[2023-03-18 21:47:30,335] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:47:30,335] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:47:30,335] [INFO] DQC Reference Directory: /var/lib/cwl/stg750a677d-4c19-4837-9c36-b3f0cd21bddb/dqc_reference
[2023-03-18 21:47:31,431] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:47:31,431] [INFO] Task started: Prodigal
[2023-03-18 21:47:31,431] [INFO] Running command: cat /var/lib/cwl/stg6fbab6fa-85b6-4e16-a35b-944720510bde/OceanDNA-b5652.fa | prodigal -d OceanDNA-b5652/cds.fna -a OceanDNA-b5652/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:47:39,692] [INFO] Task succeeded: Prodigal
[2023-03-18 21:47:39,693] [INFO] Task started: HMMsearch
[2023-03-18 21:47:39,693] [INFO] Running command: hmmsearch --tblout OceanDNA-b5652/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg750a677d-4c19-4837-9c36-b3f0cd21bddb/dqc_reference/reference_markers.hmm OceanDNA-b5652/protein.faa > /dev/null
[2023-03-18 21:47:39,870] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:47:39,870] [INFO] Found 6/6 markers.
[2023-03-18 21:47:39,884] [INFO] Query marker FASTA was written to OceanDNA-b5652/markers.fasta
[2023-03-18 21:47:39,884] [INFO] Task started: Blastn
[2023-03-18 21:47:39,884] [INFO] Running command: blastn -query OceanDNA-b5652/markers.fasta -db /var/lib/cwl/stg750a677d-4c19-4837-9c36-b3f0cd21bddb/dqc_reference/reference_markers.fasta -out OceanDNA-b5652/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:47:40,469] [INFO] Task succeeded: Blastn
[2023-03-18 21:47:40,544] [INFO] Selected 27 target genomes.
[2023-03-18 21:47:40,544] [INFO] Target genome list was writen to OceanDNA-b5652/target_genomes.txt
[2023-03-18 21:47:40,559] [INFO] Task started: fastANI
[2023-03-18 21:47:40,559] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fbab6fa-85b6-4e16-a35b-944720510bde/OceanDNA-b5652.fa --refList OceanDNA-b5652/target_genomes.txt --output OceanDNA-b5652/fastani_result.tsv --threads 1
[2023-03-18 21:47:56,073] [INFO] Task succeeded: fastANI
[2023-03-18 21:47:56,074] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg750a677d-4c19-4837-9c36-b3f0cd21bddb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:47:56,074] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg750a677d-4c19-4837-9c36-b3f0cd21bddb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:47:56,074] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:47:56,074] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 21:47:56,074] [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 21:47:56,074] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5652/tc_result.tsv
[2023-03-18 21:47:56,074] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:47:56,075] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:47:56,075] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg750a677d-4c19-4837-9c36-b3f0cd21bddb/dqc_reference/checkm_data
[2023-03-18 21:47:56,078] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:47:56,083] [INFO] Task started: CheckM
[2023-03-18 21:47:56,083] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5652/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5652/checkm_input OceanDNA-b5652/checkm_result
[2023-03-18 21:48:21,823] [INFO] Task succeeded: CheckM
[2023-03-18 21:48:21,824] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.36%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:48:21,912] [INFO] ===== Completeness check finished =====
[2023-03-18 21:48:21,912] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:48:21,912] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5652/markers.fasta)
[2023-03-18 21:48:21,914] [INFO] Task started: Blastn
[2023-03-18 21:48:21,914] [INFO] Running command: blastn -query OceanDNA-b5652/markers.fasta -db /var/lib/cwl/stg750a677d-4c19-4837-9c36-b3f0cd21bddb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5652/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:48:22,801] [INFO] Task succeeded: Blastn
[2023-03-18 21:48:22,802] [INFO] Selected 35 target genomes.
[2023-03-18 21:48:22,803] [INFO] Target genome list was writen to OceanDNA-b5652/target_genomes_gtdb.txt
[2023-03-18 21:48:22,837] [INFO] Task started: fastANI
[2023-03-18 21:48:22,837] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fbab6fa-85b6-4e16-a35b-944720510bde/OceanDNA-b5652.fa --refList OceanDNA-b5652/target_genomes_gtdb.txt --output OceanDNA-b5652/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:48:39,676] [INFO] Task succeeded: fastANI
[2023-03-18 21:48:39,679] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:48:39,679] [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_002167805.1	s__TMED14 sp002167805	76.9614	107	404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__TMED14	95.0	95.87	95.87	0.92	0.92	2	-
GCA_002682945.1	s__TMED14 sp002682945	76.8054	118	404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__TMED14	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 21:48:39,679] [INFO] GTDB search result was written to OceanDNA-b5652/result_gtdb.tsv
[2023-03-18 21:48:39,679] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:48:39,680] [INFO] DFAST_QC result json was written to OceanDNA-b5652/dqc_result.json
[2023-03-18 21:48:39,680] [INFO] DFAST_QC completed!
[2023-03-18 21:48:39,680] [INFO] Total running time: 0h1m9s