[2023-03-15 23:07:02,649] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:07:02,649] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:07:02,649] [INFO] DQC Reference Directory: /var/lib/cwl/stgeb85e9ae-67e4-4d93-89ba-e2bc446123b7/dqc_reference
[2023-03-15 23:07:03,966] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:07:03,966] [INFO] Task started: Prodigal
[2023-03-15 23:07:03,966] [INFO] Running command: cat /var/lib/cwl/stg4e1ea80c-3540-4822-9e37-de5997901fb2/OceanDNA-b23089.fa | prodigal -d OceanDNA-b23089/cds.fna -a OceanDNA-b23089/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:07:24,525] [INFO] Task succeeded: Prodigal
[2023-03-15 23:07:24,525] [INFO] Task started: HMMsearch
[2023-03-15 23:07:24,525] [INFO] Running command: hmmsearch --tblout OceanDNA-b23089/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeb85e9ae-67e4-4d93-89ba-e2bc446123b7/dqc_reference/reference_markers.hmm OceanDNA-b23089/protein.faa > /dev/null
[2023-03-15 23:07:24,732] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:07:24,732] [INFO] Found 6/6 markers.
[2023-03-15 23:07:24,758] [INFO] Query marker FASTA was written to OceanDNA-b23089/markers.fasta
[2023-03-15 23:07:24,758] [INFO] Task started: Blastn
[2023-03-15 23:07:24,759] [INFO] Running command: blastn -query OceanDNA-b23089/markers.fasta -db /var/lib/cwl/stgeb85e9ae-67e4-4d93-89ba-e2bc446123b7/dqc_reference/reference_markers.fasta -out OceanDNA-b23089/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:07:25,294] [INFO] Task succeeded: Blastn
[2023-03-15 23:07:25,295] [INFO] Selected 21 target genomes.
[2023-03-15 23:07:25,295] [INFO] Target genome list was writen to OceanDNA-b23089/target_genomes.txt
[2023-03-15 23:07:25,322] [INFO] Task started: fastANI
[2023-03-15 23:07:25,322] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e1ea80c-3540-4822-9e37-de5997901fb2/OceanDNA-b23089.fa --refList OceanDNA-b23089/target_genomes.txt --output OceanDNA-b23089/fastani_result.tsv --threads 1
[2023-03-15 23:07:43,234] [INFO] Task succeeded: fastANI
[2023-03-15 23:07:43,234] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeb85e9ae-67e4-4d93-89ba-e2bc446123b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:07:43,234] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeb85e9ae-67e4-4d93-89ba-e2bc446123b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:07:43,238] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:07:43,238] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 23:07:43,238] [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
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	74.9425	50	999	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	74.8125	50	999	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 23:07:43,240] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23089/tc_result.tsv
[2023-03-15 23:07:43,242] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:07:43,242] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:07:43,242] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeb85e9ae-67e4-4d93-89ba-e2bc446123b7/dqc_reference/checkm_data
[2023-03-15 23:07:43,243] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:07:43,250] [INFO] Task started: CheckM
[2023-03-15 23:07:43,250] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23089/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23089/checkm_input OceanDNA-b23089/checkm_result
[2023-03-15 23:08:35,079] [INFO] Task succeeded: CheckM
[2023-03-15 23:08:35,080] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:08:35,114] [INFO] ===== Completeness check finished =====
[2023-03-15 23:08:35,114] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:08:35,114] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23089/markers.fasta)
[2023-03-15 23:08:35,116] [INFO] Task started: Blastn
[2023-03-15 23:08:35,116] [INFO] Running command: blastn -query OceanDNA-b23089/markers.fasta -db /var/lib/cwl/stgeb85e9ae-67e4-4d93-89ba-e2bc446123b7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23089/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:08:35,919] [INFO] Task succeeded: Blastn
[2023-03-15 23:08:35,938] [INFO] Selected 15 target genomes.
[2023-03-15 23:08:35,938] [INFO] Target genome list was writen to OceanDNA-b23089/target_genomes_gtdb.txt
[2023-03-15 23:08:35,948] [INFO] Task started: fastANI
[2023-03-15 23:08:35,948] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e1ea80c-3540-4822-9e37-de5997901fb2/OceanDNA-b23089.fa --refList OceanDNA-b23089/target_genomes_gtdb.txt --output OceanDNA-b23089/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:08:46,365] [INFO] Task succeeded: fastANI
[2023-03-15 23:08:46,372] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:08:46,372] [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_011051855.1	s__GCA-2684655 sp011051855	77.1491	123	999	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__GCA-2684655	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872675.1	s__UBA2386 sp016872675	77.0685	151	999	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__UBA2386	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794425.1	s__JAEUHS01 sp016794425	77.0637	179	999	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__JAEUHS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794035.1	s__JAEUHS01 sp016794035	77.0103	181	999	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__JAEUHS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793265.1	s__UBA2386 sp016793265	76.9259	169	999	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__UBA2386	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016873195.1	s__VGXW01 sp016873195	76.892	131	999	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__VGXW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713175.1	s__JADJPQ01 sp016713175	76.8679	202	999	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__JADJPQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794485.1	s__UBA2386 sp016794485	76.8416	139	999	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__UBA2386	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795295.1	s__VGXW01 sp016795295	76.808	135	999	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__VGXW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002684655.1	s__GCA-2684655 sp002684655	76.5797	93	999	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__GCA-2684655	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793305.1	s__UBA2386 sp016793305	76.4644	134	999	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__UBA2386	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794565.1	s__JAEUHS01 sp016794565	76.3501	130	999	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__JAEUHS01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 23:08:46,375] [INFO] GTDB search result was written to OceanDNA-b23089/result_gtdb.tsv
[2023-03-15 23:08:46,380] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:08:46,385] [INFO] DFAST_QC result json was written to OceanDNA-b23089/dqc_result.json
[2023-03-15 23:08:46,385] [INFO] DFAST_QC completed!
[2023-03-15 23:08:46,385] [INFO] Total running time: 0h1m44s