[2023-03-19 02:05:11,578] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:05:11,578] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:05:11,578] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e5f2c97-a114-4f7e-9af2-1fb30b6fec0f/dqc_reference
[2023-03-19 02:05:13,264] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:05:13,264] [INFO] Task started: Prodigal
[2023-03-19 02:05:13,264] [INFO] Running command: cat /var/lib/cwl/stg58d5ea4d-9bb2-493d-a20d-119e089e3490/OceanDNA-b45896.fa | prodigal -d OceanDNA-b45896/cds.fna -a OceanDNA-b45896/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:05:21,693] [INFO] Task succeeded: Prodigal
[2023-03-19 02:05:21,693] [INFO] Task started: HMMsearch
[2023-03-19 02:05:21,693] [INFO] Running command: hmmsearch --tblout OceanDNA-b45896/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e5f2c97-a114-4f7e-9af2-1fb30b6fec0f/dqc_reference/reference_markers.hmm OceanDNA-b45896/protein.faa > /dev/null
[2023-03-19 02:05:21,844] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:05:21,845] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg58d5ea4d-9bb2-493d-a20d-119e089e3490/OceanDNA-b45896.fa]
[2023-03-19 02:05:21,855] [INFO] Query marker FASTA was written to OceanDNA-b45896/markers.fasta
[2023-03-19 02:05:21,855] [INFO] Task started: Blastn
[2023-03-19 02:05:21,855] [INFO] Running command: blastn -query OceanDNA-b45896/markers.fasta -db /var/lib/cwl/stg8e5f2c97-a114-4f7e-9af2-1fb30b6fec0f/dqc_reference/reference_markers.fasta -out OceanDNA-b45896/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:05:22,411] [INFO] Task succeeded: Blastn
[2023-03-19 02:05:22,412] [INFO] Selected 13 target genomes.
[2023-03-19 02:05:22,412] [INFO] Target genome list was writen to OceanDNA-b45896/target_genomes.txt
[2023-03-19 02:05:22,421] [INFO] Task started: fastANI
[2023-03-19 02:05:22,421] [INFO] Running command: fastANI --query /var/lib/cwl/stg58d5ea4d-9bb2-493d-a20d-119e089e3490/OceanDNA-b45896.fa --refList OceanDNA-b45896/target_genomes.txt --output OceanDNA-b45896/fastani_result.tsv --threads 1
[2023-03-19 02:05:33,772] [INFO] Task succeeded: fastANI
[2023-03-19 02:05:33,773] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e5f2c97-a114-4f7e-9af2-1fb30b6fec0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:05:33,773] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e5f2c97-a114-4f7e-9af2-1fb30b6fec0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:05:33,773] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:05:33,773] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 02:05:33,773] [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
--------------------------------------------------------------------------------
[2023-03-19 02:05:33,773] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45896/tc_result.tsv
[2023-03-19 02:05:33,773] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:05:33,773] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:05:33,774] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e5f2c97-a114-4f7e-9af2-1fb30b6fec0f/dqc_reference/checkm_data
[2023-03-19 02:05:33,777] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:05:33,785] [INFO] Task started: CheckM
[2023-03-19 02:05:33,785] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45896/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45896/checkm_input OceanDNA-b45896/checkm_result
[2023-03-19 02:06:00,286] [INFO] Task succeeded: CheckM
[2023-03-19 02:06:00,286] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.57%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:06:00,288] [INFO] ===== Completeness check finished =====
[2023-03-19 02:06:00,288] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:06:00,288] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45896/markers.fasta)
[2023-03-19 02:06:00,289] [INFO] Task started: Blastn
[2023-03-19 02:06:00,289] [INFO] Running command: blastn -query OceanDNA-b45896/markers.fasta -db /var/lib/cwl/stg8e5f2c97-a114-4f7e-9af2-1fb30b6fec0f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45896/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:06:00,990] [INFO] Task succeeded: Blastn
[2023-03-19 02:06:00,991] [INFO] Selected 7 target genomes.
[2023-03-19 02:06:00,991] [INFO] Target genome list was writen to OceanDNA-b45896/target_genomes_gtdb.txt
[2023-03-19 02:06:01,112] [INFO] Task started: fastANI
[2023-03-19 02:06:01,113] [INFO] Running command: fastANI --query /var/lib/cwl/stg58d5ea4d-9bb2-493d-a20d-119e089e3490/OceanDNA-b45896.fa --refList OceanDNA-b45896/target_genomes_gtdb.txt --output OceanDNA-b45896/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:06:04,187] [INFO] Task succeeded: fastANI
[2023-03-19 02:06:04,191] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 02:06:04,192] [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_003331195.1	s__UBA7441 sp003331195	99.4646	313	341	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002862945.1	s__UBA7441 sp002862945	94.3445	303	341	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	98.18	98.18	0.82	0.82	2	-
GCA_009886465.1	s__UBA7441 sp009886465	93.0038	291	341	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	97.11	97.11	0.79	0.79	2	-
GCA_905182465.1	s__UBA7441 sp905182465	91.6258	298	341	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902587165.1	s__UBA7441 sp902587165	87.6065	291	341	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729725.1	s__UBA7441 sp002729725	77.3442	92	341	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	99.86	99.86	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-19 02:06:04,192] [INFO] GTDB search result was written to OceanDNA-b45896/result_gtdb.tsv
[2023-03-19 02:06:04,192] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:06:04,193] [INFO] DFAST_QC result json was written to OceanDNA-b45896/dqc_result.json
[2023-03-19 02:06:04,193] [INFO] DFAST_QC completed!
[2023-03-19 02:06:04,193] [INFO] Total running time: 0h0m53s