[2023-03-18 20:59:43,928] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:59:43,928] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:59:43,929] [INFO] DQC Reference Directory: /var/lib/cwl/stga0424cd5-30b1-40fc-8452-abe3117b4efb/dqc_reference
[2023-03-18 20:59:45,682] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:59:45,682] [INFO] Task started: Prodigal
[2023-03-18 20:59:45,683] [INFO] Running command: cat /var/lib/cwl/stg58487216-3261-476d-bb76-b736e31f2c39/OceanDNA-b12328.fa | prodigal -d OceanDNA-b12328/cds.fna -a OceanDNA-b12328/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:59:52,400] [INFO] Task succeeded: Prodigal
[2023-03-18 20:59:52,400] [INFO] Task started: HMMsearch
[2023-03-18 20:59:52,400] [INFO] Running command: hmmsearch --tblout OceanDNA-b12328/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0424cd5-30b1-40fc-8452-abe3117b4efb/dqc_reference/reference_markers.hmm OceanDNA-b12328/protein.faa > /dev/null
[2023-03-18 20:59:52,566] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:59:52,566] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg58487216-3261-476d-bb76-b736e31f2c39/OceanDNA-b12328.fa]
[2023-03-18 20:59:52,580] [INFO] Query marker FASTA was written to OceanDNA-b12328/markers.fasta
[2023-03-18 20:59:52,581] [INFO] Task started: Blastn
[2023-03-18 20:59:52,581] [INFO] Running command: blastn -query OceanDNA-b12328/markers.fasta -db /var/lib/cwl/stga0424cd5-30b1-40fc-8452-abe3117b4efb/dqc_reference/reference_markers.fasta -out OceanDNA-b12328/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:59:53,114] [INFO] Task succeeded: Blastn
[2023-03-18 20:59:53,115] [INFO] Selected 26 target genomes.
[2023-03-18 20:59:53,115] [INFO] Target genome list was writen to OceanDNA-b12328/target_genomes.txt
[2023-03-18 20:59:53,128] [INFO] Task started: fastANI
[2023-03-18 20:59:53,129] [INFO] Running command: fastANI --query /var/lib/cwl/stg58487216-3261-476d-bb76-b736e31f2c39/OceanDNA-b12328.fa --refList OceanDNA-b12328/target_genomes.txt --output OceanDNA-b12328/fastani_result.tsv --threads 1
[2023-03-18 21:00:05,971] [INFO] Task succeeded: fastANI
[2023-03-18 21:00:05,971] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0424cd5-30b1-40fc-8452-abe3117b4efb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:00:05,971] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0424cd5-30b1-40fc-8452-abe3117b4efb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:00:05,972] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:00:05,972] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 21:00:05,972] [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 21:00:05,972] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12328/tc_result.tsv
[2023-03-18 21:00:05,972] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:00:05,972] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:00:05,972] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0424cd5-30b1-40fc-8452-abe3117b4efb/dqc_reference/checkm_data
[2023-03-18 21:00:05,975] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:00:06,004] [INFO] Task started: CheckM
[2023-03-18 21:00:06,004] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12328/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12328/checkm_input OceanDNA-b12328/checkm_result
[2023-03-18 21:00:28,609] [INFO] Task succeeded: CheckM
[2023-03-18 21:00:28,609] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.58%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 21:00:28,611] [INFO] ===== Completeness check finished =====
[2023-03-18 21:00:28,611] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:00:28,611] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12328/markers.fasta)
[2023-03-18 21:00:28,612] [INFO] Task started: Blastn
[2023-03-18 21:00:28,612] [INFO] Running command: blastn -query OceanDNA-b12328/markers.fasta -db /var/lib/cwl/stga0424cd5-30b1-40fc-8452-abe3117b4efb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12328/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:00:29,324] [INFO] Task succeeded: Blastn
[2023-03-18 21:00:29,325] [INFO] Selected 13 target genomes.
[2023-03-18 21:00:29,325] [INFO] Target genome list was writen to OceanDNA-b12328/target_genomes_gtdb.txt
[2023-03-18 21:00:29,351] [INFO] Task started: fastANI
[2023-03-18 21:00:29,351] [INFO] Running command: fastANI --query /var/lib/cwl/stg58487216-3261-476d-bb76-b736e31f2c39/OceanDNA-b12328.fa --refList OceanDNA-b12328/target_genomes_gtdb.txt --output OceanDNA-b12328/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:00:33,896] [INFO] Task succeeded: fastANI
[2023-03-18 21:00:33,902] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:00:33,902] [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_016780365.1	s__MED-G20 sp016780365	91.7871	228	270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	98.18	97.06	0.79	0.71	6	-
GCA_905182745.1	s__MED-G20 sp905182745	90.2554	146	270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002713405.1	s__MED-G20 sp002713405	88.492	229	270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181675.1	s__MED-G20 sp905181675	82.7803	204	270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182525.1	s__MED-G20 sp905182525	78.3454	138	270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	96.07	96.07	0.86	0.86	2	-
GCA_002457645.1	s__MED-G20 sp002457645	77.9358	71	270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686655.1	s__MED-G20 sp002686655	77.7186	117	270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	96.65	96.65	0.87	0.87	2	-
GCA_002691605.1	s__MED-G20 sp002691605	77.2546	103	270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	96.19	95.12	0.79	0.76	3	-
--------------------------------------------------------------------------------
[2023-03-18 21:00:33,903] [INFO] GTDB search result was written to OceanDNA-b12328/result_gtdb.tsv
[2023-03-18 21:00:33,903] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:00:33,904] [INFO] DFAST_QC result json was written to OceanDNA-b12328/dqc_result.json
[2023-03-18 21:00:33,904] [INFO] DFAST_QC completed!
[2023-03-18 21:00:33,904] [INFO] Total running time: 0h0m50s