[2023-03-18 05:35:37,307] [INFO] DFAST_QC pipeline started.
[2023-03-18 05:35:37,309] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 05:35:37,309] [INFO] DQC Reference Directory: /var/lib/cwl/stg78b20d31-a616-4033-a885-4058325df3a5/dqc_reference
[2023-03-18 05:35:38,962] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 05:35:38,963] [INFO] Task started: Prodigal
[2023-03-18 05:35:38,963] [INFO] Running command: cat /var/lib/cwl/stgb9d7a81b-ee2a-4d4d-aae4-14e89ac4db7c/OceanDNA-b39820.fa | prodigal -d OceanDNA-b39820/cds.fna -a OceanDNA-b39820/protein.faa -g 11 -q > /dev/null
[2023-03-18 05:35:50,360] [INFO] Task succeeded: Prodigal
[2023-03-18 05:35:50,361] [INFO] Task started: HMMsearch
[2023-03-18 05:35:50,361] [INFO] Running command: hmmsearch --tblout OceanDNA-b39820/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78b20d31-a616-4033-a885-4058325df3a5/dqc_reference/reference_markers.hmm OceanDNA-b39820/protein.faa > /dev/null
[2023-03-18 05:35:50,562] [INFO] Task succeeded: HMMsearch
[2023-03-18 05:35:50,562] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb9d7a81b-ee2a-4d4d-aae4-14e89ac4db7c/OceanDNA-b39820.fa]
[2023-03-18 05:35:50,580] [INFO] Query marker FASTA was written to OceanDNA-b39820/markers.fasta
[2023-03-18 05:35:50,581] [INFO] Task started: Blastn
[2023-03-18 05:35:50,581] [INFO] Running command: blastn -query OceanDNA-b39820/markers.fasta -db /var/lib/cwl/stg78b20d31-a616-4033-a885-4058325df3a5/dqc_reference/reference_markers.fasta -out OceanDNA-b39820/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:35:51,152] [INFO] Task succeeded: Blastn
[2023-03-18 05:35:51,155] [INFO] Selected 21 target genomes.
[2023-03-18 05:35:51,155] [INFO] Target genome list was writen to OceanDNA-b39820/target_genomes.txt
[2023-03-18 05:35:51,169] [INFO] Task started: fastANI
[2023-03-18 05:35:51,169] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9d7a81b-ee2a-4d4d-aae4-14e89ac4db7c/OceanDNA-b39820.fa --refList OceanDNA-b39820/target_genomes.txt --output OceanDNA-b39820/fastani_result.tsv --threads 1
[2023-03-18 05:36:03,916] [INFO] Task succeeded: fastANI
[2023-03-18 05:36:03,916] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78b20d31-a616-4033-a885-4058325df3a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 05:36:03,916] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78b20d31-a616-4033-a885-4058325df3a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 05:36:03,917] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 05:36:03,917] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 05:36:03,917] [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 05:36:03,918] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39820/tc_result.tsv
[2023-03-18 05:36:03,920] [INFO] ===== Taxonomy check completed =====
[2023-03-18 05:36:03,921] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 05:36:03,921] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78b20d31-a616-4033-a885-4058325df3a5/dqc_reference/checkm_data
[2023-03-18 05:36:03,923] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 05:36:03,929] [INFO] Task started: CheckM
[2023-03-18 05:36:03,929] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39820/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39820/checkm_input OceanDNA-b39820/checkm_result
[2023-03-18 05:36:35,837] [INFO] Task succeeded: CheckM
[2023-03-18 05:36:35,837] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 05:36:35,895] [INFO] ===== Completeness check finished =====
[2023-03-18 05:36:35,895] [INFO] ===== Start GTDB Search =====
[2023-03-18 05:36:35,895] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39820/markers.fasta)
[2023-03-18 05:36:35,896] [INFO] Task started: Blastn
[2023-03-18 05:36:35,896] [INFO] Running command: blastn -query OceanDNA-b39820/markers.fasta -db /var/lib/cwl/stg78b20d31-a616-4033-a885-4058325df3a5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39820/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:36:36,819] [INFO] Task succeeded: Blastn
[2023-03-18 05:36:36,822] [INFO] Selected 14 target genomes.
[2023-03-18 05:36:36,822] [INFO] Target genome list was writen to OceanDNA-b39820/target_genomes_gtdb.txt
[2023-03-18 05:36:36,859] [INFO] Task started: fastANI
[2023-03-18 05:36:36,859] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9d7a81b-ee2a-4d4d-aae4-14e89ac4db7c/OceanDNA-b39820.fa --refList OceanDNA-b39820/target_genomes_gtdb.txt --output OceanDNA-b39820/fastani_result_gtdb.tsv --threads 1
[2023-03-18 05:36:43,456] [INFO] Task succeeded: fastANI
[2023-03-18 05:36:43,462] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 05:36:43,462] [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_002313335.1	s__HTCC2207 sp002313335	99.2639	453	668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905181925.1	s__HTCC2207 sp905181925	82.7864	310	668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	97.26	97.26	0.84	0.84	2	-
GCA_905182275.1	s__HTCC2207 sp905182275	81.0285	379	668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014381985.1	s__HTCC2207 sp014381985	78.9196	130	668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	96.01	96.01	0.94	0.94	2	-
GCA_018654575.1	s__HTCC2207 sp018654575	78.0415	108	668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.63	99.50	0.93	0.91	15	-
GCA_012960115.1	s__HTCC2207 sp012960115	77.8743	114	668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.92	99.92	0.91	0.91	2	-
GCA_002382445.1	s__HTCC2207 sp002382445	77.4283	111	668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.82	99.82	0.95	0.95	2	-
GCA_002685195.1	s__HTCC2207 sp002685195	77.1416	83	668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	97.12	96.72	0.71	0.66	10	-
--------------------------------------------------------------------------------
[2023-03-18 05:36:43,463] [INFO] GTDB search result was written to OceanDNA-b39820/result_gtdb.tsv
[2023-03-18 05:36:43,464] [INFO] ===== GTDB Search completed =====
[2023-03-18 05:36:43,466] [INFO] DFAST_QC result json was written to OceanDNA-b39820/dqc_result.json
[2023-03-18 05:36:43,466] [INFO] DFAST_QC completed!
[2023-03-18 05:36:43,466] [INFO] Total running time: 0h1m6s