[2023-03-14 14:44:33,113] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:44:33,113] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:44:33,113] [INFO] DQC Reference Directory: /var/lib/cwl/stg11628209-d8a3-4647-86d6-df6e0ac03e5e/dqc_reference
[2023-03-14 14:44:34,301] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:44:34,302] [INFO] Task started: Prodigal
[2023-03-14 14:44:34,302] [INFO] Running command: cat /var/lib/cwl/stgbbceca31-d83b-4dae-98c2-10d2b59a3ca6/OceanDNA-b40593.fa | prodigal -d OceanDNA-b40593/cds.fna -a OceanDNA-b40593/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:44:50,607] [INFO] Task succeeded: Prodigal
[2023-03-14 14:44:50,607] [INFO] Task started: HMMsearch
[2023-03-14 14:44:50,607] [INFO] Running command: hmmsearch --tblout OceanDNA-b40593/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11628209-d8a3-4647-86d6-df6e0ac03e5e/dqc_reference/reference_markers.hmm OceanDNA-b40593/protein.faa > /dev/null
[2023-03-14 14:44:51,034] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:44:51,034] [INFO] Found 6/6 markers.
[2023-03-14 14:44:51,050] [INFO] Query marker FASTA was written to OceanDNA-b40593/markers.fasta
[2023-03-14 14:44:51,051] [INFO] Task started: Blastn
[2023-03-14 14:44:51,051] [INFO] Running command: blastn -query OceanDNA-b40593/markers.fasta -db /var/lib/cwl/stg11628209-d8a3-4647-86d6-df6e0ac03e5e/dqc_reference/reference_markers.fasta -out OceanDNA-b40593/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:44:51,783] [INFO] Task succeeded: Blastn
[2023-03-14 14:44:51,784] [INFO] Selected 21 target genomes.
[2023-03-14 14:44:51,785] [INFO] Target genome list was writen to OceanDNA-b40593/target_genomes.txt
[2023-03-14 14:44:51,796] [INFO] Task started: fastANI
[2023-03-14 14:44:51,796] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbceca31-d83b-4dae-98c2-10d2b59a3ca6/OceanDNA-b40593.fa --refList OceanDNA-b40593/target_genomes.txt --output OceanDNA-b40593/fastani_result.tsv --threads 1
[2023-03-14 14:45:03,100] [INFO] Task succeeded: fastANI
[2023-03-14 14:45:03,101] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11628209-d8a3-4647-86d6-df6e0ac03e5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:45:03,101] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11628209-d8a3-4647-86d6-df6e0ac03e5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:45:03,101] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 14:45:03,101] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 14:45:03,101] [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
--------------------------------------------------------------------------------
[2023-03-14 14:45:03,102] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40593/tc_result.tsv
[2023-03-14 14:45:03,102] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:45:03,102] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:45:03,102] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11628209-d8a3-4647-86d6-df6e0ac03e5e/dqc_reference/checkm_data
[2023-03-14 14:45:03,105] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:45:03,109] [INFO] Task started: CheckM
[2023-03-14 14:45:03,109] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40593/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40593/checkm_input OceanDNA-b40593/checkm_result
[2023-03-14 14:45:40,936] [INFO] Task succeeded: CheckM
[2023-03-14 14:45:40,936] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 2.69%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-14 14:45:40,938] [INFO] ===== Completeness check finished =====
[2023-03-14 14:45:40,938] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:45:40,939] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40593/markers.fasta)
[2023-03-14 14:45:40,940] [INFO] Task started: Blastn
[2023-03-14 14:45:40,940] [INFO] Running command: blastn -query OceanDNA-b40593/markers.fasta -db /var/lib/cwl/stg11628209-d8a3-4647-86d6-df6e0ac03e5e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40593/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:45:42,011] [INFO] Task succeeded: Blastn
[2023-03-14 14:45:42,012] [INFO] Selected 22 target genomes.
[2023-03-14 14:45:42,012] [INFO] Target genome list was writen to OceanDNA-b40593/target_genomes_gtdb.txt
[2023-03-14 14:45:42,199] [INFO] Task started: fastANI
[2023-03-14 14:45:42,199] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbceca31-d83b-4dae-98c2-10d2b59a3ca6/OceanDNA-b40593.fa --refList OceanDNA-b40593/target_genomes_gtdb.txt --output OceanDNA-b40593/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:45:52,132] [INFO] Task succeeded: fastANI
[2023-03-14 14:45:52,136] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 14:45:52,136] [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_002727755.1	s__UBA9145 sp002727755	93.991	392	614	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	97.64	97.41	0.73	0.73	3	-
GCA_902591495.1	s__UBA9145 sp902591495	92.6705	407	614	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902531515.1	s__UBA9145 sp902531515	79.1011	194	614	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002714195.1	s__UBA9145 sp002714195	78.4772	168	614	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002172295.1	s__UBA9145 sp002172295	76.4237	73	614	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-14 14:45:52,136] [INFO] GTDB search result was written to OceanDNA-b40593/result_gtdb.tsv
[2023-03-14 14:45:52,137] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:45:52,138] [INFO] DFAST_QC result json was written to OceanDNA-b40593/dqc_result.json
[2023-03-14 14:45:52,138] [INFO] DFAST_QC completed!
[2023-03-14 14:45:52,138] [INFO] Total running time: 0h1m19s