[2023-03-17 11:57:19,284] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:57:19,284] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:57:19,285] [INFO] DQC Reference Directory: /var/lib/cwl/stg18e73312-c60f-464c-80e9-c75be3c578fd/dqc_reference
[2023-03-17 11:57:20,886] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:57:20,887] [INFO] Task started: Prodigal
[2023-03-17 11:57:20,887] [INFO] Running command: cat /var/lib/cwl/stg78f9a8c6-60a8-40c8-b969-9dfd030304b0/OceanDNA-b23096.fa | prodigal -d OceanDNA-b23096/cds.fna -a OceanDNA-b23096/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:57:51,213] [INFO] Task succeeded: Prodigal
[2023-03-17 11:57:51,213] [INFO] Task started: HMMsearch
[2023-03-17 11:57:51,213] [INFO] Running command: hmmsearch --tblout OceanDNA-b23096/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18e73312-c60f-464c-80e9-c75be3c578fd/dqc_reference/reference_markers.hmm OceanDNA-b23096/protein.faa > /dev/null
[2023-03-17 11:57:51,441] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:57:51,441] [INFO] Found 6/6 markers.
[2023-03-17 11:57:51,470] [INFO] Query marker FASTA was written to OceanDNA-b23096/markers.fasta
[2023-03-17 11:57:51,471] [INFO] Task started: Blastn
[2023-03-17 11:57:51,471] [INFO] Running command: blastn -query OceanDNA-b23096/markers.fasta -db /var/lib/cwl/stg18e73312-c60f-464c-80e9-c75be3c578fd/dqc_reference/reference_markers.fasta -out OceanDNA-b23096/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:57:52,027] [INFO] Task succeeded: Blastn
[2023-03-17 11:57:52,028] [INFO] Selected 25 target genomes.
[2023-03-17 11:57:52,028] [INFO] Target genome list was writen to OceanDNA-b23096/target_genomes.txt
[2023-03-17 11:57:52,066] [INFO] Task started: fastANI
[2023-03-17 11:57:52,066] [INFO] Running command: fastANI --query /var/lib/cwl/stg78f9a8c6-60a8-40c8-b969-9dfd030304b0/OceanDNA-b23096.fa --refList OceanDNA-b23096/target_genomes.txt --output OceanDNA-b23096/fastani_result.tsv --threads 1
[2023-03-17 11:58:06,220] [INFO] Task succeeded: fastANI
[2023-03-17 11:58:06,220] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18e73312-c60f-464c-80e9-c75be3c578fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:58:06,220] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18e73312-c60f-464c-80e9-c75be3c578fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:58:06,221] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:58:06,221] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 11:58:06,221] [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 11:58:06,221] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23096/tc_result.tsv
[2023-03-17 11:58:06,221] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:58:06,221] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:58:06,221] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18e73312-c60f-464c-80e9-c75be3c578fd/dqc_reference/checkm_data
[2023-03-17 11:58:06,224] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:58:06,229] [INFO] Task started: CheckM
[2023-03-17 11:58:06,229] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23096/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23096/checkm_input OceanDNA-b23096/checkm_result
[2023-03-17 11:59:18,671] [INFO] Task succeeded: CheckM
[2023-03-17 11:59:18,671] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:59:18,851] [INFO] ===== Completeness check finished =====
[2023-03-17 11:59:18,851] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:59:18,851] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23096/markers.fasta)
[2023-03-17 11:59:18,851] [INFO] Task started: Blastn
[2023-03-17 11:59:18,851] [INFO] Running command: blastn -query OceanDNA-b23096/markers.fasta -db /var/lib/cwl/stg18e73312-c60f-464c-80e9-c75be3c578fd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23096/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:59:20,150] [INFO] Task succeeded: Blastn
[2023-03-17 11:59:20,151] [INFO] Selected 12 target genomes.
[2023-03-17 11:59:20,151] [INFO] Target genome list was writen to OceanDNA-b23096/target_genomes_gtdb.txt
[2023-03-17 11:59:20,355] [INFO] Task started: fastANI
[2023-03-17 11:59:20,355] [INFO] Running command: fastANI --query /var/lib/cwl/stg78f9a8c6-60a8-40c8-b969-9dfd030304b0/OceanDNA-b23096.fa --refList OceanDNA-b23096/target_genomes_gtdb.txt --output OceanDNA-b23096/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:59:29,417] [INFO] Task succeeded: fastANI
[2023-03-17 11:59:29,424] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:59:29,424] [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	78.2863	370	1540	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_016793265.1	s__UBA2386 sp016793265	77.7332	354	1540	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__UBA2386	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794035.1	s__JAEUHS01 sp016794035	77.7123	380	1540	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__JAEUHS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794425.1	s__JAEUHS01 sp016794425	77.6463	373	1540	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__JAEUHS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002684655.1	s__GCA-2684655 sp002684655	77.5941	282	1540	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	77.5723	311	1540	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__UBA2386	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794485.1	s__UBA2386 sp016794485	77.3132	323	1540	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__UBA2386	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002343845.1	s__UBA2386 sp002343845	77.3013	256	1540	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__UBA2386	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793305.1	s__UBA2386 sp016793305	77.1727	292	1540	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	77.0974	260	1540	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__VGXW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005776475.1	s__UBA2386 sp005776475	77.0334	323	1540	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	76.9752	261	1540	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__VGXW01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:59:29,424] [INFO] GTDB search result was written to OceanDNA-b23096/result_gtdb.tsv
[2023-03-17 11:59:29,424] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:59:29,425] [INFO] DFAST_QC result json was written to OceanDNA-b23096/dqc_result.json
[2023-03-17 11:59:29,425] [INFO] DFAST_QC completed!
[2023-03-17 11:59:29,425] [INFO] Total running time: 0h2m10s