[2024-01-25 19:45:35,375] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:45:35,377] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:45:35,377] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4c2b9aa-195e-4537-aaa9-ed28948237c6/dqc_reference
[2024-01-25 19:45:36,524] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:45:36,524] [INFO] Task started: Prodigal
[2024-01-25 19:45:36,525] [INFO] Running command: gunzip -c /var/lib/cwl/stg63f712b7-ce20-4ddc-8316-2b44ba791804/GCF_002287075.1_ASM228707v1_genomic.fna.gz | prodigal -d GCF_002287075.1_ASM228707v1_genomic.fna/cds.fna -a GCF_002287075.1_ASM228707v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:45:49,806] [INFO] Task succeeded: Prodigal
[2024-01-25 19:45:49,807] [INFO] Task started: HMMsearch
[2024-01-25 19:45:49,807] [INFO] Running command: hmmsearch --tblout GCF_002287075.1_ASM228707v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4c2b9aa-195e-4537-aaa9-ed28948237c6/dqc_reference/reference_markers.hmm GCF_002287075.1_ASM228707v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:45:50,046] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:45:50,047] [INFO] Found 6/6 markers.
[2024-01-25 19:45:50,085] [INFO] Query marker FASTA was written to GCF_002287075.1_ASM228707v1_genomic.fna/markers.fasta
[2024-01-25 19:45:50,085] [INFO] Task started: Blastn
[2024-01-25 19:45:50,085] [INFO] Running command: blastn -query GCF_002287075.1_ASM228707v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4c2b9aa-195e-4537-aaa9-ed28948237c6/dqc_reference/reference_markers.fasta -out GCF_002287075.1_ASM228707v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:50,674] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:50,677] [INFO] Selected 21 target genomes.
[2024-01-25 19:45:50,677] [INFO] Target genome list was writen to GCF_002287075.1_ASM228707v1_genomic.fna/target_genomes.txt
[2024-01-25 19:45:50,704] [INFO] Task started: fastANI
[2024-01-25 19:45:50,705] [INFO] Running command: fastANI --query /var/lib/cwl/stg63f712b7-ce20-4ddc-8316-2b44ba791804/GCF_002287075.1_ASM228707v1_genomic.fna.gz --refList GCF_002287075.1_ASM228707v1_genomic.fna/target_genomes.txt --output GCF_002287075.1_ASM228707v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:46:03,988] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:03,988] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4c2b9aa-195e-4537-aaa9-ed28948237c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:46:03,989] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4c2b9aa-195e-4537-aaa9-ed28948237c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:46:03,994] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:46:03,994] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:46:03,994] [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 sediminis	strain=DSM 21194	GCA_900182555.1	1214077	1214077	type	True	78.3144	123	1176	95	below_threshold
Aliifodinibius roseus	strain=DSM 21986	GCA_900129315.1	1194090	1194090	type	True	77.911	143	1176	95	below_threshold
Aliifodinibius halophilus	strain=2W32	GCA_011059105.1	1736908	1736908	type	True	77.8496	241	1176	95	below_threshold
Fodinibius salinus	strain=DSM 21935	GCA_008124865.1	860790	860790	type	True	77.697	199	1176	95	below_threshold
Aliifodinibius saliphilus	strain=ECH52	GCA_005869845.1	1920650	1920650	type	True	77.5397	179	1176	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:46:03,995] [INFO] DFAST Taxonomy check result was written to GCF_002287075.1_ASM228707v1_genomic.fna/tc_result.tsv
[2024-01-25 19:46:03,996] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:46:03,996] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:46:03,996] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4c2b9aa-195e-4537-aaa9-ed28948237c6/dqc_reference/checkm_data
[2024-01-25 19:46:03,997] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:46:04,035] [INFO] Task started: CheckM
[2024-01-25 19:46:04,035] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002287075.1_ASM228707v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002287075.1_ASM228707v1_genomic.fna/checkm_input GCF_002287075.1_ASM228707v1_genomic.fna/checkm_result
[2024-01-25 19:46:43,737] [INFO] Task succeeded: CheckM
[2024-01-25 19:46:43,738] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:46:43,754] [INFO] ===== Completeness check finished =====
[2024-01-25 19:46:43,754] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:46:43,754] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002287075.1_ASM228707v1_genomic.fna/markers.fasta)
[2024-01-25 19:46:43,754] [INFO] Task started: Blastn
[2024-01-25 19:46:43,755] [INFO] Running command: blastn -query GCF_002287075.1_ASM228707v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4c2b9aa-195e-4537-aaa9-ed28948237c6/dqc_reference/reference_markers_gtdb.fasta -out GCF_002287075.1_ASM228707v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:46:44,553] [INFO] Task succeeded: Blastn
[2024-01-25 19:46:44,562] [INFO] Selected 21 target genomes.
[2024-01-25 19:46:44,562] [INFO] Target genome list was writen to GCF_002287075.1_ASM228707v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:46:44,581] [INFO] Task started: fastANI
[2024-01-25 19:46:44,581] [INFO] Running command: fastANI --query /var/lib/cwl/stg63f712b7-ce20-4ddc-8316-2b44ba791804/GCF_002287075.1_ASM228707v1_genomic.fna.gz --refList GCF_002287075.1_ASM228707v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002287075.1_ASM228707v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:46:57,580] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:57,586] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:46:57,587] [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_002287075.1	s__Fodinibius sp002287075	100.0	1175	1176	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_900182555.1	s__Aliifodinibius sediminis	78.3051	124	1176	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Aliifodinibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129315.1	s__Aliifodinibius roseus	77.9347	142	1176	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Aliifodinibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011059105.1	s__Fodinibius halophilus	77.8496	241	1176	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	77.697	199	1176	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Fodinibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005869845.1	s__Fodinibius saliphilus	77.5397	179	1176	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Fodinibius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016937115.1	s__SMO-BIN1 sp016937115	76.5608	63	1176	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__SMO-BIN1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:46:57,588] [INFO] GTDB search result was written to GCF_002287075.1_ASM228707v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:46:57,588] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:46:57,594] [INFO] DFAST_QC result json was written to GCF_002287075.1_ASM228707v1_genomic.fna/dqc_result.json
[2024-01-25 19:46:57,594] [INFO] DFAST_QC completed!
[2024-01-25 19:46:57,594] [INFO] Total running time: 0h1m22s