[2023-03-18 20:59:43,923] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:59:43,923] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:59:43,923] [INFO] DQC Reference Directory: /var/lib/cwl/stg589fe0d2-9346-4baf-a0ad-4542de0bd815/dqc_reference
[2023-03-18 20:59:45,683] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:59:45,683] [INFO] Task started: Prodigal
[2023-03-18 20:59:45,683] [INFO] Running command: cat /var/lib/cwl/stg81d44c4f-9e0a-44c8-8bd1-57af4e10d527/OceanDNA-b41755.fa | prodigal -d OceanDNA-b41755/cds.fna -a OceanDNA-b41755/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:59:49,524] [INFO] Task succeeded: Prodigal
[2023-03-18 20:59:49,524] [INFO] Task started: HMMsearch
[2023-03-18 20:59:49,524] [INFO] Running command: hmmsearch --tblout OceanDNA-b41755/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg589fe0d2-9346-4baf-a0ad-4542de0bd815/dqc_reference/reference_markers.hmm OceanDNA-b41755/protein.faa > /dev/null
[2023-03-18 20:59:49,703] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:59:49,704] [INFO] Found 6/6 markers.
[2023-03-18 20:59:49,712] [INFO] Query marker FASTA was written to OceanDNA-b41755/markers.fasta
[2023-03-18 20:59:49,712] [INFO] Task started: Blastn
[2023-03-18 20:59:49,712] [INFO] Running command: blastn -query OceanDNA-b41755/markers.fasta -db /var/lib/cwl/stg589fe0d2-9346-4baf-a0ad-4542de0bd815/dqc_reference/reference_markers.fasta -out OceanDNA-b41755/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:59:51,851] [INFO] Task succeeded: Blastn
[2023-03-18 20:59:51,852] [INFO] Selected 15 target genomes.
[2023-03-18 20:59:51,852] [INFO] Target genome list was writen to OceanDNA-b41755/target_genomes.txt
[2023-03-18 20:59:51,861] [INFO] Task started: fastANI
[2023-03-18 20:59:51,861] [INFO] Running command: fastANI --query /var/lib/cwl/stg81d44c4f-9e0a-44c8-8bd1-57af4e10d527/OceanDNA-b41755.fa --refList OceanDNA-b41755/target_genomes.txt --output OceanDNA-b41755/fastani_result.tsv --threads 1
[2023-03-18 20:59:59,028] [INFO] Task succeeded: fastANI
[2023-03-18 20:59:59,029] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg589fe0d2-9346-4baf-a0ad-4542de0bd815/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:59:59,029] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg589fe0d2-9346-4baf-a0ad-4542de0bd815/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:59:59,029] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:59:59,029] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 20:59:59,030] [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 20:59:59,030] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41755/tc_result.tsv
[2023-03-18 20:59:59,030] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:59:59,030] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:59:59,030] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg589fe0d2-9346-4baf-a0ad-4542de0bd815/dqc_reference/checkm_data
[2023-03-18 20:59:59,035] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:59:59,037] [INFO] Task started: CheckM
[2023-03-18 20:59:59,037] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41755/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41755/checkm_input OceanDNA-b41755/checkm_result
[2023-03-18 21:00:15,753] [INFO] Task succeeded: CheckM
[2023-03-18 21:00:15,753] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:00:15,776] [INFO] ===== Completeness check finished =====
[2023-03-18 21:00:15,776] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:00:15,776] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41755/markers.fasta)
[2023-03-18 21:00:15,777] [INFO] Task started: Blastn
[2023-03-18 21:00:15,777] [INFO] Running command: blastn -query OceanDNA-b41755/markers.fasta -db /var/lib/cwl/stg589fe0d2-9346-4baf-a0ad-4542de0bd815/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41755/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:00:16,638] [INFO] Task succeeded: Blastn
[2023-03-18 21:00:16,639] [INFO] Selected 13 target genomes.
[2023-03-18 21:00:16,639] [INFO] Target genome list was writen to OceanDNA-b41755/target_genomes_gtdb.txt
[2023-03-18 21:00:16,655] [INFO] Task started: fastANI
[2023-03-18 21:00:16,655] [INFO] Running command: fastANI --query /var/lib/cwl/stg81d44c4f-9e0a-44c8-8bd1-57af4e10d527/OceanDNA-b41755.fa --refList OceanDNA-b41755/target_genomes_gtdb.txt --output OceanDNA-b41755/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:00:20,202] [INFO] Task succeeded: fastANI
[2023-03-18 21:00:20,208] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 21:00:20,208] [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_902616715.1	s__AG-339-G14 sp902616715	98.8092	242	249	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	98.52	98.27	0.93	0.90	8	conclusive
GCA_902527995.1	s__AG-339-G14 sp902527995	89.0121	158	249	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004213955.1	s__AG-339-G14 sp004213955	85.6289	226	249	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902536295.1	s__AG-339-G14 sp902536295	79.9406	145	249	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	97.79	97.73	0.85	0.77	3	-
GCA_902562135.1	s__AG-339-G14 sp902562135	79.8051	138	249	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	97.66	97.66	0.82	0.82	2	-
GCA_003282105.1	s__AG-339-G14 sp003282105	78.0683	94	249	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	95.52	95.11	0.79	0.67	11	-
GCA_902613455.1	s__AG-339-G14 sp902613455	77.9583	130	249	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	97.22	96.70	0.93	0.90	20	-
GCA_902635045.1	s__AG-339-G14 sp902635045	76.5334	51	249	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	98.24	96.50	0.87	0.84	4	-
--------------------------------------------------------------------------------
[2023-03-18 21:00:20,209] [INFO] GTDB search result was written to OceanDNA-b41755/result_gtdb.tsv
[2023-03-18 21:00:20,209] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:00:20,214] [INFO] DFAST_QC result json was written to OceanDNA-b41755/dqc_result.json
[2023-03-18 21:00:20,214] [INFO] DFAST_QC completed!
[2023-03-18 21:00:20,214] [INFO] Total running time: 0h0m36s