[2023-03-18 21:53:45,254] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:53:45,254] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:53:45,255] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2404c69-e58c-464c-b00d-0b52882f2007/dqc_reference
[2023-03-18 21:53:47,072] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:53:47,072] [INFO] Task started: Prodigal
[2023-03-18 21:53:47,073] [INFO] Running command: cat /var/lib/cwl/stg4b5ae8c6-f4af-4dec-bf7b-7a631fd9be9f/OceanDNA-b8668.fa | prodigal -d OceanDNA-b8668/cds.fna -a OceanDNA-b8668/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:53:52,946] [INFO] Task succeeded: Prodigal
[2023-03-18 21:53:52,946] [INFO] Task started: HMMsearch
[2023-03-18 21:53:52,947] [INFO] Running command: hmmsearch --tblout OceanDNA-b8668/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2404c69-e58c-464c-b00d-0b52882f2007/dqc_reference/reference_markers.hmm OceanDNA-b8668/protein.faa > /dev/null
[2023-03-18 21:53:53,121] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:53:53,122] [INFO] Found 6/6 markers.
[2023-03-18 21:53:53,133] [INFO] Query marker FASTA was written to OceanDNA-b8668/markers.fasta
[2023-03-18 21:53:53,134] [INFO] Task started: Blastn
[2023-03-18 21:53:53,134] [INFO] Running command: blastn -query OceanDNA-b8668/markers.fasta -db /var/lib/cwl/stgb2404c69-e58c-464c-b00d-0b52882f2007/dqc_reference/reference_markers.fasta -out OceanDNA-b8668/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:53:53,706] [INFO] Task succeeded: Blastn
[2023-03-18 21:53:53,708] [INFO] Selected 34 target genomes.
[2023-03-18 21:53:53,708] [INFO] Target genome list was writen to OceanDNA-b8668/target_genomes.txt
[2023-03-18 21:53:53,725] [INFO] Task started: fastANI
[2023-03-18 21:53:53,726] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b5ae8c6-f4af-4dec-bf7b-7a631fd9be9f/OceanDNA-b8668.fa --refList OceanDNA-b8668/target_genomes.txt --output OceanDNA-b8668/fastani_result.tsv --threads 1
[2023-03-18 21:54:12,933] [INFO] Task succeeded: fastANI
[2023-03-18 21:54:12,934] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2404c69-e58c-464c-b00d-0b52882f2007/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:54:12,934] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2404c69-e58c-464c-b00d-0b52882f2007/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:54:12,934] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:54:12,934] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 21:54:12,934] [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 21:54:12,935] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8668/tc_result.tsv
[2023-03-18 21:54:12,936] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:54:12,936] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:54:12,936] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2404c69-e58c-464c-b00d-0b52882f2007/dqc_reference/checkm_data
[2023-03-18 21:54:12,940] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:54:12,945] [INFO] Task started: CheckM
[2023-03-18 21:54:12,945] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8668/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8668/checkm_input OceanDNA-b8668/checkm_result
[2023-03-18 21:54:34,156] [INFO] Task succeeded: CheckM
[2023-03-18 21:54:34,156] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:54:34,255] [INFO] ===== Completeness check finished =====
[2023-03-18 21:54:34,255] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:54:34,255] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8668/markers.fasta)
[2023-03-18 21:54:34,256] [INFO] Task started: Blastn
[2023-03-18 21:54:34,256] [INFO] Running command: blastn -query OceanDNA-b8668/markers.fasta -db /var/lib/cwl/stgb2404c69-e58c-464c-b00d-0b52882f2007/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8668/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:54:35,169] [INFO] Task succeeded: Blastn
[2023-03-18 21:54:35,171] [INFO] Selected 18 target genomes.
[2023-03-18 21:54:35,171] [INFO] Target genome list was writen to OceanDNA-b8668/target_genomes_gtdb.txt
[2023-03-18 21:54:35,218] [INFO] Task started: fastANI
[2023-03-18 21:54:35,219] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b5ae8c6-f4af-4dec-bf7b-7a631fd9be9f/OceanDNA-b8668.fa --refList OceanDNA-b8668/target_genomes_gtdb.txt --output OceanDNA-b8668/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:54:40,041] [INFO] Task succeeded: fastANI
[2023-03-18 21:54:40,047] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:54:40,047] [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_002457735.1	s__MED-G13 sp002457735	90.3487	199	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_902525795.1	s__MED-G13 sp902525795	86.6239	180	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_902602415.1	s__MED-G13 sp902602415	86.317	222	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_902518355.1	s__MED-G13 sp902518355	77.1331	63	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_002697255.1	s__MED-G13 sp002697255	76.933	74	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	76.9268	66	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_902510475.1	s__MED-G13 sp902510475	76.7986	55	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_902560045.1	s__MED-G13 sp902560045	76.7469	57	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_002702745.1	s__MED-G13 sp002702745	76.623	58	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	-
--------------------------------------------------------------------------------
[2023-03-18 21:54:40,048] [INFO] GTDB search result was written to OceanDNA-b8668/result_gtdb.tsv
[2023-03-18 21:54:40,049] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:54:40,052] [INFO] DFAST_QC result json was written to OceanDNA-b8668/dqc_result.json
[2023-03-18 21:54:40,052] [INFO] DFAST_QC completed!
[2023-03-18 21:54:40,052] [INFO] Total running time: 0h0m55s