[2023-03-17 07:28:31,295] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:28:31,296] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:28:31,296] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e30f401-bc38-4d21-9a08-ce98e125343c/dqc_reference
[2023-03-17 07:28:33,079] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:28:33,079] [INFO] Task started: Prodigal
[2023-03-17 07:28:33,079] [INFO] Running command: cat /var/lib/cwl/stg427de2d7-4603-4a53-94f7-5eea0bb821bf/OceanDNA-b11512.fa | prodigal -d OceanDNA-b11512/cds.fna -a OceanDNA-b11512/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:28:46,433] [INFO] Task succeeded: Prodigal
[2023-03-17 07:28:46,433] [INFO] Task started: HMMsearch
[2023-03-17 07:28:46,433] [INFO] Running command: hmmsearch --tblout OceanDNA-b11512/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e30f401-bc38-4d21-9a08-ce98e125343c/dqc_reference/reference_markers.hmm OceanDNA-b11512/protein.faa > /dev/null
[2023-03-17 07:28:46,636] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:28:46,637] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg427de2d7-4603-4a53-94f7-5eea0bb821bf/OceanDNA-b11512.fa]
[2023-03-17 07:28:46,653] [INFO] Query marker FASTA was written to OceanDNA-b11512/markers.fasta
[2023-03-17 07:28:46,653] [INFO] Task started: Blastn
[2023-03-17 07:28:46,653] [INFO] Running command: blastn -query OceanDNA-b11512/markers.fasta -db /var/lib/cwl/stg5e30f401-bc38-4d21-9a08-ce98e125343c/dqc_reference/reference_markers.fasta -out OceanDNA-b11512/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:28:47,184] [INFO] Task succeeded: Blastn
[2023-03-17 07:28:47,185] [INFO] Selected 22 target genomes.
[2023-03-17 07:28:47,185] [INFO] Target genome list was writen to OceanDNA-b11512/target_genomes.txt
[2023-03-17 07:28:47,197] [INFO] Task started: fastANI
[2023-03-17 07:28:47,197] [INFO] Running command: fastANI --query /var/lib/cwl/stg427de2d7-4603-4a53-94f7-5eea0bb821bf/OceanDNA-b11512.fa --refList OceanDNA-b11512/target_genomes.txt --output OceanDNA-b11512/fastani_result.tsv --threads 1
[2023-03-17 07:29:01,718] [INFO] Task succeeded: fastANI
[2023-03-17 07:29:01,719] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e30f401-bc38-4d21-9a08-ce98e125343c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:29:01,719] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e30f401-bc38-4d21-9a08-ce98e125343c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:29:01,719] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:29:01,719] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 07:29:01,719] [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
--------------------------------------------------------------------------------
[2023-03-17 07:29:01,719] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11512/tc_result.tsv
[2023-03-17 07:29:01,720] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:29:01,720] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:29:01,720] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e30f401-bc38-4d21-9a08-ce98e125343c/dqc_reference/checkm_data
[2023-03-17 07:29:01,723] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:29:01,726] [INFO] Task started: CheckM
[2023-03-17 07:29:01,726] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11512/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11512/checkm_input OceanDNA-b11512/checkm_result
[2023-03-17 07:29:38,625] [INFO] Task succeeded: CheckM
[2023-03-17 07:29:38,625] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:29:38,627] [INFO] ===== Completeness check finished =====
[2023-03-17 07:29:38,628] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:29:38,628] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11512/markers.fasta)
[2023-03-17 07:29:38,628] [INFO] Task started: Blastn
[2023-03-17 07:29:38,628] [INFO] Running command: blastn -query OceanDNA-b11512/markers.fasta -db /var/lib/cwl/stg5e30f401-bc38-4d21-9a08-ce98e125343c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11512/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:29:39,356] [INFO] Task succeeded: Blastn
[2023-03-17 07:29:39,357] [INFO] Selected 21 target genomes.
[2023-03-17 07:29:39,358] [INFO] Target genome list was writen to OceanDNA-b11512/target_genomes_gtdb.txt
[2023-03-17 07:29:39,700] [INFO] Task started: fastANI
[2023-03-17 07:29:39,700] [INFO] Running command: fastANI --query /var/lib/cwl/stg427de2d7-4603-4a53-94f7-5eea0bb821bf/OceanDNA-b11512.fa --refList OceanDNA-b11512/target_genomes_gtdb.txt --output OceanDNA-b11512/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:29:49,999] [INFO] Task succeeded: fastANI
[2023-03-17 07:29:50,003] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 07:29:50,003] [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_002720635.1	s__GCA-002722245 sp002720635	78.992	272	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__GCA-002722245;g__GCA-002722245	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002717515.1	s__GCA-002722245 sp002717515	78.5004	281	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__GCA-002722245;g__GCA-002722245	95.0	99.42	99.42	0.83	0.83	2	-
GCA_002722245.1	s__GCA-002722245 sp002722245	77.3058	141	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__GCA-002722245;g__GCA-002722245	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182585.1	s__GCA-002722245 sp905182585	76.774	81	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__GCA-002722245;g__GCA-002722245	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 07:29:50,003] [INFO] GTDB search result was written to OceanDNA-b11512/result_gtdb.tsv
[2023-03-17 07:29:50,003] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:29:50,004] [INFO] DFAST_QC result json was written to OceanDNA-b11512/dqc_result.json
[2023-03-17 07:29:50,004] [INFO] DFAST_QC completed!
[2023-03-17 07:29:50,004] [INFO] Total running time: 0h1m19s