[2023-06-27 03:54:08,219] [INFO] DFAST_QC pipeline started.
[2023-06-27 03:54:08,222] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 03:54:08,222] [INFO] DQC Reference Directory: /var/lib/cwl/stg24d932d6-292d-4b9f-a438-5577a91e58ab/dqc_reference
[2023-06-27 03:54:09,447] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 03:54:09,448] [INFO] Task started: Prodigal
[2023-06-27 03:54:09,448] [INFO] Running command: gunzip -c /var/lib/cwl/stg26f1bb4f-a67b-41f1-bf32-7bc6a0227741/GCA_026709175.1_ASM2670917v1_genomic.fna.gz | prodigal -d GCA_026709175.1_ASM2670917v1_genomic.fna/cds.fna -a GCA_026709175.1_ASM2670917v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 03:54:14,791] [INFO] Task succeeded: Prodigal
[2023-06-27 03:54:14,792] [INFO] Task started: HMMsearch
[2023-06-27 03:54:14,792] [INFO] Running command: hmmsearch --tblout GCA_026709175.1_ASM2670917v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24d932d6-292d-4b9f-a438-5577a91e58ab/dqc_reference/reference_markers.hmm GCA_026709175.1_ASM2670917v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 03:54:15,158] [INFO] Task succeeded: HMMsearch
[2023-06-27 03:54:15,159] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg26f1bb4f-a67b-41f1-bf32-7bc6a0227741/GCA_026709175.1_ASM2670917v1_genomic.fna.gz]
[2023-06-27 03:54:15,227] [INFO] Query marker FASTA was written to GCA_026709175.1_ASM2670917v1_genomic.fna/markers.fasta
[2023-06-27 03:54:15,228] [INFO] Task started: Blastn
[2023-06-27 03:54:15,228] [INFO] Running command: blastn -query GCA_026709175.1_ASM2670917v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24d932d6-292d-4b9f-a438-5577a91e58ab/dqc_reference/reference_markers.fasta -out GCA_026709175.1_ASM2670917v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 03:54:15,800] [INFO] Task succeeded: Blastn
[2023-06-27 03:54:15,805] [INFO] Selected 7 target genomes.
[2023-06-27 03:54:15,805] [INFO] Target genome list was writen to GCA_026709175.1_ASM2670917v1_genomic.fna/target_genomes.txt
[2023-06-27 03:54:15,809] [INFO] Task started: fastANI
[2023-06-27 03:54:15,809] [INFO] Running command: fastANI --query /var/lib/cwl/stg26f1bb4f-a67b-41f1-bf32-7bc6a0227741/GCA_026709175.1_ASM2670917v1_genomic.fna.gz --refList GCA_026709175.1_ASM2670917v1_genomic.fna/target_genomes.txt --output GCA_026709175.1_ASM2670917v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 03:54:19,854] [INFO] Task succeeded: fastANI
[2023-06-27 03:54:19,855] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24d932d6-292d-4b9f-a438-5577a91e58ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 03:54:19,855] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24d932d6-292d-4b9f-a438-5577a91e58ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 03:54:19,864] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 03:54:19,864] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 03:54:19,864] [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 arenae	strain=DSM 19593	GCA_000442275.2	491388	491388	type	True	78.2087	67	355	95	below_threshold
Litoreibacter halocynthiae	strain=DSM 29467	GCA_004365635.1	1242689	1242689	type	True	77.5668	73	355	95	below_threshold
Litoreibacter ascidiaceicola	strain=DSM 100566	GCA_900129235.1	1486859	1486859	type	True	77.4332	66	355	95	below_threshold
Litoreibacter meonggei	strain=DSM 29466	GCA_003663885.1	1049199	1049199	type	True	77.4257	59	355	95	below_threshold
Litoreibacter albidus	strain=DSM 26922	GCA_900107015.1	670155	670155	type	True	77.0934	60	355	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 03:54:19,866] [INFO] DFAST Taxonomy check result was written to GCA_026709175.1_ASM2670917v1_genomic.fna/tc_result.tsv
[2023-06-27 03:54:19,867] [INFO] ===== Taxonomy check completed =====
[2023-06-27 03:54:19,867] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 03:54:19,867] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24d932d6-292d-4b9f-a438-5577a91e58ab/dqc_reference/checkm_data
[2023-06-27 03:54:19,868] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 03:54:19,894] [INFO] Task started: CheckM
[2023-06-27 03:54:19,895] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026709175.1_ASM2670917v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026709175.1_ASM2670917v1_genomic.fna/checkm_input GCA_026709175.1_ASM2670917v1_genomic.fna/checkm_result
[2023-06-27 03:54:42,269] [INFO] Task succeeded: CheckM
[2023-06-27 03:54:42,271] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.55%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 03:54:42,291] [INFO] ===== Completeness check finished =====
[2023-06-27 03:54:42,292] [INFO] ===== Start GTDB Search =====
[2023-06-27 03:54:42,292] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026709175.1_ASM2670917v1_genomic.fna/markers.fasta)
[2023-06-27 03:54:42,293] [INFO] Task started: Blastn
[2023-06-27 03:54:42,293] [INFO] Running command: blastn -query GCA_026709175.1_ASM2670917v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24d932d6-292d-4b9f-a438-5577a91e58ab/dqc_reference/reference_markers_gtdb.fasta -out GCA_026709175.1_ASM2670917v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 03:54:42,955] [INFO] Task succeeded: Blastn
[2023-06-27 03:54:42,960] [INFO] Selected 8 target genomes.
[2023-06-27 03:54:42,960] [INFO] Target genome list was writen to GCA_026709175.1_ASM2670917v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 03:54:42,967] [INFO] Task started: fastANI
[2023-06-27 03:54:42,967] [INFO] Running command: fastANI --query /var/lib/cwl/stg26f1bb4f-a67b-41f1-bf32-7bc6a0227741/GCA_026709175.1_ASM2670917v1_genomic.fna.gz --refList GCA_026709175.1_ASM2670917v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026709175.1_ASM2670917v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 03:54:46,916] [INFO] Task succeeded: fastANI
[2023-06-27 03:54:46,924] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 03:54:46,925] [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_000442275.2	s__Litoreibacter arenae	78.2087	67	355	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004365635.1	s__Litoreibacter halocynthiae	77.5668	73	355	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129235.1	s__Litoreibacter ascidiaceicola	77.4332	66	355	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	77.4257	59	355	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	77.0934	60	355	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 03:54:46,927] [INFO] GTDB search result was written to GCA_026709175.1_ASM2670917v1_genomic.fna/result_gtdb.tsv
[2023-06-27 03:54:46,927] [INFO] ===== GTDB Search completed =====
[2023-06-27 03:54:46,935] [INFO] DFAST_QC result json was written to GCA_026709175.1_ASM2670917v1_genomic.fna/dqc_result.json
[2023-06-27 03:54:46,935] [INFO] DFAST_QC completed!
[2023-06-27 03:54:46,935] [INFO] Total running time: 0h0m39s