[2023-03-15 17:05:43,620] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:05:43,620] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:05:43,621] [INFO] DQC Reference Directory: /var/lib/cwl/stgb804757a-66bf-4252-831c-d69ce3e00f52/dqc_reference
[2023-03-15 17:05:45,975] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:05:45,976] [INFO] Task started: Prodigal
[2023-03-15 17:05:45,976] [INFO] Running command: cat /var/lib/cwl/stg2d134c8f-cee6-4c3f-a5ff-ed240e2af025/OceanDNA-b16235.fa | prodigal -d OceanDNA-b16235/cds.fna -a OceanDNA-b16235/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:05:53,493] [INFO] Task succeeded: Prodigal
[2023-03-15 17:05:53,493] [INFO] Task started: HMMsearch
[2023-03-15 17:05:53,493] [INFO] Running command: hmmsearch --tblout OceanDNA-b16235/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb804757a-66bf-4252-831c-d69ce3e00f52/dqc_reference/reference_markers.hmm OceanDNA-b16235/protein.faa > /dev/null
[2023-03-15 17:05:53,689] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:05:53,690] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg2d134c8f-cee6-4c3f-a5ff-ed240e2af025/OceanDNA-b16235.fa]
[2023-03-15 17:05:53,702] [INFO] Query marker FASTA was written to OceanDNA-b16235/markers.fasta
[2023-03-15 17:05:53,704] [INFO] Task started: Blastn
[2023-03-15 17:05:53,704] [INFO] Running command: blastn -query OceanDNA-b16235/markers.fasta -db /var/lib/cwl/stgb804757a-66bf-4252-831c-d69ce3e00f52/dqc_reference/reference_markers.fasta -out OceanDNA-b16235/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:05:56,334] [INFO] Task succeeded: Blastn
[2023-03-15 17:05:56,336] [INFO] Selected 5 target genomes.
[2023-03-15 17:05:56,336] [INFO] Target genome list was writen to OceanDNA-b16235/target_genomes.txt
[2023-03-15 17:05:56,343] [INFO] Task started: fastANI
[2023-03-15 17:05:56,343] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d134c8f-cee6-4c3f-a5ff-ed240e2af025/OceanDNA-b16235.fa --refList OceanDNA-b16235/target_genomes.txt --output OceanDNA-b16235/fastani_result.tsv --threads 1
[2023-03-15 17:06:00,144] [INFO] Task succeeded: fastANI
[2023-03-15 17:06:00,144] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb804757a-66bf-4252-831c-d69ce3e00f52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:06:00,145] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb804757a-66bf-4252-831c-d69ce3e00f52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:06:00,145] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:06:00,145] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 17:06:00,145] [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
--------------------------------------------------------------------------------
[2023-03-15 17:06:00,146] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16235/tc_result.tsv
[2023-03-15 17:06:00,146] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:06:00,146] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:06:00,146] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb804757a-66bf-4252-831c-d69ce3e00f52/dqc_reference/checkm_data
[2023-03-15 17:06:00,158] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:06:00,164] [INFO] Task started: CheckM
[2023-03-15 17:06:00,164] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16235/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16235/checkm_input OceanDNA-b16235/checkm_result
[2023-03-15 17:06:27,364] [INFO] Task succeeded: CheckM
[2023-03-15 17:06:27,365] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.78%
Contamintation: 5.21%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 17:06:27,367] [INFO] ===== Completeness check finished =====
[2023-03-15 17:06:27,367] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:06:27,367] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16235/markers.fasta)
[2023-03-15 17:06:27,369] [INFO] Task started: Blastn
[2023-03-15 17:06:27,369] [INFO] Running command: blastn -query OceanDNA-b16235/markers.fasta -db /var/lib/cwl/stgb804757a-66bf-4252-831c-d69ce3e00f52/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16235/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:06:28,245] [INFO] Task succeeded: Blastn
[2023-03-15 17:06:28,246] [INFO] Selected 8 target genomes.
[2023-03-15 17:06:28,246] [INFO] Target genome list was writen to OceanDNA-b16235/target_genomes_gtdb.txt
[2023-03-15 17:06:28,255] [INFO] Task started: fastANI
[2023-03-15 17:06:28,255] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d134c8f-cee6-4c3f-a5ff-ed240e2af025/OceanDNA-b16235.fa --refList OceanDNA-b16235/target_genomes_gtdb.txt --output OceanDNA-b16235/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:06:31,265] [INFO] Task succeeded: fastANI
[2023-03-15 17:06:31,269] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 17:06:31,269] [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
GCF_000760295.1	s__Prochlorococcus_C sp000760295	81.2444	120	149	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_C	95.0	99.99	99.99	0.99	0.99	3	-
GCF_000011485.1	s__Prochlorococcus_C marinus_B	80.6326	115	149	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_C	95.0	96.34	95.12	0.90	0.85	19	-
GCA_003214855.1	s__Prochlorococcus_C sp003214855	79.9892	88	149	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 17:06:31,270] [INFO] GTDB search result was written to OceanDNA-b16235/result_gtdb.tsv
[2023-03-15 17:06:31,270] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:06:31,271] [INFO] DFAST_QC result json was written to OceanDNA-b16235/dqc_result.json
[2023-03-15 17:06:31,272] [INFO] DFAST_QC completed!
[2023-03-15 17:06:31,272] [INFO] Total running time: 0h0m48s