[2023-03-19 01:33:27,245] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:33:27,245] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:33:27,245] [INFO] DQC Reference Directory: /var/lib/cwl/stg4bd1b854-c629-4a6f-9112-391a91777383/dqc_reference
[2023-03-19 01:33:28,378] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:33:28,378] [INFO] Task started: Prodigal
[2023-03-19 01:33:28,378] [INFO] Running command: cat /var/lib/cwl/stgcf4754ed-3135-42cf-8238-77587be96f03/OceanDNA-b8673.fa | prodigal -d OceanDNA-b8673/cds.fna -a OceanDNA-b8673/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:33:33,277] [INFO] Task succeeded: Prodigal
[2023-03-19 01:33:33,277] [INFO] Task started: HMMsearch
[2023-03-19 01:33:33,277] [INFO] Running command: hmmsearch --tblout OceanDNA-b8673/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4bd1b854-c629-4a6f-9112-391a91777383/dqc_reference/reference_markers.hmm OceanDNA-b8673/protein.faa > /dev/null
[2023-03-19 01:33:33,422] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:33:33,423] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgcf4754ed-3135-42cf-8238-77587be96f03/OceanDNA-b8673.fa]
[2023-03-19 01:33:33,429] [INFO] Query marker FASTA was written to OceanDNA-b8673/markers.fasta
[2023-03-19 01:33:33,429] [INFO] Task started: Blastn
[2023-03-19 01:33:33,429] [INFO] Running command: blastn -query OceanDNA-b8673/markers.fasta -db /var/lib/cwl/stg4bd1b854-c629-4a6f-9112-391a91777383/dqc_reference/reference_markers.fasta -out OceanDNA-b8673/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:33:33,945] [INFO] Task succeeded: Blastn
[2023-03-19 01:33:33,946] [INFO] Selected 25 target genomes.
[2023-03-19 01:33:33,946] [INFO] Target genome list was writen to OceanDNA-b8673/target_genomes.txt
[2023-03-19 01:33:33,963] [INFO] Task started: fastANI
[2023-03-19 01:33:33,963] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf4754ed-3135-42cf-8238-77587be96f03/OceanDNA-b8673.fa --refList OceanDNA-b8673/target_genomes.txt --output OceanDNA-b8673/fastani_result.tsv --threads 1
[2023-03-19 01:33:47,513] [INFO] Task succeeded: fastANI
[2023-03-19 01:33:47,513] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4bd1b854-c629-4a6f-9112-391a91777383/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:33:47,513] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4bd1b854-c629-4a6f-9112-391a91777383/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:33:47,514] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:33:47,514] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:33:47,514] [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
--------------------------------------------------------------------------------
[2023-03-19 01:33:47,514] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8673/tc_result.tsv
[2023-03-19 01:33:47,514] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:33:47,514] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:33:47,514] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4bd1b854-c629-4a6f-9112-391a91777383/dqc_reference/checkm_data
[2023-03-19 01:33:47,517] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:33:47,523] [INFO] Task started: CheckM
[2023-03-19 01:33:47,523] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8673/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8673/checkm_input OceanDNA-b8673/checkm_result
[2023-03-19 01:34:05,938] [INFO] Task succeeded: CheckM
[2023-03-19 01:34:05,939] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:34:05,940] [INFO] ===== Completeness check finished =====
[2023-03-19 01:34:05,940] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:34:05,940] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8673/markers.fasta)
[2023-03-19 01:34:05,941] [INFO] Task started: Blastn
[2023-03-19 01:34:05,942] [INFO] Running command: blastn -query OceanDNA-b8673/markers.fasta -db /var/lib/cwl/stg4bd1b854-c629-4a6f-9112-391a91777383/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8673/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:34:06,634] [INFO] Task succeeded: Blastn
[2023-03-19 01:34:06,635] [INFO] Selected 11 target genomes.
[2023-03-19 01:34:06,635] [INFO] Target genome list was writen to OceanDNA-b8673/target_genomes_gtdb.txt
[2023-03-19 01:34:06,645] [INFO] Task started: fastANI
[2023-03-19 01:34:06,646] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf4754ed-3135-42cf-8238-77587be96f03/OceanDNA-b8673.fa --refList OceanDNA-b8673/target_genomes_gtdb.txt --output OceanDNA-b8673/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:34:08,962] [INFO] Task succeeded: fastANI
[2023-03-19 01:34:08,968] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:34:08,969] [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_902602415.1	s__MED-G13 sp902602415	90.2866	212	268	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	99.01	98.13	0.87	0.81	5	-
GCA_902525795.1	s__MED-G13 sp902525795	89.0465	178	268	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002457735.1	s__MED-G13 sp002457735	88.1083	196	268	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902557655.1	s__MED-G13 sp902557655	77.5243	68	268	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	99.84	99.84	0.82	0.82	2	-
GCA_902560045.1	s__MED-G13 sp902560045	77.5073	59	268	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	99.04	98.52	0.67	0.66	3	-
GCA_002697255.1	s__MED-G13 sp002697255	77.0636	83	268	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902510415.1	s__MED-G13 sp902510415	77.0245	72	268	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	98.10	98.10	0.69	0.69	2	-
GCA_902518355.1	s__MED-G13 sp902518355	76.9931	71	268	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	96.57	96.00	0.86	0.83	4	-
GCA_902604715.1	s__MED-G13 sp902604715	76.8649	76	268	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	97.66	97.66	0.81	0.81	2	-
GCA_902626365.1	s__MED-G13 sp902626365	76.7444	78	268	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	96.07	96.07	0.74	0.74	2	-
--------------------------------------------------------------------------------
[2023-03-19 01:34:08,969] [INFO] GTDB search result was written to OceanDNA-b8673/result_gtdb.tsv
[2023-03-19 01:34:08,969] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:34:08,970] [INFO] DFAST_QC result json was written to OceanDNA-b8673/dqc_result.json
[2023-03-19 01:34:08,970] [INFO] DFAST_QC completed!
[2023-03-19 01:34:08,970] [INFO] Total running time: 0h0m42s