[2023-03-18 02:13:49,844] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:13:49,844] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:13:49,844] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e395865-2c9c-46c4-8ff6-f4df8ab05dec/dqc_reference
[2023-03-18 02:13:50,969] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:13:50,970] [INFO] Task started: Prodigal
[2023-03-18 02:13:50,970] [INFO] Running command: cat /var/lib/cwl/stg312917ae-e74f-4610-a1be-84ad32744202/OceanDNA-b45686.fa | prodigal -d OceanDNA-b45686/cds.fna -a OceanDNA-b45686/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:14:02,614] [INFO] Task succeeded: Prodigal
[2023-03-18 02:14:02,614] [INFO] Task started: HMMsearch
[2023-03-18 02:14:02,614] [INFO] Running command: hmmsearch --tblout OceanDNA-b45686/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e395865-2c9c-46c4-8ff6-f4df8ab05dec/dqc_reference/reference_markers.hmm OceanDNA-b45686/protein.faa > /dev/null
[2023-03-18 02:14:02,757] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:14:02,758] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg312917ae-e74f-4610-a1be-84ad32744202/OceanDNA-b45686.fa]
[2023-03-18 02:14:02,774] [INFO] Query marker FASTA was written to OceanDNA-b45686/markers.fasta
[2023-03-18 02:14:02,775] [INFO] Task started: Blastn
[2023-03-18 02:14:02,775] [INFO] Running command: blastn -query OceanDNA-b45686/markers.fasta -db /var/lib/cwl/stg8e395865-2c9c-46c4-8ff6-f4df8ab05dec/dqc_reference/reference_markers.fasta -out OceanDNA-b45686/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:14:03,248] [INFO] Task succeeded: Blastn
[2023-03-18 02:14:03,249] [INFO] Selected 8 target genomes.
[2023-03-18 02:14:03,249] [INFO] Target genome list was writen to OceanDNA-b45686/target_genomes.txt
[2023-03-18 02:14:03,253] [INFO] Task started: fastANI
[2023-03-18 02:14:03,253] [INFO] Running command: fastANI --query /var/lib/cwl/stg312917ae-e74f-4610-a1be-84ad32744202/OceanDNA-b45686.fa --refList OceanDNA-b45686/target_genomes.txt --output OceanDNA-b45686/fastani_result.tsv --threads 1
[2023-03-18 02:14:06,484] [INFO] Task succeeded: fastANI
[2023-03-18 02:14:06,484] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e395865-2c9c-46c4-8ff6-f4df8ab05dec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:14:06,484] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e395865-2c9c-46c4-8ff6-f4df8ab05dec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:14:06,484] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:14:06,484] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 02:14:06,484] [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
--------------------------------------------------------------------------------
[2023-03-18 02:14:06,485] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45686/tc_result.tsv
[2023-03-18 02:14:06,485] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:14:06,485] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:14:06,485] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e395865-2c9c-46c4-8ff6-f4df8ab05dec/dqc_reference/checkm_data
[2023-03-18 02:14:06,488] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:14:06,491] [INFO] Task started: CheckM
[2023-03-18 02:14:06,491] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45686/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45686/checkm_input OceanDNA-b45686/checkm_result
[2023-03-18 02:14:40,659] [INFO] Task succeeded: CheckM
[2023-03-18 02:14:40,659] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:14:40,696] [INFO] ===== Completeness check finished =====
[2023-03-18 02:14:40,696] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:14:40,697] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45686/markers.fasta)
[2023-03-18 02:14:40,698] [INFO] Task started: Blastn
[2023-03-18 02:14:40,698] [INFO] Running command: blastn -query OceanDNA-b45686/markers.fasta -db /var/lib/cwl/stg8e395865-2c9c-46c4-8ff6-f4df8ab05dec/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45686/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:14:41,105] [INFO] Task succeeded: Blastn
[2023-03-18 02:14:41,106] [INFO] Selected 10 target genomes.
[2023-03-18 02:14:41,106] [INFO] Target genome list was writen to OceanDNA-b45686/target_genomes_gtdb.txt
[2023-03-18 02:14:41,115] [INFO] Task started: fastANI
[2023-03-18 02:14:41,115] [INFO] Running command: fastANI --query /var/lib/cwl/stg312917ae-e74f-4610-a1be-84ad32744202/OceanDNA-b45686.fa --refList OceanDNA-b45686/target_genomes_gtdb.txt --output OceanDNA-b45686/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:14:45,701] [INFO] Task succeeded: fastANI
[2023-03-18 02:14:45,705] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 02:14:45,705] [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_002168015.1	s__MB11C04 sp002168015	97.6352	378	470	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002167265.1	s__MB11C04 sp002167265	79.7666	74	470	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902612125.1	s__MB11C04 sp902612125	77.655	60	470	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689665.1	s__MB11C04 sp002689665	77.3174	79	470	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 02:14:45,705] [INFO] GTDB search result was written to OceanDNA-b45686/result_gtdb.tsv
[2023-03-18 02:14:45,706] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:14:45,706] [INFO] DFAST_QC result json was written to OceanDNA-b45686/dqc_result.json
[2023-03-18 02:14:45,706] [INFO] DFAST_QC completed!
[2023-03-18 02:14:45,706] [INFO] Total running time: 0h0m56s