[2023-03-17 00:45:47,248] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:45:47,249] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:45:47,249] [INFO] DQC Reference Directory: /var/lib/cwl/stg7108ea86-5b09-4b99-9629-04287b29d993/dqc_reference
[2023-03-17 00:45:48,369] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:45:48,369] [INFO] Task started: Prodigal
[2023-03-17 00:45:48,369] [INFO] Running command: cat /var/lib/cwl/stg51499286-fe63-43db-b6ee-c38676a67286/OceanDNA-b4914.fa | prodigal -d OceanDNA-b4914/cds.fna -a OceanDNA-b4914/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:45:54,365] [INFO] Task succeeded: Prodigal
[2023-03-17 00:45:54,365] [INFO] Task started: HMMsearch
[2023-03-17 00:45:54,365] [INFO] Running command: hmmsearch --tblout OceanDNA-b4914/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7108ea86-5b09-4b99-9629-04287b29d993/dqc_reference/reference_markers.hmm OceanDNA-b4914/protein.faa > /dev/null
[2023-03-17 00:45:54,514] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:45:54,515] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg51499286-fe63-43db-b6ee-c38676a67286/OceanDNA-b4914.fa]
[2023-03-17 00:45:54,524] [INFO] Query marker FASTA was written to OceanDNA-b4914/markers.fasta
[2023-03-17 00:45:54,525] [INFO] Task started: Blastn
[2023-03-17 00:45:54,525] [INFO] Running command: blastn -query OceanDNA-b4914/markers.fasta -db /var/lib/cwl/stg7108ea86-5b09-4b99-9629-04287b29d993/dqc_reference/reference_markers.fasta -out OceanDNA-b4914/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:45:54,957] [INFO] Task succeeded: Blastn
[2023-03-17 00:45:54,957] [INFO] Selected 12 target genomes.
[2023-03-17 00:45:54,958] [INFO] Target genome list was writen to OceanDNA-b4914/target_genomes.txt
[2023-03-17 00:45:55,041] [INFO] Task started: fastANI
[2023-03-17 00:45:55,041] [INFO] Running command: fastANI --query /var/lib/cwl/stg51499286-fe63-43db-b6ee-c38676a67286/OceanDNA-b4914.fa --refList OceanDNA-b4914/target_genomes.txt --output OceanDNA-b4914/fastani_result.tsv --threads 1
[2023-03-17 00:46:01,574] [INFO] Task succeeded: fastANI
[2023-03-17 00:46:01,574] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7108ea86-5b09-4b99-9629-04287b29d993/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:46:01,574] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7108ea86-5b09-4b99-9629-04287b29d993/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:46:01,575] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:46:01,575] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 00:46:01,575] [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
--------------------------------------------------------------------------------
[2023-03-17 00:46:01,575] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4914/tc_result.tsv
[2023-03-17 00:46:01,575] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:46:01,575] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:46:01,575] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7108ea86-5b09-4b99-9629-04287b29d993/dqc_reference/checkm_data
[2023-03-17 00:46:01,578] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:46:01,580] [INFO] Task started: CheckM
[2023-03-17 00:46:01,580] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4914/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4914/checkm_input OceanDNA-b4914/checkm_result
[2023-03-17 00:46:25,077] [INFO] Task succeeded: CheckM
[2023-03-17 00:46:25,077] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:46:25,079] [INFO] ===== Completeness check finished =====
[2023-03-17 00:46:25,079] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:46:25,079] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4914/markers.fasta)
[2023-03-17 00:46:25,079] [INFO] Task started: Blastn
[2023-03-17 00:46:25,079] [INFO] Running command: blastn -query OceanDNA-b4914/markers.fasta -db /var/lib/cwl/stg7108ea86-5b09-4b99-9629-04287b29d993/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4914/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:46:26,175] [INFO] Task succeeded: Blastn
[2023-03-17 00:46:26,176] [INFO] Selected 10 target genomes.
[2023-03-17 00:46:26,176] [INFO] Target genome list was writen to OceanDNA-b4914/target_genomes_gtdb.txt
[2023-03-17 00:46:26,562] [INFO] Task started: fastANI
[2023-03-17 00:46:26,562] [INFO] Running command: fastANI --query /var/lib/cwl/stg51499286-fe63-43db-b6ee-c38676a67286/OceanDNA-b4914.fa --refList OceanDNA-b4914/target_genomes_gtdb.txt --output OceanDNA-b4914/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:46:29,591] [INFO] Task succeeded: fastANI
[2023-03-17 00:46:29,596] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 00:46:29,596] [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_018695965.1	s__GCA-002697625 sp018695965	81.3632	179	319	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	98.45	97.65	0.78	0.72	6	-
GCA_002710495.1	s__GCA-002697625 sp002710495	80.9182	230	319	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902514225.1	s__GCA-002697625 sp902514225	79.161	103	319	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018647945.1	s__GCA-002697625 sp018647945	77.6039	128	319	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	99.64	99.58	0.90	0.90	3	-
GCA_905478555.1	s__GCA-002697625 sp905478555	77.2751	140	319	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	96.63	96.63	0.87	0.87	2	-
GCA_002712715.1	s__GCA-2712715 sp002712715	76.6128	66	319	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2712715	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 00:46:29,596] [INFO] GTDB search result was written to OceanDNA-b4914/result_gtdb.tsv
[2023-03-17 00:46:29,596] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:46:29,597] [INFO] DFAST_QC result json was written to OceanDNA-b4914/dqc_result.json
[2023-03-17 00:46:29,597] [INFO] DFAST_QC completed!
[2023-03-17 00:46:29,597] [INFO] Total running time: 0h0m42s