[2023-03-17 08:04:06,987] [INFO] DFAST_QC pipeline started.
[2023-03-17 08:04:06,987] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 08:04:06,987] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd12dd30-d3f8-4bf7-bc73-36b18167ec48/dqc_reference
[2023-03-17 08:04:08,770] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 08:04:08,770] [INFO] Task started: Prodigal
[2023-03-17 08:04:08,770] [INFO] Running command: cat /var/lib/cwl/stg1a855f85-fd78-4c81-a0d8-671b683e3c3d/OceanDNA-b34792.fa | prodigal -d OceanDNA-b34792/cds.fna -a OceanDNA-b34792/protein.faa -g 11 -q > /dev/null
[2023-03-17 08:04:16,330] [INFO] Task succeeded: Prodigal
[2023-03-17 08:04:16,331] [INFO] Task started: HMMsearch
[2023-03-17 08:04:16,331] [INFO] Running command: hmmsearch --tblout OceanDNA-b34792/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd12dd30-d3f8-4bf7-bc73-36b18167ec48/dqc_reference/reference_markers.hmm OceanDNA-b34792/protein.faa > /dev/null
[2023-03-17 08:04:16,497] [INFO] Task succeeded: HMMsearch
[2023-03-17 08:04:16,498] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg1a855f85-fd78-4c81-a0d8-671b683e3c3d/OceanDNA-b34792.fa]
[2023-03-17 08:04:16,514] [INFO] Query marker FASTA was written to OceanDNA-b34792/markers.fasta
[2023-03-17 08:04:16,514] [INFO] Task started: Blastn
[2023-03-17 08:04:16,514] [INFO] Running command: blastn -query OceanDNA-b34792/markers.fasta -db /var/lib/cwl/stgcd12dd30-d3f8-4bf7-bc73-36b18167ec48/dqc_reference/reference_markers.fasta -out OceanDNA-b34792/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:04:17,004] [INFO] Task succeeded: Blastn
[2023-03-17 08:04:17,005] [INFO] Selected 18 target genomes.
[2023-03-17 08:04:17,005] [INFO] Target genome list was writen to OceanDNA-b34792/target_genomes.txt
[2023-03-17 08:04:17,015] [INFO] Task started: fastANI
[2023-03-17 08:04:17,015] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a855f85-fd78-4c81-a0d8-671b683e3c3d/OceanDNA-b34792.fa --refList OceanDNA-b34792/target_genomes.txt --output OceanDNA-b34792/fastani_result.tsv --threads 1
[2023-03-17 08:04:28,149] [INFO] Task succeeded: fastANI
[2023-03-17 08:04:28,149] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd12dd30-d3f8-4bf7-bc73-36b18167ec48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 08:04:28,150] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd12dd30-d3f8-4bf7-bc73-36b18167ec48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 08:04:28,154] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 08:04:28,154] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 08:04:28,154] [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
Glaciecola pallidula	strain=DSM 14239	GCA_000428905.1	56807	56807	type	True	81.8341	262	334	95	below_threshold
Glaciecola pallidula	strain=ACAM 615	GCA_000315035.1	56807	56807	type	True	81.7826	263	334	95	below_threshold
Glaciecola nitratireducens	strain=FR1064	GCA_000226565.1	300231	300231	type	True	78.9064	175	334	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 08:04:28,154] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34792/tc_result.tsv
[2023-03-17 08:04:28,154] [INFO] ===== Taxonomy check completed =====
[2023-03-17 08:04:28,154] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 08:04:28,154] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd12dd30-d3f8-4bf7-bc73-36b18167ec48/dqc_reference/checkm_data
[2023-03-17 08:04:28,155] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 08:04:28,170] [INFO] Task started: CheckM
[2023-03-17 08:04:28,170] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34792/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34792/checkm_input OceanDNA-b34792/checkm_result
[2023-03-17 08:04:52,671] [INFO] Task succeeded: CheckM
[2023-03-17 08:04:52,671] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 08:04:52,673] [INFO] ===== Completeness check finished =====
[2023-03-17 08:04:52,673] [INFO] ===== Start GTDB Search =====
[2023-03-17 08:04:52,673] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34792/markers.fasta)
[2023-03-17 08:04:52,675] [INFO] Task started: Blastn
[2023-03-17 08:04:52,675] [INFO] Running command: blastn -query OceanDNA-b34792/markers.fasta -db /var/lib/cwl/stgcd12dd30-d3f8-4bf7-bc73-36b18167ec48/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34792/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:04:53,308] [INFO] Task succeeded: Blastn
[2023-03-17 08:04:53,309] [INFO] Selected 16 target genomes.
[2023-03-17 08:04:53,309] [INFO] Target genome list was writen to OceanDNA-b34792/target_genomes_gtdb.txt
[2023-03-17 08:04:53,461] [INFO] Task started: fastANI
[2023-03-17 08:04:53,461] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a855f85-fd78-4c81-a0d8-671b683e3c3d/OceanDNA-b34792.fa --refList OceanDNA-b34792/target_genomes_gtdb.txt --output OceanDNA-b34792/fastani_result_gtdb.tsv --threads 1
[2023-03-17 08:05:03,344] [INFO] Task succeeded: fastANI
[2023-03-17 08:05:03,347] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 08:05:03,347] [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_000428905.1	s__Glaciecola pallidula	81.8341	262	334	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002836745.1	s__Glaciecola sp002836745	81.677	257	334	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000226565.1	s__Glaciecola nitratireducens	78.9064	175	334	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479945.1	s__Glaciecola sp905479945	78.0213	98	334	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 08:05:03,348] [INFO] GTDB search result was written to OceanDNA-b34792/result_gtdb.tsv
[2023-03-17 08:05:03,348] [INFO] ===== GTDB Search completed =====
[2023-03-17 08:05:03,348] [INFO] DFAST_QC result json was written to OceanDNA-b34792/dqc_result.json
[2023-03-17 08:05:03,348] [INFO] DFAST_QC completed!
[2023-03-17 08:05:03,348] [INFO] Total running time: 0h0m56s