[2023-03-18 01:43:46,138] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:43:46,139] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:43:46,139] [INFO] DQC Reference Directory: /var/lib/cwl/stg11de5e0f-9c86-421c-a6d5-346caf3dee6a/dqc_reference
[2023-03-18 01:43:47,235] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:43:47,236] [INFO] Task started: Prodigal
[2023-03-18 01:43:47,236] [INFO] Running command: cat /var/lib/cwl/stg8e6e0f32-1a99-446c-8ab0-ee88f885eec2/OceanDNA-b4526.fa | prodigal -d OceanDNA-b4526/cds.fna -a OceanDNA-b4526/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:44:07,257] [INFO] Task succeeded: Prodigal
[2023-03-18 01:44:07,258] [INFO] Task started: HMMsearch
[2023-03-18 01:44:07,258] [INFO] Running command: hmmsearch --tblout OceanDNA-b4526/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11de5e0f-9c86-421c-a6d5-346caf3dee6a/dqc_reference/reference_markers.hmm OceanDNA-b4526/protein.faa > /dev/null
[2023-03-18 01:44:07,473] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:44:07,473] [INFO] Found 6/6 markers.
[2023-03-18 01:44:07,505] [INFO] Query marker FASTA was written to OceanDNA-b4526/markers.fasta
[2023-03-18 01:44:07,506] [INFO] Task started: Blastn
[2023-03-18 01:44:07,506] [INFO] Running command: blastn -query OceanDNA-b4526/markers.fasta -db /var/lib/cwl/stg11de5e0f-9c86-421c-a6d5-346caf3dee6a/dqc_reference/reference_markers.fasta -out OceanDNA-b4526/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:44:08,030] [INFO] Task succeeded: Blastn
[2023-03-18 01:44:08,036] [INFO] Selected 28 target genomes.
[2023-03-18 01:44:08,036] [INFO] Target genome list was writen to OceanDNA-b4526/target_genomes.txt
[2023-03-18 01:44:08,053] [INFO] Task started: fastANI
[2023-03-18 01:44:08,054] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e6e0f32-1a99-446c-8ab0-ee88f885eec2/OceanDNA-b4526.fa --refList OceanDNA-b4526/target_genomes.txt --output OceanDNA-b4526/fastani_result.tsv --threads 1
[2023-03-18 01:44:23,718] [INFO] Task succeeded: fastANI
[2023-03-18 01:44:23,719] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11de5e0f-9c86-421c-a6d5-346caf3dee6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:44:23,719] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11de5e0f-9c86-421c-a6d5-346caf3dee6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:44:23,719] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:44:23,719] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 01:44:23,719] [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 01:44:23,722] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4526/tc_result.tsv
[2023-03-18 01:44:23,724] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:44:23,724] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:44:23,725] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11de5e0f-9c86-421c-a6d5-346caf3dee6a/dqc_reference/checkm_data
[2023-03-18 01:44:23,728] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:44:23,820] [INFO] Task started: CheckM
[2023-03-18 01:44:23,820] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4526/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4526/checkm_input OceanDNA-b4526/checkm_result
[2023-03-18 01:45:16,672] [INFO] Task succeeded: CheckM
[2023-03-18 01:45:16,673] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.94%
Contamintation: 0.84%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:45:16,729] [INFO] ===== Completeness check finished =====
[2023-03-18 01:45:16,729] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:45:16,729] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4526/markers.fasta)
[2023-03-18 01:45:16,730] [INFO] Task started: Blastn
[2023-03-18 01:45:16,731] [INFO] Running command: blastn -query OceanDNA-b4526/markers.fasta -db /var/lib/cwl/stg11de5e0f-9c86-421c-a6d5-346caf3dee6a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4526/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:45:17,425] [INFO] Task succeeded: Blastn
[2023-03-18 01:45:17,436] [INFO] Selected 26 target genomes.
[2023-03-18 01:45:17,436] [INFO] Target genome list was writen to OceanDNA-b4526/target_genomes_gtdb.txt
[2023-03-18 01:45:17,510] [INFO] Task started: fastANI
[2023-03-18 01:45:17,510] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e6e0f32-1a99-446c-8ab0-ee88f885eec2/OceanDNA-b4526.fa --refList OceanDNA-b4526/target_genomes_gtdb.txt --output OceanDNA-b4526/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:45:31,025] [INFO] Task succeeded: fastANI
[2023-03-18 01:45:31,027] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:45:31,027] [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_002705995.1	s__GCA-2705995 sp002705995	99.3198	813	828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Salibacteraceae;g__GCA-2705995	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-18 01:45:31,031] [INFO] GTDB search result was written to OceanDNA-b4526/result_gtdb.tsv
[2023-03-18 01:45:31,040] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:45:31,043] [INFO] DFAST_QC result json was written to OceanDNA-b4526/dqc_result.json
[2023-03-18 01:45:31,044] [INFO] DFAST_QC completed!
[2023-03-18 01:45:31,044] [INFO] Total running time: 0h1m45s