[2024-01-24 14:12:15,424] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:15,427] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:15,428] [INFO] DQC Reference Directory: /var/lib/cwl/stgead71d56-ef0e-467b-bc29-9215c0ab8d45/dqc_reference
[2024-01-24 14:12:16,822] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:16,823] [INFO] Task started: Prodigal
[2024-01-24 14:12:16,823] [INFO] Running command: gunzip -c /var/lib/cwl/stg038a0616-f889-4ed0-aeb5-aeaabfdbd8bb/GCF_011059105.1_ASM1105910v1_genomic.fna.gz | prodigal -d GCF_011059105.1_ASM1105910v1_genomic.fna/cds.fna -a GCF_011059105.1_ASM1105910v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:35,909] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:35,909] [INFO] Task started: HMMsearch
[2024-01-24 14:12:35,909] [INFO] Running command: hmmsearch --tblout GCF_011059105.1_ASM1105910v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgead71d56-ef0e-467b-bc29-9215c0ab8d45/dqc_reference/reference_markers.hmm GCF_011059105.1_ASM1105910v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:36,287] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:36,289] [INFO] Found 6/6 markers.
[2024-01-24 14:12:36,324] [INFO] Query marker FASTA was written to GCF_011059105.1_ASM1105910v1_genomic.fna/markers.fasta
[2024-01-24 14:12:36,325] [INFO] Task started: Blastn
[2024-01-24 14:12:36,325] [INFO] Running command: blastn -query GCF_011059105.1_ASM1105910v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgead71d56-ef0e-467b-bc29-9215c0ab8d45/dqc_reference/reference_markers.fasta -out GCF_011059105.1_ASM1105910v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:36,949] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:36,952] [INFO] Selected 16 target genomes.
[2024-01-24 14:12:36,952] [INFO] Target genome list was writen to GCF_011059105.1_ASM1105910v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:36,971] [INFO] Task started: fastANI
[2024-01-24 14:12:36,972] [INFO] Running command: fastANI --query /var/lib/cwl/stg038a0616-f889-4ed0-aeb5-aeaabfdbd8bb/GCF_011059105.1_ASM1105910v1_genomic.fna.gz --refList GCF_011059105.1_ASM1105910v1_genomic.fna/target_genomes.txt --output GCF_011059105.1_ASM1105910v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:51,569] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:51,570] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgead71d56-ef0e-467b-bc29-9215c0ab8d45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:51,570] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgead71d56-ef0e-467b-bc29-9215c0ab8d45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:51,576] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:12:51,577] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:51,577] [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
Aliifodinibius halophilus	strain=2W32	GCA_011059105.1	1736908	1736908	type	True	100.0	1357	1360	95	conclusive
Aliifodinibius saliphilus	strain=ECH52	GCA_005869845.1	1920650	1920650	type	True	80.5794	732	1360	95	below_threshold
Fodinibius salinus	strain=DSM 21935	GCA_008124865.1	860790	860790	type	True	77.7128	190	1360	95	below_threshold
Aliifodinibius roseus	strain=DSM 21986	GCA_900129315.1	1194090	1194090	type	True	77.4214	107	1360	95	below_threshold
Aliifodinibius sediminis	strain=DSM 21194	GCA_900182555.1	1214077	1214077	type	True	77.1905	121	1360	95	below_threshold
Halalkalibaculum roseum	strain=YR4-1	GCA_011059145.1	2709311	2709311	type	True	76.2395	67	1360	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:51,581] [INFO] DFAST Taxonomy check result was written to GCF_011059105.1_ASM1105910v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:51,582] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:51,582] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:51,582] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgead71d56-ef0e-467b-bc29-9215c0ab8d45/dqc_reference/checkm_data
[2024-01-24 14:12:51,583] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:51,625] [INFO] Task started: CheckM
[2024-01-24 14:12:51,625] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011059105.1_ASM1105910v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011059105.1_ASM1105910v1_genomic.fna/checkm_input GCF_011059105.1_ASM1105910v1_genomic.fna/checkm_result
[2024-01-24 14:13:44,493] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:44,495] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:44,517] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:44,517] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:44,518] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011059105.1_ASM1105910v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:44,518] [INFO] Task started: Blastn
[2024-01-24 14:13:44,518] [INFO] Running command: blastn -query GCF_011059105.1_ASM1105910v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgead71d56-ef0e-467b-bc29-9215c0ab8d45/dqc_reference/reference_markers_gtdb.fasta -out GCF_011059105.1_ASM1105910v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:45,301] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:45,305] [INFO] Selected 16 target genomes.
[2024-01-24 14:13:45,305] [INFO] Target genome list was writen to GCF_011059105.1_ASM1105910v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:45,380] [INFO] Task started: fastANI
[2024-01-24 14:13:45,381] [INFO] Running command: fastANI --query /var/lib/cwl/stg038a0616-f889-4ed0-aeb5-aeaabfdbd8bb/GCF_011059105.1_ASM1105910v1_genomic.fna.gz --refList GCF_011059105.1_ASM1105910v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011059105.1_ASM1105910v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:56,447] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:56,460] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:56,460] [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_011059105.1	s__Fodinibius halophilus	100.0	1357	1360	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_005869845.1	s__Fodinibius saliphilus	80.563	734	1360	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Fodinibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002287075.1	s__Fodinibius sp002287075	77.9032	225	1360	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Fodinibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124865.1	s__Fodinibius salinus	77.7128	190	1360	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	77.4214	107	1360	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	77.1905	121	1360	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Aliifodinibius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:56,463] [INFO] GTDB search result was written to GCF_011059105.1_ASM1105910v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:56,463] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:56,468] [INFO] DFAST_QC result json was written to GCF_011059105.1_ASM1105910v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:56,468] [INFO] DFAST_QC completed!
[2024-01-24 14:13:56,468] [INFO] Total running time: 0h1m41s