[2023-03-15 07:25:31,262] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:25:31,265] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:25:31,265] [INFO] DQC Reference Directory: /var/lib/cwl/stgd757f352-3308-4f07-9364-4dc8c7839539/dqc_reference
[2023-03-15 07:25:32,918] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:25:32,918] [INFO] Task started: Prodigal
[2023-03-15 07:25:32,918] [INFO] Running command: cat /var/lib/cwl/stg880448c9-a11b-4568-b45e-9c72e217171e/OceanDNA-b8783.fa | prodigal -d OceanDNA-b8783/cds.fna -a OceanDNA-b8783/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:25:37,723] [INFO] Task succeeded: Prodigal
[2023-03-15 07:25:37,723] [INFO] Task started: HMMsearch
[2023-03-15 07:25:37,723] [INFO] Running command: hmmsearch --tblout OceanDNA-b8783/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd757f352-3308-4f07-9364-4dc8c7839539/dqc_reference/reference_markers.hmm OceanDNA-b8783/protein.faa > /dev/null
[2023-03-15 07:25:37,867] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:25:37,868] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg880448c9-a11b-4568-b45e-9c72e217171e/OceanDNA-b8783.fa]
[2023-03-15 07:25:37,881] [INFO] Query marker FASTA was written to OceanDNA-b8783/markers.fasta
[2023-03-15 07:25:37,881] [INFO] Task started: Blastn
[2023-03-15 07:25:37,881] [INFO] Running command: blastn -query OceanDNA-b8783/markers.fasta -db /var/lib/cwl/stgd757f352-3308-4f07-9364-4dc8c7839539/dqc_reference/reference_markers.fasta -out OceanDNA-b8783/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:25:38,320] [INFO] Task succeeded: Blastn
[2023-03-15 07:25:38,323] [INFO] Selected 11 target genomes.
[2023-03-15 07:25:38,324] [INFO] Target genome list was writen to OceanDNA-b8783/target_genomes.txt
[2023-03-15 07:25:38,328] [INFO] Task started: fastANI
[2023-03-15 07:25:38,329] [INFO] Running command: fastANI --query /var/lib/cwl/stg880448c9-a11b-4568-b45e-9c72e217171e/OceanDNA-b8783.fa --refList OceanDNA-b8783/target_genomes.txt --output OceanDNA-b8783/fastani_result.tsv --threads 1
[2023-03-15 07:25:44,852] [INFO] Task succeeded: fastANI
[2023-03-15 07:25:44,853] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd757f352-3308-4f07-9364-4dc8c7839539/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:25:44,853] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd757f352-3308-4f07-9364-4dc8c7839539/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:25:44,853] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:25:44,853] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 07:25:44,853] [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
--------------------------------------------------------------------------------
[2023-03-15 07:25:44,856] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8783/tc_result.tsv
[2023-03-15 07:25:44,862] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:25:44,862] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:25:44,862] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd757f352-3308-4f07-9364-4dc8c7839539/dqc_reference/checkm_data
[2023-03-15 07:25:44,865] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:25:44,953] [INFO] Task started: CheckM
[2023-03-15 07:25:44,953] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8783/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8783/checkm_input OceanDNA-b8783/checkm_result
[2023-03-15 07:26:03,684] [INFO] Task succeeded: CheckM
[2023-03-15 07:26:03,685] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 6.77%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 07:26:03,770] [INFO] ===== Completeness check finished =====
[2023-03-15 07:26:03,770] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:26:03,770] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8783/markers.fasta)
[2023-03-15 07:26:03,771] [INFO] Task started: Blastn
[2023-03-15 07:26:03,771] [INFO] Running command: blastn -query OceanDNA-b8783/markers.fasta -db /var/lib/cwl/stgd757f352-3308-4f07-9364-4dc8c7839539/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8783/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:26:04,210] [INFO] Task succeeded: Blastn
[2023-03-15 07:26:04,220] [INFO] Selected 8 target genomes.
[2023-03-15 07:26:04,220] [INFO] Target genome list was writen to OceanDNA-b8783/target_genomes_gtdb.txt
[2023-03-15 07:26:04,228] [INFO] Task started: fastANI
[2023-03-15 07:26:04,228] [INFO] Running command: fastANI --query /var/lib/cwl/stg880448c9-a11b-4568-b45e-9c72e217171e/OceanDNA-b8783.fa --refList OceanDNA-b8783/target_genomes_gtdb.txt --output OceanDNA-b8783/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:26:06,007] [INFO] Task succeeded: fastANI
[2023-03-15 07:26:06,011] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:26:06,012] [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_902598295.1	s__MED-G14 sp902598295	92.9145	190	247	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902614065.1	s__MED-G14 sp002697465	86.2371	199	247	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	97.49	95.51	0.88	0.84	14	-
GCA_902586095.1	s__MED-G14 sp902586095	85.0722	152	247	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902544085.1	s__MED-G14 sp902544085	85.0579	192	247	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	99.92	99.92	0.94	0.94	2	-
GCA_902609185.1	s__MED-G14 sp902609185	82.0938	117	247	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003331875.1	s__MED-G14 sp003331875	81.8245	163	247	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 07:26:06,014] [INFO] GTDB search result was written to OceanDNA-b8783/result_gtdb.tsv
[2023-03-15 07:26:06,017] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:26:06,020] [INFO] DFAST_QC result json was written to OceanDNA-b8783/dqc_result.json
[2023-03-15 07:26:06,021] [INFO] DFAST_QC completed!
[2023-03-15 07:26:06,021] [INFO] Total running time: 0h0m35s