[2023-03-14 13:16:12,732] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:16:12,732] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:16:12,732] [INFO] DQC Reference Directory: /var/lib/cwl/stge7914e89-aaca-4c57-a8fa-bc745f98226f/dqc_reference
[2023-03-14 13:16:17,395] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:16:17,396] [INFO] Task started: Prodigal
[2023-03-14 13:16:17,396] [INFO] Running command: cat /var/lib/cwl/stge5b22c98-05cd-438a-83c4-250c500b676d/OceanDNA-b26937.fa | prodigal -d OceanDNA-b26937/cds.fna -a OceanDNA-b26937/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:16:23,515] [INFO] Task succeeded: Prodigal
[2023-03-14 13:16:23,515] [INFO] Task started: HMMsearch
[2023-03-14 13:16:23,515] [INFO] Running command: hmmsearch --tblout OceanDNA-b26937/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7914e89-aaca-4c57-a8fa-bc745f98226f/dqc_reference/reference_markers.hmm OceanDNA-b26937/protein.faa > /dev/null
[2023-03-14 13:16:23,738] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:16:23,739] [INFO] Found 6/6 markers.
[2023-03-14 13:16:23,747] [INFO] Query marker FASTA was written to OceanDNA-b26937/markers.fasta
[2023-03-14 13:16:23,748] [INFO] Task started: Blastn
[2023-03-14 13:16:23,748] [INFO] Running command: blastn -query OceanDNA-b26937/markers.fasta -db /var/lib/cwl/stge7914e89-aaca-4c57-a8fa-bc745f98226f/dqc_reference/reference_markers.fasta -out OceanDNA-b26937/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:16:28,030] [INFO] Task succeeded: Blastn
[2023-03-14 13:16:28,032] [INFO] Selected 14 target genomes.
[2023-03-14 13:16:28,032] [INFO] Target genome list was writen to OceanDNA-b26937/target_genomes.txt
[2023-03-14 13:16:28,044] [INFO] Task started: fastANI
[2023-03-14 13:16:28,044] [INFO] Running command: fastANI --query /var/lib/cwl/stge5b22c98-05cd-438a-83c4-250c500b676d/OceanDNA-b26937.fa --refList OceanDNA-b26937/target_genomes.txt --output OceanDNA-b26937/fastani_result.tsv --threads 1
[2023-03-14 13:16:34,051] [INFO] Task succeeded: fastANI
[2023-03-14 13:16:34,051] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7914e89-aaca-4c57-a8fa-bc745f98226f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:16:34,051] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7914e89-aaca-4c57-a8fa-bc745f98226f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:16:34,051] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:16:34,051] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 13:16:34,051] [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
--------------------------------------------------------------------------------
[2023-03-14 13:16:34,052] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26937/tc_result.tsv
[2023-03-14 13:16:34,052] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:16:34,052] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:16:34,052] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7914e89-aaca-4c57-a8fa-bc745f98226f/dqc_reference/checkm_data
[2023-03-14 13:16:34,062] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:16:34,065] [INFO] Task started: CheckM
[2023-03-14 13:16:34,065] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26937/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26937/checkm_input OceanDNA-b26937/checkm_result
[2023-03-14 13:17:03,310] [INFO] Task succeeded: CheckM
[2023-03-14 13:17:03,311] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 13:17:03,313] [INFO] ===== Completeness check finished =====
[2023-03-14 13:17:03,313] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:17:03,313] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26937/markers.fasta)
[2023-03-14 13:17:03,314] [INFO] Task started: Blastn
[2023-03-14 13:17:03,315] [INFO] Running command: blastn -query OceanDNA-b26937/markers.fasta -db /var/lib/cwl/stge7914e89-aaca-4c57-a8fa-bc745f98226f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26937/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:17:04,556] [INFO] Task succeeded: Blastn
[2023-03-14 13:17:04,558] [INFO] Selected 28 target genomes.
[2023-03-14 13:17:04,558] [INFO] Target genome list was writen to OceanDNA-b26937/target_genomes_gtdb.txt
[2023-03-14 13:17:04,605] [INFO] Task started: fastANI
[2023-03-14 13:17:04,605] [INFO] Running command: fastANI --query /var/lib/cwl/stge5b22c98-05cd-438a-83c4-250c500b676d/OceanDNA-b26937.fa --refList OceanDNA-b26937/target_genomes_gtdb.txt --output OceanDNA-b26937/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:17:11,393] [INFO] Task succeeded: fastANI
[2023-03-14 13:17:11,396] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 13:17:11,396] [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_002168075.1	s__TMED25 sp002168075	76.7078	61	340	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__TMED25;g__TMED25	95.0	98.97	97.02	0.94	0.90	4	-
GCA_902613795.1	s__TMED25 sp902613795	76.5873	57	340	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__TMED25;g__TMED25	95.0	99.47	99.34	0.93	0.93	3	-
GCA_002704755.1	s__TMED25 sp002704755	76.5231	52	340	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__TMED25;g__TMED25	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-14 13:17:11,397] [INFO] GTDB search result was written to OceanDNA-b26937/result_gtdb.tsv
[2023-03-14 13:17:11,397] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:17:11,398] [INFO] DFAST_QC result json was written to OceanDNA-b26937/dqc_result.json
[2023-03-14 13:17:11,398] [INFO] DFAST_QC completed!
[2023-03-14 13:17:11,398] [INFO] Total running time: 0h0m59s