491388	type	True	84.1312	786	1222	95	below_threshold
Litoreibacter janthinus	strain=DSM 26921	GCA_900111945.1	670154	670154	type	True	81.527	732	1222	95	below_threshold
Litoreibacter albidus	strain=DSM 26922	GCA_900107015.1	670155	670155	type	True	80.9302	677	1222	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	78.0001	184	1222	95	below_threshold
Phaeobacter piscinae	strain=P14	GCA_002407245.1	1580596	1580596	type	True	77.3145	189	1222	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	77.0801	179	1222	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.0795	179	1222	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	76.7839	161	1222	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	76.7211	191	1222	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:13,449] [INFO] DFAST Taxonomy check result was written to GCF_004365635.1_ASM436563v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:13,450] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:13,450] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:13,450] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10a0fa7e-520f-4459-945c-168f3585d930/dqc_reference/checkm_data
[2024-01-24 15:11:13,451] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:13,491] [INFO] Task started: CheckM
[2024-01-24 15:11:13,491] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004365635.1_ASM436563v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004365635.1_ASM436563v1_genomic.fna/checkm_input GCF_004365635.1_ASM436563v1_genomic.fna/checkm_result
[2024-01-24 15:11:54,701] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:54,702] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:54,722] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:54,723] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:54,723] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004365635.1_ASM436563v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:54,724] [INFO] Task started: Blastn
[2024-01-24 15:11:54,724] [INFO] Running command: blastn -query GCF_004365635.1_ASM436563v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10a0fa7e-520f-4459-945c-168f3585d930/dqc_reference/reference_markers_gtdb.fasta -out GCF_004365635.1_ASM436563v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:55,887] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:55,891] [INFO] Selected 7 target genomes.
[2024-01-24 15:11:55,891] [INFO] Target genome list was writen to GCF_004365635.1_ASM436563v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:55,896] [INFO] Task started: fastANI
[2024-01-24 15:11:55,896] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb190e96-d290-4236-a64e-ef76c5132f6d/GCF_004365635.1_ASM436563v1_genomic.fna.gz --refList GCF_004365635.1_ASM436563v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004365635.1_ASM436563v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:02,100] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:02,107] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:02,107] [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_004365635.1	s__Litoreibacter halocynthiae	100.0	1222	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900129235.1	s__Litoreibacter ascidiaceicola	92.8435	1066	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003663885.1	s__Litoreibacter meonggei	86.4291	882	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000442275.2	s__Litoreibacter arenae	84.1312	786	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111945.1	s__Litoreibacter janthinus	81.5464	730	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107015.1	s__Litoreibacter albidus	80.9302	677	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792925.1	s__Gemmobacter sp016792925	76.5495	166	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:12:02,108] [INFO] GTDB search result was written to GCF_004365635.1_ASM436563v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:02,109] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:02,112] [INFO] DFAST_QC result json was written to GCF_004365635.1_ASM436563v1_genomic.fna/dqc_result.json
[2024-01-24 15:12:02,112] [INFO] DFAST_QC completed!
[2024-01-24 15:12:02,112] [INFO] Total running time: 0h1m13s