[2023-03-17 10:52:36,373] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:52:36,373] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:52:36,373] [INFO] DQC Reference Directory: /var/lib/cwl/stgbcdad42e-6960-401f-811b-a6abe9ea76cd/dqc_reference
[2023-03-17 10:52:38,606] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:52:38,606] [INFO] Task started: Prodigal
[2023-03-17 10:52:38,606] [INFO] Running command: cat /var/lib/cwl/stgddabc4a3-5959-44db-877c-bc3eb8ac80ac/OceanDNA-b17743.fa | prodigal -d OceanDNA-b17743/cds.fna -a OceanDNA-b17743/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:53:12,333] [INFO] Task succeeded: Prodigal
[2023-03-17 10:53:12,333] [INFO] Task started: HMMsearch
[2023-03-17 10:53:12,333] [INFO] Running command: hmmsearch --tblout OceanDNA-b17743/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbcdad42e-6960-401f-811b-a6abe9ea76cd/dqc_reference/reference_markers.hmm OceanDNA-b17743/protein.faa > /dev/null
[2023-03-17 10:53:12,583] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:53:12,584] [INFO] Found 6/6 markers.
[2023-03-17 10:53:12,623] [INFO] Query marker FASTA was written to OceanDNA-b17743/markers.fasta
[2023-03-17 10:53:12,624] [INFO] Task started: Blastn
[2023-03-17 10:53:12,624] [INFO] Running command: blastn -query OceanDNA-b17743/markers.fasta -db /var/lib/cwl/stgbcdad42e-6960-401f-811b-a6abe9ea76cd/dqc_reference/reference_markers.fasta -out OceanDNA-b17743/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:53:13,166] [INFO] Task succeeded: Blastn
[2023-03-17 10:53:13,168] [INFO] Selected 29 target genomes.
[2023-03-17 10:53:13,168] [INFO] Target genome list was writen to OceanDNA-b17743/target_genomes.txt
[2023-03-17 10:53:13,258] [INFO] Task started: fastANI
[2023-03-17 10:53:13,258] [INFO] Running command: fastANI --query /var/lib/cwl/stgddabc4a3-5959-44db-877c-bc3eb8ac80ac/OceanDNA-b17743.fa --refList OceanDNA-b17743/target_genomes.txt --output OceanDNA-b17743/fastani_result.tsv --threads 1
[2023-03-17 10:53:36,607] [INFO] Task succeeded: fastANI
[2023-03-17 10:53:36,607] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbcdad42e-6960-401f-811b-a6abe9ea76cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:53:36,607] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbcdad42e-6960-401f-811b-a6abe9ea76cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:53:36,608] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:53:36,608] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 10:53:36,608] [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 10:53:36,608] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17743/tc_result.tsv
[2023-03-17 10:53:36,609] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:53:36,609] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:53:36,609] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbcdad42e-6960-401f-811b-a6abe9ea76cd/dqc_reference/checkm_data
[2023-03-17 10:53:36,612] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:53:36,620] [INFO] Task started: CheckM
[2023-03-17 10:53:36,620] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17743/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17743/checkm_input OceanDNA-b17743/checkm_result
[2023-03-17 10:54:56,543] [INFO] Task succeeded: CheckM
[2023-03-17 10:54:56,543] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 10:54:56,548] [INFO] ===== Completeness check finished =====
[2023-03-17 10:54:56,548] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:54:56,548] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17743/markers.fasta)
[2023-03-17 10:54:56,548] [INFO] Task started: Blastn
[2023-03-17 10:54:56,548] [INFO] Running command: blastn -query OceanDNA-b17743/markers.fasta -db /var/lib/cwl/stgbcdad42e-6960-401f-811b-a6abe9ea76cd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17743/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:54:57,320] [INFO] Task succeeded: Blastn
[2023-03-17 10:54:57,321] [INFO] Selected 20 target genomes.
[2023-03-17 10:54:57,321] [INFO] Target genome list was writen to OceanDNA-b17743/target_genomes_gtdb.txt
[2023-03-17 10:54:57,418] [INFO] Task started: fastANI
[2023-03-17 10:54:57,418] [INFO] Running command: fastANI --query /var/lib/cwl/stgddabc4a3-5959-44db-877c-bc3eb8ac80ac/OceanDNA-b17743.fa --refList OceanDNA-b17743/target_genomes_gtdb.txt --output OceanDNA-b17743/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:55:11,732] [INFO] Task succeeded: fastANI
[2023-03-17 10:55:11,737] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 10:55:11,737] [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_002712305.1	s__UBA12574 sp002712305	98.7031	1373	1728	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__UBA12574	95.0	98.27	97.81	0.83	0.79	3	conclusive
GCA_018660835.1	s__UBA12574 sp018660835	78.1195	631	1728	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__UBA12574	95.0	99.93	99.91	0.98	0.97	7	-
GCA_018673255.1	s__UBA12574 sp018673255	77.3236	516	1728	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__UBA12574	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002726335.1	s__UBA8231 sp002726335	76.7423	195	1728	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__UBA8231	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002725915.1	s__GCA-2725915 sp002725915	76.0796	66	1728	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2725915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016187725.1	s__SICG01 sp016187725	75.5951	74	1728	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__SICG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 10:55:11,740] [INFO] GTDB search result was written to OceanDNA-b17743/result_gtdb.tsv
[2023-03-17 10:55:11,746] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:55:11,749] [INFO] DFAST_QC result json was written to OceanDNA-b17743/dqc_result.json
[2023-03-17 10:55:11,749] [INFO] DFAST_QC completed!
[2023-03-17 10:55:11,749] [INFO] Total running time: 0h2m35s