[2023-03-16 07:00:26,549] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:00:26,550] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:00:26,550] [INFO] DQC Reference Directory: /var/lib/cwl/stgd7182a53-48c5-4e8a-8d42-d6d441048f12/dqc_reference
[2023-03-16 07:00:27,684] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:00:27,685] [INFO] Task started: Prodigal
[2023-03-16 07:00:27,685] [INFO] Running command: cat /var/lib/cwl/stgd32476d7-3cb3-4422-90e8-23bb78cbdb05/OceanDNA-b9171.fa | prodigal -d OceanDNA-b9171/cds.fna -a OceanDNA-b9171/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:00:37,932] [INFO] Task succeeded: Prodigal
[2023-03-16 07:00:37,932] [INFO] Task started: HMMsearch
[2023-03-16 07:00:37,932] [INFO] Running command: hmmsearch --tblout OceanDNA-b9171/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd7182a53-48c5-4e8a-8d42-d6d441048f12/dqc_reference/reference_markers.hmm OceanDNA-b9171/protein.faa > /dev/null
[2023-03-16 07:00:38,107] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:00:38,107] [INFO] Found 6/6 markers.
[2023-03-16 07:00:38,124] [INFO] Query marker FASTA was written to OceanDNA-b9171/markers.fasta
[2023-03-16 07:00:38,125] [INFO] Task started: Blastn
[2023-03-16 07:00:38,125] [INFO] Running command: blastn -query OceanDNA-b9171/markers.fasta -db /var/lib/cwl/stgd7182a53-48c5-4e8a-8d42-d6d441048f12/dqc_reference/reference_markers.fasta -out OceanDNA-b9171/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:00:38,748] [INFO] Task succeeded: Blastn
[2023-03-16 07:00:38,750] [INFO] Selected 30 target genomes.
[2023-03-16 07:00:38,750] [INFO] Target genome list was writen to OceanDNA-b9171/target_genomes.txt
[2023-03-16 07:00:38,784] [INFO] Task started: fastANI
[2023-03-16 07:00:38,784] [INFO] Running command: fastANI --query /var/lib/cwl/stgd32476d7-3cb3-4422-90e8-23bb78cbdb05/OceanDNA-b9171.fa --refList OceanDNA-b9171/target_genomes.txt --output OceanDNA-b9171/fastani_result.tsv --threads 1
[2023-03-16 07:00:56,166] [INFO] Task succeeded: fastANI
[2023-03-16 07:00:56,167] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd7182a53-48c5-4e8a-8d42-d6d441048f12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:00:56,167] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd7182a53-48c5-4e8a-8d42-d6d441048f12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:00:56,167] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:00:56,167] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 07:00:56,167] [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 07:00:56,169] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9171/tc_result.tsv
[2023-03-16 07:00:56,169] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:00:56,169] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:00:56,170] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd7182a53-48c5-4e8a-8d42-d6d441048f12/dqc_reference/checkm_data
[2023-03-16 07:00:56,213] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:00:56,400] [INFO] Task started: CheckM
[2023-03-16 07:00:56,400] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9171/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9171/checkm_input OceanDNA-b9171/checkm_result
[2023-03-16 07:01:27,323] [INFO] Task succeeded: CheckM
[2023-03-16 07:01:27,324] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.29%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:01:27,334] [INFO] ===== Completeness check finished =====
[2023-03-16 07:01:27,334] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:01:27,334] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9171/markers.fasta)
[2023-03-16 07:01:27,335] [INFO] Task started: Blastn
[2023-03-16 07:01:27,335] [INFO] Running command: blastn -query OceanDNA-b9171/markers.fasta -db /var/lib/cwl/stgd7182a53-48c5-4e8a-8d42-d6d441048f12/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9171/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:01:28,302] [INFO] Task succeeded: Blastn
[2023-03-16 07:01:28,304] [INFO] Selected 21 target genomes.
[2023-03-16 07:01:28,304] [INFO] Target genome list was writen to OceanDNA-b9171/target_genomes_gtdb.txt
[2023-03-16 07:01:28,397] [INFO] Task started: fastANI
[2023-03-16 07:01:28,397] [INFO] Running command: fastANI --query /var/lib/cwl/stgd32476d7-3cb3-4422-90e8-23bb78cbdb05/OceanDNA-b9171.fa --refList OceanDNA-b9171/target_genomes_gtdb.txt --output OceanDNA-b9171/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:01:37,374] [INFO] Task succeeded: fastANI
[2023-03-16 07:01:37,380] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 07:01:37,380] [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_902546725.1	s__MS024-2A sp902546725	78.1895	156	511	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002705385.1	s__MS024-2A sp002705385	78.0248	161	511	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002167945.1	s__MS024-2A sp002167945	77.929	165	511	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017851655.1	s__MS024-2A sp017851655	77.6796	151	511	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.55	99.53	0.87	0.86	3	-
GCA_017858055.1	s__MS024-2A sp002384715	77.1115	147	511	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.54	99.54	0.94	0.94	2	-
GCA_009886625.1	s__MS024-2A sp009886625	76.8803	99	511	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480425.1	s__MS024-2A sp905480425	76.2033	92	511	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	95.11	95.11	0.87	0.87	2	-
GCA_905182305.1	s__MS024-2A sp905182305	76.1436	85	511	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 07:01:37,382] [INFO] GTDB search result was written to OceanDNA-b9171/result_gtdb.tsv
[2023-03-16 07:01:37,383] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:01:37,385] [INFO] DFAST_QC result json was written to OceanDNA-b9171/dqc_result.json
[2023-03-16 07:01:37,385] [INFO] DFAST_QC completed!
[2023-03-16 07:01:37,385] [INFO] Total running time: 0h1m11s