[2023-03-18 23:44:06,361] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:44:06,361] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:44:06,361] [INFO] DQC Reference Directory: /var/lib/cwl/stg885b0325-ff00-4f96-a54f-01c870768c5e/dqc_reference
[2023-03-18 23:44:07,521] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:44:07,521] [INFO] Task started: Prodigal
[2023-03-18 23:44:07,522] [INFO] Running command: cat /var/lib/cwl/stge25ca9e4-0339-4643-8f5c-6922ebadfd51/OceanDNA-b37042.fa | prodigal -d OceanDNA-b37042/cds.fna -a OceanDNA-b37042/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:44:21,373] [INFO] Task succeeded: Prodigal
[2023-03-18 23:44:21,373] [INFO] Task started: HMMsearch
[2023-03-18 23:44:21,373] [INFO] Running command: hmmsearch --tblout OceanDNA-b37042/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg885b0325-ff00-4f96-a54f-01c870768c5e/dqc_reference/reference_markers.hmm OceanDNA-b37042/protein.faa > /dev/null
[2023-03-18 23:44:21,586] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:44:21,586] [INFO] Found 6/6 markers.
[2023-03-18 23:44:21,605] [INFO] Query marker FASTA was written to OceanDNA-b37042/markers.fasta
[2023-03-18 23:44:21,606] [INFO] Task started: Blastn
[2023-03-18 23:44:21,606] [INFO] Running command: blastn -query OceanDNA-b37042/markers.fasta -db /var/lib/cwl/stg885b0325-ff00-4f96-a54f-01c870768c5e/dqc_reference/reference_markers.fasta -out OceanDNA-b37042/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:44:22,179] [INFO] Task succeeded: Blastn
[2023-03-18 23:44:22,179] [INFO] Selected 30 target genomes.
[2023-03-18 23:44:22,180] [INFO] Target genome list was writen to OceanDNA-b37042/target_genomes.txt
[2023-03-18 23:44:22,199] [INFO] Task started: fastANI
[2023-03-18 23:44:22,199] [INFO] Running command: fastANI --query /var/lib/cwl/stge25ca9e4-0339-4643-8f5c-6922ebadfd51/OceanDNA-b37042.fa --refList OceanDNA-b37042/target_genomes.txt --output OceanDNA-b37042/fastani_result.tsv --threads 1
[2023-03-18 23:44:41,144] [INFO] Task succeeded: fastANI
[2023-03-18 23:44:41,144] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg885b0325-ff00-4f96-a54f-01c870768c5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:44:41,144] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg885b0325-ff00-4f96-a54f-01c870768c5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:44:41,144] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:44:41,145] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:44:41,145] [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 23:44:41,145] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37042/tc_result.tsv
[2023-03-18 23:44:41,145] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:44:41,145] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:44:41,145] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg885b0325-ff00-4f96-a54f-01c870768c5e/dqc_reference/checkm_data
[2023-03-18 23:44:41,148] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:44:41,181] [INFO] Task started: CheckM
[2023-03-18 23:44:41,181] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37042/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37042/checkm_input OceanDNA-b37042/checkm_result
[2023-03-18 23:45:19,395] [INFO] Task succeeded: CheckM
[2023-03-18 23:45:19,396] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 23:45:19,402] [INFO] ===== Completeness check finished =====
[2023-03-18 23:45:19,402] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:45:19,402] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37042/markers.fasta)
[2023-03-18 23:45:19,403] [INFO] Task started: Blastn
[2023-03-18 23:45:19,403] [INFO] Running command: blastn -query OceanDNA-b37042/markers.fasta -db /var/lib/cwl/stg885b0325-ff00-4f96-a54f-01c870768c5e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37042/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:45:20,289] [INFO] Task succeeded: Blastn
[2023-03-18 23:45:20,294] [INFO] Selected 25 target genomes.
[2023-03-18 23:45:20,294] [INFO] Target genome list was writen to OceanDNA-b37042/target_genomes_gtdb.txt
[2023-03-18 23:45:20,326] [INFO] Task started: fastANI
[2023-03-18 23:45:20,326] [INFO] Running command: fastANI --query /var/lib/cwl/stge25ca9e4-0339-4643-8f5c-6922ebadfd51/OceanDNA-b37042.fa --refList OceanDNA-b37042/target_genomes_gtdb.txt --output OceanDNA-b37042/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:45:33,815] [INFO] Task succeeded: fastANI
[2023-03-18 23:45:33,820] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:45:33,821] [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_902565895.1	s__UBA4421 sp902565895	95.8913	442	752	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	96.81	96.81	0.58	0.58	2	conclusive
GCA_002170355.2	s__UBA4421 sp002170355	77.8434	159	752	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002690405.1	s__UBA4421 sp002690405	77.7789	145	752	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	98.88	98.84	0.89	0.88	4	-
GCA_002684495.1	s__UBA4421 sp002684495	77.3529	174	752	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002704325.1	s__UBA4421 sp002704325	77.2995	83	752	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002725095.1	s__UBA4421 sp002725095	77.0974	93	752	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	99.07	99.07	0.73	0.73	2	-
GCA_002348825.1	s__UBA4421 sp002348825	76.8876	105	752	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	99.36	99.22	0.85	0.84	3	-
--------------------------------------------------------------------------------
[2023-03-18 23:45:33,821] [INFO] GTDB search result was written to OceanDNA-b37042/result_gtdb.tsv
[2023-03-18 23:45:33,822] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:45:33,824] [INFO] DFAST_QC result json was written to OceanDNA-b37042/dqc_result.json
[2023-03-18 23:45:33,824] [INFO] DFAST_QC completed!
[2023-03-18 23:45:33,824] [INFO] Total running time: 0h1m27s