[2023-03-19 02:46:09,199] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:46:09,199] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:46:09,199] [INFO] DQC Reference Directory: /var/lib/cwl/stg0caba00b-ae8b-45e0-9a1d-8d5ffe3dec9f/dqc_reference
[2023-03-19 02:46:10,315] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:46:10,316] [INFO] Task started: Prodigal
[2023-03-19 02:46:10,316] [INFO] Running command: cat /var/lib/cwl/stgb83149b3-33d6-4c67-b63c-9e3f3cb75892/OceanDNA-b4799.fa | prodigal -d OceanDNA-b4799/cds.fna -a OceanDNA-b4799/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:46:19,267] [INFO] Task succeeded: Prodigal
[2023-03-19 02:46:19,267] [INFO] Task started: HMMsearch
[2023-03-19 02:46:19,267] [INFO] Running command: hmmsearch --tblout OceanDNA-b4799/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0caba00b-ae8b-45e0-9a1d-8d5ffe3dec9f/dqc_reference/reference_markers.hmm OceanDNA-b4799/protein.faa > /dev/null
[2023-03-19 02:46:19,441] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:46:19,442] [INFO] Found 6/6 markers.
[2023-03-19 02:46:19,455] [INFO] Query marker FASTA was written to OceanDNA-b4799/markers.fasta
[2023-03-19 02:46:19,456] [INFO] Task started: Blastn
[2023-03-19 02:46:19,456] [INFO] Running command: blastn -query OceanDNA-b4799/markers.fasta -db /var/lib/cwl/stg0caba00b-ae8b-45e0-9a1d-8d5ffe3dec9f/dqc_reference/reference_markers.fasta -out OceanDNA-b4799/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:46:20,026] [INFO] Task succeeded: Blastn
[2023-03-19 02:46:20,028] [INFO] Selected 26 target genomes.
[2023-03-19 02:46:20,028] [INFO] Target genome list was writen to OceanDNA-b4799/target_genomes.txt
[2023-03-19 02:46:20,105] [INFO] Task started: fastANI
[2023-03-19 02:46:20,105] [INFO] Running command: fastANI --query /var/lib/cwl/stgb83149b3-33d6-4c67-b63c-9e3f3cb75892/OceanDNA-b4799.fa --refList OceanDNA-b4799/target_genomes.txt --output OceanDNA-b4799/fastani_result.tsv --threads 1
[2023-03-19 02:46:35,699] [INFO] Task succeeded: fastANI
[2023-03-19 02:46:35,700] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0caba00b-ae8b-45e0-9a1d-8d5ffe3dec9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:46:35,700] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0caba00b-ae8b-45e0-9a1d-8d5ffe3dec9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:46:35,700] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:46:35,700] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 02:46:35,700] [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
--------------------------------------------------------------------------------
[2023-03-19 02:46:35,701] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4799/tc_result.tsv
[2023-03-19 02:46:35,702] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:46:35,702] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:46:35,702] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0caba00b-ae8b-45e0-9a1d-8d5ffe3dec9f/dqc_reference/checkm_data
[2023-03-19 02:46:35,705] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:46:35,708] [INFO] Task started: CheckM
[2023-03-19 02:46:35,708] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4799/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4799/checkm_input OceanDNA-b4799/checkm_result
[2023-03-19 02:47:02,567] [INFO] Task succeeded: CheckM
[2023-03-19 02:47:02,568] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.11%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:47:02,571] [INFO] ===== Completeness check finished =====
[2023-03-19 02:47:02,571] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:47:02,571] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4799/markers.fasta)
[2023-03-19 02:47:02,572] [INFO] Task started: Blastn
[2023-03-19 02:47:02,572] [INFO] Running command: blastn -query OceanDNA-b4799/markers.fasta -db /var/lib/cwl/stg0caba00b-ae8b-45e0-9a1d-8d5ffe3dec9f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4799/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:47:03,514] [INFO] Task succeeded: Blastn
[2023-03-19 02:47:03,515] [INFO] Selected 21 target genomes.
[2023-03-19 02:47:03,515] [INFO] Target genome list was writen to OceanDNA-b4799/target_genomes_gtdb.txt
[2023-03-19 02:47:03,630] [INFO] Task started: fastANI
[2023-03-19 02:47:03,630] [INFO] Running command: fastANI --query /var/lib/cwl/stgb83149b3-33d6-4c67-b63c-9e3f3cb75892/OceanDNA-b4799.fa --refList OceanDNA-b4799/target_genomes_gtdb.txt --output OceanDNA-b4799/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:47:11,048] [INFO] Task succeeded: fastANI
[2023-03-19 02:47:11,056] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:47:11,056] [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_905181585.1	s__CAJIYG01 sp905181585	85.6658	466	508	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__CAJIYG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018675825.1	s__GCA-002715885 sp018675825	77.3053	121	508	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002715885	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902579065.1	s__GCA-002715885 sp902579065	77.2688	100	508	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002715885	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689735.1	s__GCA-002715885 sp002689735	76.9652	84	508	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002715885	95.0	96.30	96.30	0.76	0.76	2	-
GCA_014239655.1	s__GCA-002715885 sp014239655	76.8656	138	508	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002715885	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478185.1	s__UWMA-0277 sp905478185	76.7197	87	508	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	96.67	96.67	0.88	0.88	2	-
GCA_018664745.1	s__UWMA-0277 sp018664745	76.6865	59	508	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479165.1	s__UWMA-0277 sp905479165	76.4747	67	508	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478765.1	s__UWMA-0277 sp905478765	76.4571	87	508	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002697505.1	s__GCA-2697505 sp002697505	76.2982	67	508	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2697505	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014384505.1	s__UWMA-0277 sp014384505	76.1137	67	508	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002728175.1	s__GCA-2697505 sp002728175	76.063	81	508	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2697505	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902627575.1	s__GCA-2711125 sp902627575	75.7145	66	508	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2711125	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:47:11,057] [INFO] GTDB search result was written to OceanDNA-b4799/result_gtdb.tsv
[2023-03-19 02:47:11,058] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:47:11,059] [INFO] DFAST_QC result json was written to OceanDNA-b4799/dqc_result.json
[2023-03-19 02:47:11,059] [INFO] DFAST_QC completed!
[2023-03-19 02:47:11,059] [INFO] Total running time: 0h1m2s