[2023-03-15 22:06:34,771] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:06:34,771] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:06:34,771] [INFO] DQC Reference Directory: /var/lib/cwl/stg50319a98-30ab-4c84-b44b-e11907b2edac/dqc_reference
[2023-03-15 22:06:35,885] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:06:35,885] [INFO] Task started: Prodigal
[2023-03-15 22:06:35,885] [INFO] Running command: cat /var/lib/cwl/stg36ee6983-ce60-4bd3-b7a5-240242f0e3b8/OceanDNA-b25183.fa | prodigal -d OceanDNA-b25183/cds.fna -a OceanDNA-b25183/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:06:38,538] [INFO] Task succeeded: Prodigal
[2023-03-15 22:06:38,539] [INFO] Task started: HMMsearch
[2023-03-15 22:06:38,539] [INFO] Running command: hmmsearch --tblout OceanDNA-b25183/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50319a98-30ab-4c84-b44b-e11907b2edac/dqc_reference/reference_markers.hmm OceanDNA-b25183/protein.faa > /dev/null
[2023-03-15 22:06:38,687] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:06:38,687] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg36ee6983-ce60-4bd3-b7a5-240242f0e3b8/OceanDNA-b25183.fa]
[2023-03-15 22:06:38,694] [INFO] Query marker FASTA was written to OceanDNA-b25183/markers.fasta
[2023-03-15 22:06:38,695] [INFO] Task started: Blastn
[2023-03-15 22:06:38,695] [INFO] Running command: blastn -query OceanDNA-b25183/markers.fasta -db /var/lib/cwl/stg50319a98-30ab-4c84-b44b-e11907b2edac/dqc_reference/reference_markers.fasta -out OceanDNA-b25183/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:06:39,266] [INFO] Task succeeded: Blastn
[2023-03-15 22:06:39,267] [INFO] Selected 16 target genomes.
[2023-03-15 22:06:39,267] [INFO] Target genome list was writen to OceanDNA-b25183/target_genomes.txt
[2023-03-15 22:06:39,278] [INFO] Task started: fastANI
[2023-03-15 22:06:39,278] [INFO] Running command: fastANI --query /var/lib/cwl/stg36ee6983-ce60-4bd3-b7a5-240242f0e3b8/OceanDNA-b25183.fa --refList OceanDNA-b25183/target_genomes.txt --output OceanDNA-b25183/fastani_result.tsv --threads 1
[2023-03-15 22:06:45,433] [INFO] Task succeeded: fastANI
[2023-03-15 22:06:45,433] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50319a98-30ab-4c84-b44b-e11907b2edac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:06:45,433] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50319a98-30ab-4c84-b44b-e11907b2edac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:06:45,433] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:06:45,433] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 22:06:45,434] [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
--------------------------------------------------------------------------------
[2023-03-15 22:06:45,434] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25183/tc_result.tsv
[2023-03-15 22:06:45,434] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:06:45,434] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:06:45,434] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50319a98-30ab-4c84-b44b-e11907b2edac/dqc_reference/checkm_data
[2023-03-15 22:06:45,438] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:06:45,440] [INFO] Task started: CheckM
[2023-03-15 22:06:45,440] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25183/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25183/checkm_input OceanDNA-b25183/checkm_result
[2023-03-15 22:06:58,733] [INFO] Task succeeded: CheckM
[2023-03-15 22:06:58,733] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.20%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 22:06:58,734] [INFO] ===== Completeness check finished =====
[2023-03-15 22:06:58,735] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:06:58,735] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25183/markers.fasta)
[2023-03-15 22:06:58,735] [INFO] Task started: Blastn
[2023-03-15 22:06:58,735] [INFO] Running command: blastn -query OceanDNA-b25183/markers.fasta -db /var/lib/cwl/stg50319a98-30ab-4c84-b44b-e11907b2edac/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25183/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:06:59,412] [INFO] Task succeeded: Blastn
[2023-03-15 22:06:59,413] [INFO] Selected 15 target genomes.
[2023-03-15 22:06:59,413] [INFO] Target genome list was writen to OceanDNA-b25183/target_genomes_gtdb.txt
[2023-03-15 22:06:59,425] [INFO] Task started: fastANI
[2023-03-15 22:06:59,425] [INFO] Running command: fastANI --query /var/lib/cwl/stg36ee6983-ce60-4bd3-b7a5-240242f0e3b8/OceanDNA-b25183.fa --refList OceanDNA-b25183/target_genomes_gtdb.txt --output OceanDNA-b25183/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:07:02,047] [INFO] Task succeeded: fastANI
[2023-03-15 22:07:02,051] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 22:07:02,052] [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_905182145.1	s__CACCCN01 sp905182145	83.7892	100	148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__CACCCN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016777745.1	s__CACCCN01 sp016777745	83.532	67	148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__CACCCN01	95.0	99.44	99.44	0.52	0.52	2	-
GCA_905182445.1	s__CACCCN01 sp905182445	82.5635	92	148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__CACCCN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902544525.1	s__CACCCN01 sp902544525	78.9749	106	148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__CACCCN01	95.0	95.77	95.63	0.82	0.80	3	-
GCA_905182345.1	s__CACCCN01 sp905182345	78.7948	94	148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__CACCCN01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 22:07:02,052] [INFO] GTDB search result was written to OceanDNA-b25183/result_gtdb.tsv
[2023-03-15 22:07:02,052] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:07:02,053] [INFO] DFAST_QC result json was written to OceanDNA-b25183/dqc_result.json
[2023-03-15 22:07:02,053] [INFO] DFAST_QC completed!
[2023-03-15 22:07:02,053] [INFO] Total running time: 0h0m27s