[2023-03-17 02:03:49,498] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:03:49,499] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:03:49,499] [INFO] DQC Reference Directory: /var/lib/cwl/stg03571f18-71b5-4fcc-a8fc-75fa3878b0cf/dqc_reference
[2023-03-17 02:03:50,614] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:03:50,614] [INFO] Task started: Prodigal
[2023-03-17 02:03:50,614] [INFO] Running command: cat /var/lib/cwl/stg13e0f154-9c05-4db3-95d5-e45bf02abc5c/OceanDNA-b25733.fa | prodigal -d OceanDNA-b25733/cds.fna -a OceanDNA-b25733/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:03:52,939] [INFO] Task succeeded: Prodigal
[2023-03-17 02:03:52,939] [INFO] Task started: HMMsearch
[2023-03-17 02:03:52,939] [INFO] Running command: hmmsearch --tblout OceanDNA-b25733/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03571f18-71b5-4fcc-a8fc-75fa3878b0cf/dqc_reference/reference_markers.hmm OceanDNA-b25733/protein.faa > /dev/null
[2023-03-17 02:03:53,056] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:03:53,056] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg13e0f154-9c05-4db3-95d5-e45bf02abc5c/OceanDNA-b25733.fa]
[2023-03-17 02:03:53,061] [INFO] Query marker FASTA was written to OceanDNA-b25733/markers.fasta
[2023-03-17 02:03:53,061] [INFO] Task started: Blastn
[2023-03-17 02:03:53,061] [INFO] Running command: blastn -query OceanDNA-b25733/markers.fasta -db /var/lib/cwl/stg03571f18-71b5-4fcc-a8fc-75fa3878b0cf/dqc_reference/reference_markers.fasta -out OceanDNA-b25733/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:03:53,873] [INFO] Task succeeded: Blastn
[2023-03-17 02:03:53,873] [INFO] Selected 9 target genomes.
[2023-03-17 02:03:53,874] [INFO] Target genome list was writen to OceanDNA-b25733/target_genomes.txt
[2023-03-17 02:03:53,879] [INFO] Task started: fastANI
[2023-03-17 02:03:53,879] [INFO] Running command: fastANI --query /var/lib/cwl/stg13e0f154-9c05-4db3-95d5-e45bf02abc5c/OceanDNA-b25733.fa --refList OceanDNA-b25733/target_genomes.txt --output OceanDNA-b25733/fastani_result.tsv --threads 1
[2023-03-17 02:03:57,216] [INFO] Task succeeded: fastANI
[2023-03-17 02:03:57,217] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03571f18-71b5-4fcc-a8fc-75fa3878b0cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:03:57,217] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03571f18-71b5-4fcc-a8fc-75fa3878b0cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:03:57,217] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:03:57,217] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 02:03:57,217] [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 02:03:57,217] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25733/tc_result.tsv
[2023-03-17 02:03:57,217] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:03:57,218] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:03:57,218] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03571f18-71b5-4fcc-a8fc-75fa3878b0cf/dqc_reference/checkm_data
[2023-03-17 02:03:57,220] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:03:57,222] [INFO] Task started: CheckM
[2023-03-17 02:03:57,222] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25733/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25733/checkm_input OceanDNA-b25733/checkm_result
[2023-03-17 02:04:09,614] [INFO] Task succeeded: CheckM
[2023-03-17 02:04:09,615] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.65%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:04:09,616] [INFO] ===== Completeness check finished =====
[2023-03-17 02:04:09,616] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:04:09,616] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25733/markers.fasta)
[2023-03-17 02:04:09,616] [INFO] Task started: Blastn
[2023-03-17 02:04:09,616] [INFO] Running command: blastn -query OceanDNA-b25733/markers.fasta -db /var/lib/cwl/stg03571f18-71b5-4fcc-a8fc-75fa3878b0cf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25733/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:04:11,108] [INFO] Task succeeded: Blastn
[2023-03-17 02:04:11,109] [INFO] Selected 19 target genomes.
[2023-03-17 02:04:11,109] [INFO] Target genome list was writen to OceanDNA-b25733/target_genomes_gtdb.txt
[2023-03-17 02:04:11,678] [INFO] Task started: fastANI
[2023-03-17 02:04:11,678] [INFO] Running command: fastANI --query /var/lib/cwl/stg13e0f154-9c05-4db3-95d5-e45bf02abc5c/OceanDNA-b25733.fa --refList OceanDNA-b25733/target_genomes_gtdb.txt --output OceanDNA-b25733/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:04:14,709] [INFO] Task succeeded: fastANI
[2023-03-17 02:04:14,715] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 02:04:14,715] [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_902608305.1	s__Pelagibacter sp902608305	94.1781	72	123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902592985.1	s__Pelagibacter sp902592985	80.1787	88	123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902597425.1	s__Pelagibacter sp902597425	79.5345	57	123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003215185.1	s__Pelagibacter sp003215185	78.8213	55	123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902634695.1	s__Pelagibacter sp902634695	78.1091	51	123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902564565.1	s__Pelagibacter sp902564565	77.7371	52	123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902608975.1	s__Pelagibacter sp902608975	77.3852	50	123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902583345.1	s__Pelagibacter sp902583345	77.2665	52	123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902573385.1	s__Pelagibacter sp902573385	77.0918	51	123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 02:04:14,715] [INFO] GTDB search result was written to OceanDNA-b25733/result_gtdb.tsv
[2023-03-17 02:04:14,716] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:04:14,716] [INFO] DFAST_QC result json was written to OceanDNA-b25733/dqc_result.json
[2023-03-17 02:04:14,717] [INFO] DFAST_QC completed!
[2023-03-17 02:04:14,717] [INFO] Total running time: 0h0m25s