[2024-01-24 13:09:43,435] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:43,437] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:43,437] [INFO] DQC Reference Directory: /var/lib/cwl/stgb57051f7-c99b-47b6-8b38-263828c5b8a1/dqc_reference
[2024-01-24 13:09:44,668] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:44,669] [INFO] Task started: Prodigal
[2024-01-24 13:09:44,669] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ecacafd-da44-4fcb-9d0d-7d4c3ef99089/GCF_008124865.1_ASM812486v1_genomic.fna.gz | prodigal -d GCF_008124865.1_ASM812486v1_genomic.fna/cds.fna -a GCF_008124865.1_ASM812486v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:57,436] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:57,437] [INFO] Task started: HMMsearch
[2024-01-24 13:09:57,437] [INFO] Running command: hmmsearch --tblout GCF_008124865.1_ASM812486v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb57051f7-c99b-47b6-8b38-263828c5b8a1/dqc_reference/reference_markers.hmm GCF_008124865.1_ASM812486v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:57,676] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:57,678] [INFO] Found 6/6 markers.
[2024-01-24 13:09:57,705] [INFO] Query marker FASTA was written to GCF_008124865.1_ASM812486v1_genomic.fna/markers.fasta
[2024-01-24 13:09:57,705] [INFO] Task started: Blastn
[2024-01-24 13:09:57,705] [INFO] Running command: blastn -query GCF_008124865.1_ASM812486v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb57051f7-c99b-47b6-8b38-263828c5b8a1/dqc_reference/reference_markers.fasta -out GCF_008124865.1_ASM812486v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:58,295] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:58,299] [INFO] Selected 20 target genomes.
[2024-01-24 13:09:58,300] [INFO] Target genome list was writen to GCF_008124865.1_ASM812486v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:58,309] [INFO] Task started: fastANI
[2024-01-24 13:09:58,309] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ecacafd-da44-4fcb-9d0d-7d4c3ef99089/GCF_008124865.1_ASM812486v1_genomic.fna.gz --refList GCF_008124865.1_ASM812486v1_genomic.fna/target_genomes.txt --output GCF_008124865.1_ASM812486v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:11,929] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:11,929] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb57051f7-c99b-47b6-8b38-263828c5b8a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:11,930] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb57051f7-c99b-47b6-8b38-263828c5b8a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:11,939] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:11,939] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:11,939] [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
Fodinibius salinus	strain=DSM 21935	GCA_008124865.1	860790	860790	type	True	100.0	951	951	95	conclusive
Aliifodinibius halophilus	strain=2W32	GCA_011059105.1	1736908	1736908	type	True	77.6177	203	951	95	below_threshold
Aliifodinibius roseus	strain=DSM 21986	GCA_900129315.1	1194090	1194090	type	True	77.3187	74	951	95	below_threshold
Aliifodinibius sediminis	strain=DSM 21194	GCA_900182555.1	1214077	1214077	type	True	77.2114	105	951	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:11,940] [INFO] DFAST Taxonomy check result was written to GCF_008124865.1_ASM812486v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:11,941] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:11,941] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:11,941] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb57051f7-c99b-47b6-8b38-263828c5b8a1/dqc_reference/checkm_data
[2024-01-24 13:10:11,942] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:11,971] [INFO] Task started: CheckM
[2024-01-24 13:10:11,971] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008124865.1_ASM812486v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008124865.1_ASM812486v1_genomic.fna/checkm_input GCF_008124865.1_ASM812486v1_genomic.fna/checkm_result
[2024-01-24 13:10:52,828] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:52,830] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:52,852] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:52,853] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:52,854] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008124865.1_ASM812486v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:52,854] [INFO] Task started: Blastn
[2024-01-24 13:10:52,854] [INFO] Running command: blastn -query GCF_008124865.1_ASM812486v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb57051f7-c99b-47b6-8b38-263828c5b8a1/dqc_reference/reference_markers_gtdb.fasta -out GCF_008124865.1_ASM812486v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:53,701] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:53,714] [INFO] Selected 19 target genomes.
[2024-01-24 13:10:53,715] [INFO] Target genome list was writen to GCF_008124865.1_ASM812486v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:53,768] [INFO] Task started: fastANI
[2024-01-24 13:10:53,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ecacafd-da44-4fcb-9d0d-7d4c3ef99089/GCF_008124865.1_ASM812486v1_genomic.fna.gz --refList GCF_008124865.1_ASM812486v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008124865.1_ASM812486v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:04,189] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:04,199] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:04,199] [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_008124865.1	s__Fodinibius salinus	100.0	951	951	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Fodinibius	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002287075.1	s__Fodinibius sp002287075	77.8739	199	951	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Fodinibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011059105.1	s__Fodinibius halophilus	77.5864	205	951	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Fodinibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129315.1	s__Aliifodinibius roseus	77.3187	74	951	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Aliifodinibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182555.1	s__Aliifodinibius sediminis	77.2114	105	951	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Aliifodinibius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016937115.1	s__SMO-BIN1 sp016937115	76.2377	52	951	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__SMO-BIN1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:04,201] [INFO] GTDB search result was written to GCF_008124865.1_ASM812486v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:04,201] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:04,204] [INFO] DFAST_QC result json was written to GCF_008124865.1_ASM812486v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:04,204] [INFO] DFAST_QC completed!
[2024-01-24 13:11:04,204] [INFO] Total running time: 0h1m21s