[2023-03-15 17:50:47,194] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:50:47,194] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:50:47,194] [INFO] DQC Reference Directory: /var/lib/cwl/stge9c942b1-b6c8-40ef-ab5c-ad0cecd7d170/dqc_reference
[2023-03-15 17:50:48,325] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:50:48,325] [INFO] Task started: Prodigal
[2023-03-15 17:50:48,325] [INFO] Running command: cat /var/lib/cwl/stgc8dfb381-b392-491d-a6e5-d83d0d564e6b/OceanDNA-b22944.fa | prodigal -d OceanDNA-b22944/cds.fna -a OceanDNA-b22944/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:51:22,393] [INFO] Task succeeded: Prodigal
[2023-03-15 17:51:22,393] [INFO] Task started: HMMsearch
[2023-03-15 17:51:22,393] [INFO] Running command: hmmsearch --tblout OceanDNA-b22944/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9c942b1-b6c8-40ef-ab5c-ad0cecd7d170/dqc_reference/reference_markers.hmm OceanDNA-b22944/protein.faa > /dev/null
[2023-03-15 17:51:22,646] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:51:22,646] [INFO] Found 6/6 markers.
[2023-03-15 17:51:22,674] [INFO] Query marker FASTA was written to OceanDNA-b22944/markers.fasta
[2023-03-15 17:51:22,676] [INFO] Task started: Blastn
[2023-03-15 17:51:22,676] [INFO] Running command: blastn -query OceanDNA-b22944/markers.fasta -db /var/lib/cwl/stge9c942b1-b6c8-40ef-ab5c-ad0cecd7d170/dqc_reference/reference_markers.fasta -out OceanDNA-b22944/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:51:23,218] [INFO] Task succeeded: Blastn
[2023-03-15 17:51:23,219] [INFO] Selected 21 target genomes.
[2023-03-15 17:51:23,219] [INFO] Target genome list was writen to OceanDNA-b22944/target_genomes.txt
[2023-03-15 17:51:23,233] [INFO] Task started: fastANI
[2023-03-15 17:51:23,233] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8dfb381-b392-491d-a6e5-d83d0d564e6b/OceanDNA-b22944.fa --refList OceanDNA-b22944/target_genomes.txt --output OceanDNA-b22944/fastani_result.tsv --threads 1
[2023-03-15 17:51:40,583] [INFO] Task succeeded: fastANI
[2023-03-15 17:51:40,583] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9c942b1-b6c8-40ef-ab5c-ad0cecd7d170/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:51:40,583] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9c942b1-b6c8-40ef-ab5c-ad0cecd7d170/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:51:40,588] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:51:40,588] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 17:51:40,588] [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
Maioricimonas rarisocia	strain=Mal4	GCA_007747795.1	2528026	2528026	type	True	75.5218	94	1749	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	75.367	52	1749	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	75.1924	54	1749	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	75.1266	72	1749	95	below_threshold
Paludisphaera rhizosphaereae	strain=JC665	GCA_011065895.1	2711216	2711216	type	True	74.9709	53	1749	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 17:51:40,589] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22944/tc_result.tsv
[2023-03-15 17:51:40,589] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:51:40,590] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:51:40,590] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9c942b1-b6c8-40ef-ab5c-ad0cecd7d170/dqc_reference/checkm_data
[2023-03-15 17:51:40,590] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:51:40,598] [INFO] Task started: CheckM
[2023-03-15 17:51:40,598] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22944/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22944/checkm_input OceanDNA-b22944/checkm_result
[2023-03-15 17:53:20,936] [INFO] Task succeeded: CheckM
[2023-03-15 17:53:20,937] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:53:20,941] [INFO] ===== Completeness check finished =====
[2023-03-15 17:53:20,941] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:53:20,941] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22944/markers.fasta)
[2023-03-15 17:53:20,943] [INFO] Task started: Blastn
[2023-03-15 17:53:20,943] [INFO] Running command: blastn -query OceanDNA-b22944/markers.fasta -db /var/lib/cwl/stge9c942b1-b6c8-40ef-ab5c-ad0cecd7d170/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22944/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:53:21,885] [INFO] Task succeeded: Blastn
[2023-03-15 17:53:21,886] [INFO] Selected 26 target genomes.
[2023-03-15 17:53:21,886] [INFO] Target genome list was writen to OceanDNA-b22944/target_genomes_gtdb.txt
[2023-03-15 17:53:21,919] [INFO] Task started: fastANI
[2023-03-15 17:53:21,920] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8dfb381-b392-491d-a6e5-d83d0d564e6b/OceanDNA-b22944.fa --refList OceanDNA-b22944/target_genomes_gtdb.txt --output OceanDNA-b22944/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:53:43,240] [INFO] Task succeeded: fastANI
[2023-03-15 17:53:43,245] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 17:53:43,245] [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_002724315.1	s__UBA8437 sp002724315	77.9735	652	1749	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__UBA8437	95.0	97.85	97.85	0.87	0.87	2	-
GCA_003445035.1	s__UBA8437 sp003445035	77.9419	655	1749	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__UBA8437	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002726205.1	s__GCA-2726205 sp002726205	77.0832	415	1749	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__GCA-2726205	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007747795.1	s__Maioricimonas rarisocia	75.5218	94	1749	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Maioricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001610835.1	s__Planctomyces_A sp001610835	75.261	72	1749	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Planctomyces_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795125.1	s__JAEUIG01 sp016795125	75.0948	53	1749	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JAEUIG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 17:53:43,246] [INFO] GTDB search result was written to OceanDNA-b22944/result_gtdb.tsv
[2023-03-15 17:53:43,249] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:53:43,252] [INFO] DFAST_QC result json was written to OceanDNA-b22944/dqc_result.json
[2023-03-15 17:53:43,252] [INFO] DFAST_QC completed!
[2023-03-15 17:53:43,252] [INFO] Total running time: 0h2m56s