[2023-03-17 13:01:51,481] [INFO] DFAST_QC pipeline started.
[2023-03-17 13:01:51,481] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 13:01:51,481] [INFO] DQC Reference Directory: /var/lib/cwl/stgfdaac0a4-61b7-4a18-8bbe-fab697880ddd/dqc_reference
[2023-03-17 13:01:52,676] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 13:01:52,676] [INFO] Task started: Prodigal
[2023-03-17 13:01:52,676] [INFO] Running command: cat /var/lib/cwl/stgfd2aa014-d3f9-46b9-af97-b865aa44d02a/OceanDNA-b28610.fa | prodigal -d OceanDNA-b28610/cds.fna -a OceanDNA-b28610/protein.faa -g 11 -q > /dev/null
[2023-03-17 13:02:00,742] [INFO] Task succeeded: Prodigal
[2023-03-17 13:02:00,743] [INFO] Task started: HMMsearch
[2023-03-17 13:02:00,743] [INFO] Running command: hmmsearch --tblout OceanDNA-b28610/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfdaac0a4-61b7-4a18-8bbe-fab697880ddd/dqc_reference/reference_markers.hmm OceanDNA-b28610/protein.faa > /dev/null
[2023-03-17 13:02:00,963] [INFO] Task succeeded: HMMsearch
[2023-03-17 13:02:00,964] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfd2aa014-d3f9-46b9-af97-b865aa44d02a/OceanDNA-b28610.fa]
[2023-03-17 13:02:00,979] [INFO] Query marker FASTA was written to OceanDNA-b28610/markers.fasta
[2023-03-17 13:02:00,979] [INFO] Task started: Blastn
[2023-03-17 13:02:00,979] [INFO] Running command: blastn -query OceanDNA-b28610/markers.fasta -db /var/lib/cwl/stgfdaac0a4-61b7-4a18-8bbe-fab697880ddd/dqc_reference/reference_markers.fasta -out OceanDNA-b28610/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:02:01,548] [INFO] Task succeeded: Blastn
[2023-03-17 13:02:01,549] [INFO] Selected 29 target genomes.
[2023-03-17 13:02:01,549] [INFO] Target genome list was writen to OceanDNA-b28610/target_genomes.txt
[2023-03-17 13:02:01,565] [INFO] Task started: fastANI
[2023-03-17 13:02:01,565] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd2aa014-d3f9-46b9-af97-b865aa44d02a/OceanDNA-b28610.fa --refList OceanDNA-b28610/target_genomes.txt --output OceanDNA-b28610/fastani_result.tsv --threads 1
[2023-03-17 13:02:23,514] [INFO] Task succeeded: fastANI
[2023-03-17 13:02:23,514] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfdaac0a4-61b7-4a18-8bbe-fab697880ddd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 13:02:23,514] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfdaac0a4-61b7-4a18-8bbe-fab697880ddd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 13:02:23,515] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 13:02:23,515] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 13:02:23,515] [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
--------------------------------------------------------------------------------
[2023-03-17 13:02:23,515] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28610/tc_result.tsv
[2023-03-17 13:02:23,515] [INFO] ===== Taxonomy check completed =====
[2023-03-17 13:02:23,515] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 13:02:23,515] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfdaac0a4-61b7-4a18-8bbe-fab697880ddd/dqc_reference/checkm_data
[2023-03-17 13:02:23,518] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 13:02:23,522] [INFO] Task started: CheckM
[2023-03-17 13:02:23,522] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28610/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28610/checkm_input OceanDNA-b28610/checkm_result
[2023-03-17 13:02:49,379] [INFO] Task succeeded: CheckM
[2023-03-17 13:02:49,380] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 48.73%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 13:02:49,382] [INFO] ===== Completeness check finished =====
[2023-03-17 13:02:49,382] [INFO] ===== Start GTDB Search =====
[2023-03-17 13:02:49,382] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28610/markers.fasta)
[2023-03-17 13:02:49,382] [INFO] Task started: Blastn
[2023-03-17 13:02:49,382] [INFO] Running command: blastn -query OceanDNA-b28610/markers.fasta -db /var/lib/cwl/stgfdaac0a4-61b7-4a18-8bbe-fab697880ddd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28610/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:02:50,250] [INFO] Task succeeded: Blastn
[2023-03-17 13:02:50,250] [INFO] Selected 21 target genomes.
[2023-03-17 13:02:50,251] [INFO] Target genome list was writen to OceanDNA-b28610/target_genomes_gtdb.txt
[2023-03-17 13:02:50,481] [INFO] Task started: fastANI
[2023-03-17 13:02:50,481] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd2aa014-d3f9-46b9-af97-b865aa44d02a/OceanDNA-b28610.fa --refList OceanDNA-b28610/target_genomes_gtdb.txt --output OceanDNA-b28610/fastani_result_gtdb.tsv --threads 1
[2023-03-17 13:03:02,645] [INFO] Task succeeded: fastANI
[2023-03-17 13:03:02,648] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 13:03:02,648] [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
GCA_002336405.1	s__CPC320 sp002336405	81.1994	213	323	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CPC320	95.0	98.74	97.78	0.79	0.51	9	-
GCA_002684375.1	s__CPC320 sp002684375	80.6987	209	323	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CPC320	95.0	98.52	98.26	0.79	0.72	8	-
--------------------------------------------------------------------------------
[2023-03-17 13:03:02,648] [INFO] GTDB search result was written to OceanDNA-b28610/result_gtdb.tsv
[2023-03-17 13:03:02,648] [INFO] ===== GTDB Search completed =====
[2023-03-17 13:03:02,649] [INFO] DFAST_QC result json was written to OceanDNA-b28610/dqc_result.json
[2023-03-17 13:03:02,649] [INFO] DFAST_QC completed!
[2023-03-17 13:03:02,649] [INFO] Total running time: 0h1m11s