[2023-03-18 00:05:54,478] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:05:54,478] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:05:54,478] [INFO] DQC Reference Directory: /var/lib/cwl/stg0bd1ed9d-a8c4-41f7-8d8f-19c91e3527f4/dqc_reference
[2023-03-18 00:05:55,568] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:05:55,569] [INFO] Task started: Prodigal
[2023-03-18 00:05:55,569] [INFO] Running command: cat /var/lib/cwl/stg38e48621-0e04-4ff6-aff5-6f31938529ee/OceanDNA-b8544.fa | prodigal -d OceanDNA-b8544/cds.fna -a OceanDNA-b8544/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:05:58,301] [INFO] Task succeeded: Prodigal
[2023-03-18 00:05:58,301] [INFO] Task started: HMMsearch
[2023-03-18 00:05:58,301] [INFO] Running command: hmmsearch --tblout OceanDNA-b8544/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0bd1ed9d-a8c4-41f7-8d8f-19c91e3527f4/dqc_reference/reference_markers.hmm OceanDNA-b8544/protein.faa > /dev/null
[2023-03-18 00:05:58,443] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:05:58,443] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg38e48621-0e04-4ff6-aff5-6f31938529ee/OceanDNA-b8544.fa]
[2023-03-18 00:05:58,450] [INFO] Query marker FASTA was written to OceanDNA-b8544/markers.fasta
[2023-03-18 00:05:58,451] [INFO] Task started: Blastn
[2023-03-18 00:05:58,452] [INFO] Running command: blastn -query OceanDNA-b8544/markers.fasta -db /var/lib/cwl/stg0bd1ed9d-a8c4-41f7-8d8f-19c91e3527f4/dqc_reference/reference_markers.fasta -out OceanDNA-b8544/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:05:59,016] [INFO] Task succeeded: Blastn
[2023-03-18 00:05:59,017] [INFO] Selected 21 target genomes.
[2023-03-18 00:05:59,017] [INFO] Target genome list was writen to OceanDNA-b8544/target_genomes.txt
[2023-03-18 00:05:59,034] [INFO] Task started: fastANI
[2023-03-18 00:05:59,035] [INFO] Running command: fastANI --query /var/lib/cwl/stg38e48621-0e04-4ff6-aff5-6f31938529ee/OceanDNA-b8544.fa --refList OceanDNA-b8544/target_genomes.txt --output OceanDNA-b8544/fastani_result.tsv --threads 1
[2023-03-18 00:06:09,859] [INFO] Task succeeded: fastANI
[2023-03-18 00:06:09,859] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0bd1ed9d-a8c4-41f7-8d8f-19c91e3527f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:06:09,859] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0bd1ed9d-a8c4-41f7-8d8f-19c91e3527f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:06:09,859] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:06:09,859] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:06:09,859] [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 00:06:09,860] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8544/tc_result.tsv
[2023-03-18 00:06:09,860] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:06:09,860] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:06:09,860] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0bd1ed9d-a8c4-41f7-8d8f-19c91e3527f4/dqc_reference/checkm_data
[2023-03-18 00:06:09,863] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:06:09,929] [INFO] Task started: CheckM
[2023-03-18 00:06:09,929] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8544/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8544/checkm_input OceanDNA-b8544/checkm_result
[2023-03-18 00:06:24,350] [INFO] Task succeeded: CheckM
[2023-03-18 00:06:24,350] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.39%
Contamintation: 6.08%
Strain heterogeneity: 60.00%
--------------------------------------------------------------------------------
[2023-03-18 00:06:24,352] [INFO] ===== Completeness check finished =====
[2023-03-18 00:06:24,352] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:06:24,352] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8544/markers.fasta)
[2023-03-18 00:06:24,353] [INFO] Task started: Blastn
[2023-03-18 00:06:24,353] [INFO] Running command: blastn -query OceanDNA-b8544/markers.fasta -db /var/lib/cwl/stg0bd1ed9d-a8c4-41f7-8d8f-19c91e3527f4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8544/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:06:25,064] [INFO] Task succeeded: Blastn
[2023-03-18 00:06:25,065] [INFO] Selected 10 target genomes.
[2023-03-18 00:06:25,065] [INFO] Target genome list was writen to OceanDNA-b8544/target_genomes_gtdb.txt
[2023-03-18 00:06:25,079] [INFO] Task started: fastANI
[2023-03-18 00:06:25,079] [INFO] Running command: fastANI --query /var/lib/cwl/stg38e48621-0e04-4ff6-aff5-6f31938529ee/OceanDNA-b8544.fa --refList OceanDNA-b8544/target_genomes_gtdb.txt --output OceanDNA-b8544/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:06:26,770] [INFO] Task succeeded: fastANI
[2023-03-18 00:06:26,775] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:06:26,775] [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_902516925.1	s__MED-G11 sp902516925	97.7828	52	64	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902593165.1	s__MED-G11 sp902593165	90.5685	52	64	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	96.69	96.69	0.86	0.86	2	-
GCA_902622595.1	s__MED-G11 sp902622595	85.4285	57	64	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	96.81	96.16	0.93	0.91	12	-
GCA_902620455.1	s__MED-G11 sp902620455	85.0051	58	64	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	99.20	98.53	0.88	0.86	7	-
GCA_902629505.1	s__MED-G11 sp902629505	84.8352	53	64	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902523665.1	s__MED-G11 sp902523665	84.2222	54	64	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905380995.1	s__MED-G11 sp905380995	83.8951	54	64	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:06:26,776] [INFO] GTDB search result was written to OceanDNA-b8544/result_gtdb.tsv
[2023-03-18 00:06:26,776] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:06:26,776] [INFO] DFAST_QC result json was written to OceanDNA-b8544/dqc_result.json
[2023-03-18 00:06:26,777] [INFO] DFAST_QC completed!
[2023-03-18 00:06:26,777] [INFO] Total running time: 0h0m32s