[2024-01-24 11:35:22,541] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:22,547] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:22,547] [INFO] DQC Reference Directory: /var/lib/cwl/stgff6b92a8-2261-4cbf-b215-5459190ef1c5/dqc_reference
[2024-01-24 11:35:26,239] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:26,240] [INFO] Task started: Prodigal
[2024-01-24 11:35:26,241] [INFO] Running command: gunzip -c /var/lib/cwl/stg590c8334-6fec-4dc4-8f5f-f809a1b15df8/GCF_026229185.1_ASM2622918v1_genomic.fna.gz | prodigal -d GCF_026229185.1_ASM2622918v1_genomic.fna/cds.fna -a GCF_026229185.1_ASM2622918v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:48,244] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:48,244] [INFO] Task started: HMMsearch
[2024-01-24 11:35:48,245] [INFO] Running command: hmmsearch --tblout GCF_026229185.1_ASM2622918v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff6b92a8-2261-4cbf-b215-5459190ef1c5/dqc_reference/reference_markers.hmm GCF_026229185.1_ASM2622918v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:48,598] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:48,600] [INFO] Found 6/6 markers.
[2024-01-24 11:35:48,641] [INFO] Query marker FASTA was written to GCF_026229185.1_ASM2622918v1_genomic.fna/markers.fasta
[2024-01-24 11:35:48,641] [INFO] Task started: Blastn
[2024-01-24 11:35:48,642] [INFO] Running command: blastn -query GCF_026229185.1_ASM2622918v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff6b92a8-2261-4cbf-b215-5459190ef1c5/dqc_reference/reference_markers.fasta -out GCF_026229185.1_ASM2622918v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:49,294] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:49,299] [INFO] Selected 18 target genomes.
[2024-01-24 11:35:49,300] [INFO] Target genome list was writen to GCF_026229185.1_ASM2622918v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:49,308] [INFO] Task started: fastANI
[2024-01-24 11:35:49,308] [INFO] Running command: fastANI --query /var/lib/cwl/stg590c8334-6fec-4dc4-8f5f-f809a1b15df8/GCF_026229185.1_ASM2622918v1_genomic.fna.gz --refList GCF_026229185.1_ASM2622918v1_genomic.fna/target_genomes.txt --output GCF_026229185.1_ASM2622918v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:36:01,205] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:01,206] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff6b92a8-2261-4cbf-b215-5459190ef1c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:36:01,206] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff6b92a8-2261-4cbf-b215-5459190ef1c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:36:01,214] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:36:01,215] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:36:01,215] [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	78.5826	240	1596	95	below_threshold
Aliifodinibius halophilus	strain=2W32	GCA_011059105.1	1736908	1736908	type	True	77.8996	169	1596	95	below_threshold
Aliifodinibius roseus	strain=DSM 21986	GCA_900129315.1	1194090	1194090	type	True	77.7957	229	1596	95	below_threshold
Aliifodinibius saliphilus	strain=ECH52	GCA_005869845.1	1920650	1920650	type	True	77.0931	129	1596	95	below_threshold
Fodinibius salinus	strain=DSM 21935	GCA_008124865.1	860790	860790	type	True	76.9754	130	1596	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:36:01,217] [INFO] DFAST Taxonomy check result was written to GCF_026229185.1_ASM2622918v1_genomic.fna/tc_result.tsv
[2024-01-24 11:36:01,217] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:36:01,217] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:36:01,218] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff6b92a8-2261-4cbf-b215-5459190ef1c5/dqc_reference/checkm_data
[2024-01-24 11:36:01,219] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:36:01,268] [INFO] Task started: CheckM
[2024-01-24 11:36:01,268] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026229185.1_ASM2622918v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026229185.1_ASM2622918v1_genomic.fna/checkm_input GCF_026229185.1_ASM2622918v1_genomic.fna/checkm_result
[2024-01-24 11:37:04,606] [INFO] Task succeeded: CheckM
[2024-01-24 11:37:04,608] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:37:04,628] [INFO] ===== Completeness check finished =====
[2024-01-24 11:37:04,629] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:37:04,629] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026229185.1_ASM2622918v1_genomic.fna/markers.fasta)
[2024-01-24 11:37:04,630] [INFO] Task started: Blastn
[2024-01-24 11:37:04,630] [INFO] Running command: blastn -query GCF_026229185.1_ASM2622918v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff6b92a8-2261-4cbf-b215-5459190ef1c5/dqc_reference/reference_markers_gtdb.fasta -out GCF_026229185.1_ASM2622918v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:37:05,474] [INFO] Task succeeded: Blastn
[2024-01-24 11:37:05,477] [INFO] Selected 21 target genomes.
[2024-01-24 11:37:05,477] [INFO] Target genome list was writen to GCF_026229185.1_ASM2622918v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:37:05,512] [INFO] Task started: fastANI
[2024-01-24 11:37:05,512] [INFO] Running command: fastANI --query /var/lib/cwl/stg590c8334-6fec-4dc4-8f5f-f809a1b15df8/GCF_026229185.1_ASM2622918v1_genomic.fna.gz --refList GCF_026229185.1_ASM2622918v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026229185.1_ASM2622918v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:37:16,377] [INFO] Task succeeded: fastANI
[2024-01-24 11:37:16,390] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:37:16,391] [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	78.7496	156	1596	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Fodinibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182555.1	s__Aliifodinibius sediminis	78.5937	240	1596	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	77.9205	168	1596	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	77.7809	230	1596	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Aliifodinibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005869845.1	s__Fodinibius saliphilus	77.1141	128	1596	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	76.9617	130	1596	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	75.9949	68	1596	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 11:37:16,392] [INFO] GTDB search result was written to GCF_026229185.1_ASM2622918v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:37:16,393] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:37:16,396] [INFO] DFAST_QC result json was written to GCF_026229185.1_ASM2622918v1_genomic.fna/dqc_result.json
[2024-01-24 11:37:16,398] [INFO] DFAST_QC completed!
[2024-01-24 11:37:16,399] [INFO] Total running time: 0h1m54s