[2023-03-16 02:38:05,013] [INFO] DFAST_QC pipeline started.
[2023-03-16 02:38:05,013] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 02:38:05,013] [INFO] DQC Reference Directory: /var/lib/cwl/stg7daf97c9-77cf-480c-8a03-a31517dc50db/dqc_reference
[2023-03-16 02:38:06,150] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 02:38:06,151] [INFO] Task started: Prodigal
[2023-03-16 02:38:06,151] [INFO] Running command: cat /var/lib/cwl/stgfd506d3b-3383-46e6-9d04-87d62b1638ab/OceanDNA-b25472.fa | prodigal -d OceanDNA-b25472/cds.fna -a OceanDNA-b25472/protein.faa -g 11 -q > /dev/null
[2023-03-16 02:38:10,974] [INFO] Task succeeded: Prodigal
[2023-03-16 02:38:10,974] [INFO] Task started: HMMsearch
[2023-03-16 02:38:10,974] [INFO] Running command: hmmsearch --tblout OceanDNA-b25472/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7daf97c9-77cf-480c-8a03-a31517dc50db/dqc_reference/reference_markers.hmm OceanDNA-b25472/protein.faa > /dev/null
[2023-03-16 02:38:11,163] [INFO] Task succeeded: HMMsearch
[2023-03-16 02:38:11,163] [INFO] Found 6/6 markers.
[2023-03-16 02:38:11,170] [INFO] Query marker FASTA was written to OceanDNA-b25472/markers.fasta
[2023-03-16 02:38:11,171] [INFO] Task started: Blastn
[2023-03-16 02:38:11,171] [INFO] Running command: blastn -query OceanDNA-b25472/markers.fasta -db /var/lib/cwl/stg7daf97c9-77cf-480c-8a03-a31517dc50db/dqc_reference/reference_markers.fasta -out OceanDNA-b25472/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:38:11,749] [INFO] Task succeeded: Blastn
[2023-03-16 02:38:11,749] [INFO] Selected 20 target genomes.
[2023-03-16 02:38:11,750] [INFO] Target genome list was writen to OceanDNA-b25472/target_genomes.txt
[2023-03-16 02:38:11,761] [INFO] Task started: fastANI
[2023-03-16 02:38:11,761] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd506d3b-3383-46e6-9d04-87d62b1638ab/OceanDNA-b25472.fa --refList OceanDNA-b25472/target_genomes.txt --output OceanDNA-b25472/fastani_result.tsv --threads 1
[2023-03-16 02:38:19,910] [INFO] Task succeeded: fastANI
[2023-03-16 02:38:19,911] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7daf97c9-77cf-480c-8a03-a31517dc50db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 02:38:19,911] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7daf97c9-77cf-480c-8a03-a31517dc50db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 02:38:19,911] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 02:38:19,911] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 02:38:19,911] [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 02:38:19,911] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25472/tc_result.tsv
[2023-03-16 02:38:19,911] [INFO] ===== Taxonomy check completed =====
[2023-03-16 02:38:19,911] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 02:38:19,912] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7daf97c9-77cf-480c-8a03-a31517dc50db/dqc_reference/checkm_data
[2023-03-16 02:38:19,914] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 02:38:19,916] [INFO] Task started: CheckM
[2023-03-16 02:38:19,916] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25472/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25472/checkm_input OceanDNA-b25472/checkm_result
[2023-03-16 02:38:37,824] [INFO] Task succeeded: CheckM
[2023-03-16 02:38:37,825] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 02:38:37,826] [INFO] ===== Completeness check finished =====
[2023-03-16 02:38:37,827] [INFO] ===== Start GTDB Search =====
[2023-03-16 02:38:37,827] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25472/markers.fasta)
[2023-03-16 02:38:37,827] [INFO] Task started: Blastn
[2023-03-16 02:38:37,827] [INFO] Running command: blastn -query OceanDNA-b25472/markers.fasta -db /var/lib/cwl/stg7daf97c9-77cf-480c-8a03-a31517dc50db/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25472/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:38:38,737] [INFO] Task succeeded: Blastn
[2023-03-16 02:38:38,737] [INFO] Selected 15 target genomes.
[2023-03-16 02:38:38,738] [INFO] Target genome list was writen to OceanDNA-b25472/target_genomes_gtdb.txt
[2023-03-16 02:38:39,278] [INFO] Task started: fastANI
[2023-03-16 02:38:39,278] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd506d3b-3383-46e6-9d04-87d62b1638ab/OceanDNA-b25472.fa --refList OceanDNA-b25472/target_genomes_gtdb.txt --output OceanDNA-b25472/fastani_result_gtdb.tsv --threads 1
[2023-03-16 02:38:42,245] [INFO] Task succeeded: fastANI
[2023-03-16 02:38:42,250] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 02:38:42,250] [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_003280495.1	s__GCA-002704185 sp003280495	95.2382	216	311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__GCA-002704185	95.0	97.25	95.35	0.85	0.71	6	conclusive
GCA_902517865.1	s__GCA-002704185 sp902517865	93.8307	249	311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__GCA-002704185	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002704185.1	s__GCA-002704185 sp002704185	82.2517	120	311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__GCA-002704185	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008638005.1	s__HIMB114 sp008638005	76.5215	54	311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__HIMB114	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003209195.1	s__HIMB114 sp003209195	76.3893	56	311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__HIMB114	95.0	99.64	99.28	0.95	0.90	3	-
GCA_008638205.1	s__IMCC9063 sp008638205	76.2278	51	311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__IMCC9063	95.0	97.30	96.70	0.84	0.65	4	-
--------------------------------------------------------------------------------
[2023-03-16 02:38:42,250] [INFO] GTDB search result was written to OceanDNA-b25472/result_gtdb.tsv
[2023-03-16 02:38:42,251] [INFO] ===== GTDB Search completed =====
[2023-03-16 02:38:42,251] [INFO] DFAST_QC result json was written to OceanDNA-b25472/dqc_result.json
[2023-03-16 02:38:42,251] [INFO] DFAST_QC completed!
[2023-03-16 02:38:42,251] [INFO] Total running time: 0h0m37s