[2023-03-18 02:07:08,171] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:07:08,174] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:07:08,174] [INFO] DQC Reference Directory: /var/lib/cwl/stg210269c6-9246-42e8-84b5-e429cbbc7127/dqc_reference
[2023-03-18 02:07:09,333] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:07:09,334] [INFO] Task started: Prodigal
[2023-03-18 02:07:09,334] [INFO] Running command: cat /var/lib/cwl/stg17da1f41-e57a-43ad-9376-d3359b05f516/OceanDNA-b36864.fa | prodigal -d OceanDNA-b36864/cds.fna -a OceanDNA-b36864/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:07:34,970] [INFO] Task succeeded: Prodigal
[2023-03-18 02:07:34,971] [INFO] Task started: HMMsearch
[2023-03-18 02:07:34,971] [INFO] Running command: hmmsearch --tblout OceanDNA-b36864/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg210269c6-9246-42e8-84b5-e429cbbc7127/dqc_reference/reference_markers.hmm OceanDNA-b36864/protein.faa > /dev/null
[2023-03-18 02:07:35,183] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:07:35,184] [INFO] Found 6/6 markers.
[2023-03-18 02:07:35,209] [INFO] Query marker FASTA was written to OceanDNA-b36864/markers.fasta
[2023-03-18 02:07:35,210] [INFO] Task started: Blastn
[2023-03-18 02:07:35,211] [INFO] Running command: blastn -query OceanDNA-b36864/markers.fasta -db /var/lib/cwl/stg210269c6-9246-42e8-84b5-e429cbbc7127/dqc_reference/reference_markers.fasta -out OceanDNA-b36864/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:07:35,898] [INFO] Task succeeded: Blastn
[2023-03-18 02:07:35,899] [INFO] Selected 29 target genomes.
[2023-03-18 02:07:35,899] [INFO] Target genome list was writen to OceanDNA-b36864/target_genomes.txt
[2023-03-18 02:07:35,980] [INFO] Task started: fastANI
[2023-03-18 02:07:35,981] [INFO] Running command: fastANI --query /var/lib/cwl/stg17da1f41-e57a-43ad-9376-d3359b05f516/OceanDNA-b36864.fa --refList OceanDNA-b36864/target_genomes.txt --output OceanDNA-b36864/fastani_result.tsv --threads 1
[2023-03-18 02:07:56,107] [INFO] Task succeeded: fastANI
[2023-03-18 02:07:56,108] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg210269c6-9246-42e8-84b5-e429cbbc7127/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:07:56,108] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg210269c6-9246-42e8-84b5-e429cbbc7127/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:07:56,108] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:07:56,108] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 02:07:56,108] [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
--------------------------------------------------------------------------------
[2023-03-18 02:07:56,108] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36864/tc_result.tsv
[2023-03-18 02:07:56,109] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:07:56,109] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:07:56,109] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg210269c6-9246-42e8-84b5-e429cbbc7127/dqc_reference/checkm_data
[2023-03-18 02:07:56,119] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:07:56,130] [INFO] Task started: CheckM
[2023-03-18 02:07:56,130] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36864/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36864/checkm_input OceanDNA-b36864/checkm_result
[2023-03-18 02:08:59,108] [INFO] Task succeeded: CheckM
[2023-03-18 02:08:59,109] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:08:59,111] [INFO] ===== Completeness check finished =====
[2023-03-18 02:08:59,111] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:08:59,112] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36864/markers.fasta)
[2023-03-18 02:08:59,113] [INFO] Task started: Blastn
[2023-03-18 02:08:59,113] [INFO] Running command: blastn -query OceanDNA-b36864/markers.fasta -db /var/lib/cwl/stg210269c6-9246-42e8-84b5-e429cbbc7127/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36864/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:09:00,356] [INFO] Task succeeded: Blastn
[2023-03-18 02:09:00,357] [INFO] Selected 22 target genomes.
[2023-03-18 02:09:00,358] [INFO] Target genome list was writen to OceanDNA-b36864/target_genomes_gtdb.txt
[2023-03-18 02:09:00,374] [INFO] Task started: fastANI
[2023-03-18 02:09:00,374] [INFO] Running command: fastANI --query /var/lib/cwl/stg17da1f41-e57a-43ad-9376-d3359b05f516/OceanDNA-b36864.fa --refList OceanDNA-b36864/target_genomes_gtdb.txt --output OceanDNA-b36864/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:09:12,732] [INFO] Task succeeded: fastANI
[2023-03-18 02:09:12,736] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 02:09:12,737] [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_002327525.1	s__UBA2168 sp002327525	99.8114	1115	1332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA2168	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003247835.1	s__SZUA-309 sp003247835	76.1702	94	1332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__SZUA-309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002480525.1	s__UBA7803 sp002480525	76.0103	140	1332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA7803	95.0	99.35	98.95	0.83	0.81	3	-
GCA_009843635.1	s__UBA2168 sp009843635	75.8447	102	1332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA2168	95.0	97.76	96.95	0.89	0.86	7	-
GCA_004357385.1	s__SMWF01 sp004357385	75.6464	57	1332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__SMWF01	95.0	99.34	99.34	0.91	0.91	2	-
GCA_003248125.1	s__SZUA-521 sp003248125	75.4647	56	1332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__SZUA-521	95.0	99.60	99.60	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-03-18 02:09:12,737] [INFO] GTDB search result was written to OceanDNA-b36864/result_gtdb.tsv
[2023-03-18 02:09:12,737] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:09:12,738] [INFO] DFAST_QC result json was written to OceanDNA-b36864/dqc_result.json
[2023-03-18 02:09:12,738] [INFO] DFAST_QC completed!
[2023-03-18 02:09:12,738] [INFO] Total running time: 0h2m5s