[2023-03-16 09:53:50,315] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:53:50,315] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:53:50,316] [INFO] DQC Reference Directory: /var/lib/cwl/stg315a93c3-1524-449a-8146-46f0b374090c/dqc_reference
[2023-03-16 09:53:51,393] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:53:51,395] [INFO] Task started: Prodigal
[2023-03-16 09:53:51,395] [INFO] Running command: cat /var/lib/cwl/stg5ce47416-be8e-494f-871f-146478c5d256/OceanDNA-b21351.fa | prodigal -d OceanDNA-b21351/cds.fna -a OceanDNA-b21351/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:53:58,180] [INFO] Task succeeded: Prodigal
[2023-03-16 09:53:58,181] [INFO] Task started: HMMsearch
[2023-03-16 09:53:58,181] [INFO] Running command: hmmsearch --tblout OceanDNA-b21351/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg315a93c3-1524-449a-8146-46f0b374090c/dqc_reference/reference_markers.hmm OceanDNA-b21351/protein.faa > /dev/null
[2023-03-16 09:53:58,352] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:53:58,353] [INFO] Found 6/6 markers.
[2023-03-16 09:53:58,365] [INFO] Query marker FASTA was written to OceanDNA-b21351/markers.fasta
[2023-03-16 09:53:58,367] [INFO] Task started: Blastn
[2023-03-16 09:53:58,367] [INFO] Running command: blastn -query OceanDNA-b21351/markers.fasta -db /var/lib/cwl/stg315a93c3-1524-449a-8146-46f0b374090c/dqc_reference/reference_markers.fasta -out OceanDNA-b21351/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:53:58,944] [INFO] Task succeeded: Blastn
[2023-03-16 09:53:58,945] [INFO] Selected 18 target genomes.
[2023-03-16 09:53:58,946] [INFO] Target genome list was writen to OceanDNA-b21351/target_genomes.txt
[2023-03-16 09:53:58,956] [INFO] Task started: fastANI
[2023-03-16 09:53:58,956] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ce47416-be8e-494f-871f-146478c5d256/OceanDNA-b21351.fa --refList OceanDNA-b21351/target_genomes.txt --output OceanDNA-b21351/fastani_result.tsv --threads 1
[2023-03-16 09:54:06,500] [INFO] Task succeeded: fastANI
[2023-03-16 09:54:06,500] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg315a93c3-1524-449a-8146-46f0b374090c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:54:06,501] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg315a93c3-1524-449a-8146-46f0b374090c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:54:06,501] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:54:06,501] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 09:54:06,501] [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
--------------------------------------------------------------------------------
[2023-03-16 09:54:06,501] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21351/tc_result.tsv
[2023-03-16 09:54:06,501] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:54:06,501] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:54:06,502] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg315a93c3-1524-449a-8146-46f0b374090c/dqc_reference/checkm_data
[2023-03-16 09:54:06,556] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:54:06,605] [INFO] Task started: CheckM
[2023-03-16 09:54:06,605] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21351/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21351/checkm_input OceanDNA-b21351/checkm_result
[2023-03-16 09:54:30,751] [INFO] Task succeeded: CheckM
[2023-03-16 09:54:30,752] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.87%
Contamintation: 6.71%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 09:54:30,754] [INFO] ===== Completeness check finished =====
[2023-03-16 09:54:30,754] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:54:30,754] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21351/markers.fasta)
[2023-03-16 09:54:30,755] [INFO] Task started: Blastn
[2023-03-16 09:54:30,755] [INFO] Running command: blastn -query OceanDNA-b21351/markers.fasta -db /var/lib/cwl/stg315a93c3-1524-449a-8146-46f0b374090c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21351/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:54:31,720] [INFO] Task succeeded: Blastn
[2023-03-16 09:54:31,721] [INFO] Selected 28 target genomes.
[2023-03-16 09:54:31,721] [INFO] Target genome list was writen to OceanDNA-b21351/target_genomes_gtdb.txt
[2023-03-16 09:54:31,751] [INFO] Task started: fastANI
[2023-03-16 09:54:31,751] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ce47416-be8e-494f-871f-146478c5d256/OceanDNA-b21351.fa --refList OceanDNA-b21351/target_genomes_gtdb.txt --output OceanDNA-b21351/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:54:39,484] [INFO] Task succeeded: fastANI
[2023-03-16 09:54:39,489] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 09:54:39,490] [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_002721515.1	s__UBA8687 sp002721515	98.3783	265	393	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__UBA8687	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002697825.1	s__UBA8687 sp002697825	81.2982	227	393	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__UBA8687	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013349585.1	s__UBA8687 sp013349585	76.4661	92	393	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__UBA8687	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009873655.1	s__UBA8687 sp009873655	76.3417	104	393	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__UBA8687	95.0	99.50	99.47	0.94	0.93	3	-
GCA_018665625.1	s__UBA8687 sp018665625	76.3197	115	393	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__UBA8687	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 09:54:39,490] [INFO] GTDB search result was written to OceanDNA-b21351/result_gtdb.tsv
[2023-03-16 09:54:39,490] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:54:39,491] [INFO] DFAST_QC result json was written to OceanDNA-b21351/dqc_result.json
[2023-03-16 09:54:39,491] [INFO] DFAST_QC completed!
[2023-03-16 09:54:39,491] [INFO] Total running time: 0h0m49s