[2023-03-17 11:08:00,429] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:08:00,429] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:08:00,429] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd5f0a8c-a79c-4957-9c68-411993ff3f5d/dqc_reference
[2023-03-17 11:08:01,576] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:08:01,576] [INFO] Task started: Prodigal
[2023-03-17 11:08:01,576] [INFO] Running command: cat /var/lib/cwl/stgb9253a0b-dea3-4a53-ae9a-a44e9d18a967/OceanDNA-b16286.fa | prodigal -d OceanDNA-b16286/cds.fna -a OceanDNA-b16286/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:08:07,851] [INFO] Task succeeded: Prodigal
[2023-03-17 11:08:07,851] [INFO] Task started: HMMsearch
[2023-03-17 11:08:07,851] [INFO] Running command: hmmsearch --tblout OceanDNA-b16286/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd5f0a8c-a79c-4957-9c68-411993ff3f5d/dqc_reference/reference_markers.hmm OceanDNA-b16286/protein.faa > /dev/null
[2023-03-17 11:08:07,999] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:08:07,999] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb9253a0b-dea3-4a53-ae9a-a44e9d18a967/OceanDNA-b16286.fa]
[2023-03-17 11:08:08,009] [INFO] Query marker FASTA was written to OceanDNA-b16286/markers.fasta
[2023-03-17 11:08:08,010] [INFO] Task started: Blastn
[2023-03-17 11:08:08,010] [INFO] Running command: blastn -query OceanDNA-b16286/markers.fasta -db /var/lib/cwl/stgdd5f0a8c-a79c-4957-9c68-411993ff3f5d/dqc_reference/reference_markers.fasta -out OceanDNA-b16286/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:08:08,509] [INFO] Task succeeded: Blastn
[2023-03-17 11:08:08,510] [INFO] Selected 17 target genomes.
[2023-03-17 11:08:08,510] [INFO] Target genome list was writen to OceanDNA-b16286/target_genomes.txt
[2023-03-17 11:08:08,519] [INFO] Task started: fastANI
[2023-03-17 11:08:08,519] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9253a0b-dea3-4a53-ae9a-a44e9d18a967/OceanDNA-b16286.fa --refList OceanDNA-b16286/target_genomes.txt --output OceanDNA-b16286/fastani_result.tsv --threads 1
[2023-03-17 11:08:16,354] [INFO] Task succeeded: fastANI
[2023-03-17 11:08:16,355] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd5f0a8c-a79c-4957-9c68-411993ff3f5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:08:16,355] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd5f0a8c-a79c-4957-9c68-411993ff3f5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:08:16,355] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:08:16,355] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 11:08:16,355] [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 11:08:16,355] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16286/tc_result.tsv
[2023-03-17 11:08:16,355] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:08:16,356] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:08:16,356] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd5f0a8c-a79c-4957-9c68-411993ff3f5d/dqc_reference/checkm_data
[2023-03-17 11:08:16,359] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:08:16,379] [INFO] Task started: CheckM
[2023-03-17 11:08:16,380] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16286/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16286/checkm_input OceanDNA-b16286/checkm_result
[2023-03-17 11:08:37,680] [INFO] Task succeeded: CheckM
[2023-03-17 11:08:37,680] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:08:37,682] [INFO] ===== Completeness check finished =====
[2023-03-17 11:08:37,682] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:08:37,683] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16286/markers.fasta)
[2023-03-17 11:08:37,683] [INFO] Task started: Blastn
[2023-03-17 11:08:37,683] [INFO] Running command: blastn -query OceanDNA-b16286/markers.fasta -db /var/lib/cwl/stgdd5f0a8c-a79c-4957-9c68-411993ff3f5d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16286/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:08:38,447] [INFO] Task succeeded: Blastn
[2023-03-17 11:08:38,449] [INFO] Selected 13 target genomes.
[2023-03-17 11:08:38,449] [INFO] Target genome list was writen to OceanDNA-b16286/target_genomes_gtdb.txt
[2023-03-17 11:08:38,535] [INFO] Task started: fastANI
[2023-03-17 11:08:38,535] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9253a0b-dea3-4a53-ae9a-a44e9d18a967/OceanDNA-b16286.fa --refList OceanDNA-b16286/target_genomes_gtdb.txt --output OceanDNA-b16286/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:08:41,930] [INFO] Task succeeded: fastANI
[2023-03-17 11:08:41,940] [INFO] Found 13 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-17 11:08:41,940] [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_000011465.1	s__Prochlorococcus_A pastoris	97.1075	339	346	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	96.02	95.34	0.92	0.85	31	inconclusive
GCA_003279855.1	s__Prochlorococcus_A sp003279855	95.0607	326	346	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_003279935.1	s__Prochlorococcus_A sp003279935	94.9947	290	346	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003211655.1	s__Prochlorococcus_A sp003211655	94.9416	193	346	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003282425.1	s__Prochlorococcus_A sp003282425	94.569	162	346	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	95.44	95.44	0.78	0.78	2	-
GCA_902609995.1	s__Prochlorococcus_A sp902609995	94.4399	197	346	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003282225.1	s__Prochlorococcus_A sp003282225	93.908	198	346	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902526435.1	s__Prochlorococcus_A sp902526435	93.7102	228	346	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003210825.1	s__Prochlorococcus_A sp003210825	93.4975	232	346	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003211315.1	s__Prochlorococcus_A sp003211315	92.9452	260	346	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003211135.1	s__Prochlorococcus_A sp003211135	92.7891	278	346	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003209065.1	s__Prochlorococcus_A sp003209065	92.2411	283	346	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003208695.1	s__Prochlorococcus_A sp003208695	91.5401	153	346	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:08:41,940] [INFO] GTDB search result was written to OceanDNA-b16286/result_gtdb.tsv
[2023-03-17 11:08:41,940] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:08:41,941] [INFO] DFAST_QC result json was written to OceanDNA-b16286/dqc_result.json
[2023-03-17 11:08:41,941] [INFO] DFAST_QC completed!
[2023-03-17 11:08:41,942] [INFO] Total running time: 0h0m42s