[2023-03-15 04:45:50,515] [INFO] DFAST_QC pipeline started.
[2023-03-15 04:45:50,517] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 04:45:50,517] [INFO] DQC Reference Directory: /var/lib/cwl/stg96ee9fac-f7e5-4c68-9f3f-8ef99f4c22ba/dqc_reference
[2023-03-15 04:45:51,652] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 04:45:51,652] [INFO] Task started: Prodigal
[2023-03-15 04:45:51,652] [INFO] Running command: cat /var/lib/cwl/stga6239bc4-5147-4611-bb72-ae58477ca8c2/OceanDNA-b5779.fa | prodigal -d OceanDNA-b5779/cds.fna -a OceanDNA-b5779/protein.faa -g 11 -q > /dev/null
[2023-03-15 04:46:05,902] [INFO] Task succeeded: Prodigal
[2023-03-15 04:46:05,902] [INFO] Task started: HMMsearch
[2023-03-15 04:46:05,902] [INFO] Running command: hmmsearch --tblout OceanDNA-b5779/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg96ee9fac-f7e5-4c68-9f3f-8ef99f4c22ba/dqc_reference/reference_markers.hmm OceanDNA-b5779/protein.faa > /dev/null
[2023-03-15 04:46:06,084] [INFO] Task succeeded: HMMsearch
[2023-03-15 04:46:06,084] [INFO] Found 6/6 markers.
[2023-03-15 04:46:06,118] [INFO] Query marker FASTA was written to OceanDNA-b5779/markers.fasta
[2023-03-15 04:46:06,119] [INFO] Task started: Blastn
[2023-03-15 04:46:06,119] [INFO] Running command: blastn -query OceanDNA-b5779/markers.fasta -db /var/lib/cwl/stg96ee9fac-f7e5-4c68-9f3f-8ef99f4c22ba/dqc_reference/reference_markers.fasta -out OceanDNA-b5779/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:46:06,672] [INFO] Task succeeded: Blastn
[2023-03-15 04:46:06,678] [INFO] Selected 33 target genomes.
[2023-03-15 04:46:06,679] [INFO] Target genome list was writen to OceanDNA-b5779/target_genomes.txt
[2023-03-15 04:46:06,700] [INFO] Task started: fastANI
[2023-03-15 04:46:06,700] [INFO] Running command: fastANI --query /var/lib/cwl/stga6239bc4-5147-4611-bb72-ae58477ca8c2/OceanDNA-b5779.fa --refList OceanDNA-b5779/target_genomes.txt --output OceanDNA-b5779/fastani_result.tsv --threads 1
[2023-03-15 04:46:25,002] [INFO] Task succeeded: fastANI
[2023-03-15 04:46:25,003] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg96ee9fac-f7e5-4c68-9f3f-8ef99f4c22ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 04:46:25,003] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg96ee9fac-f7e5-4c68-9f3f-8ef99f4c22ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 04:46:25,003] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 04:46:25,003] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 04:46:25,003] [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
--------------------------------------------------------------------------------
[2023-03-15 04:46:25,004] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5779/tc_result.tsv
[2023-03-15 04:46:25,005] [INFO] ===== Taxonomy check completed =====
[2023-03-15 04:46:25,005] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 04:46:25,005] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg96ee9fac-f7e5-4c68-9f3f-8ef99f4c22ba/dqc_reference/checkm_data
[2023-03-15 04:46:25,008] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 04:46:25,013] [INFO] Task started: CheckM
[2023-03-15 04:46:25,013] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5779/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5779/checkm_input OceanDNA-b5779/checkm_result
[2023-03-15 04:47:04,541] [INFO] Task succeeded: CheckM
[2023-03-15 04:47:04,541] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 04:47:04,586] [INFO] ===== Completeness check finished =====
[2023-03-15 04:47:04,586] [INFO] ===== Start GTDB Search =====
[2023-03-15 04:47:04,586] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5779/markers.fasta)
[2023-03-15 04:47:04,586] [INFO] Task started: Blastn
[2023-03-15 04:47:04,586] [INFO] Running command: blastn -query OceanDNA-b5779/markers.fasta -db /var/lib/cwl/stg96ee9fac-f7e5-4c68-9f3f-8ef99f4c22ba/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5779/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:47:05,373] [INFO] Task succeeded: Blastn
[2023-03-15 04:47:05,375] [INFO] Selected 10 target genomes.
[2023-03-15 04:47:05,375] [INFO] Target genome list was writen to OceanDNA-b5779/target_genomes_gtdb.txt
[2023-03-15 04:47:05,385] [INFO] Task started: fastANI
[2023-03-15 04:47:05,385] [INFO] Running command: fastANI --query /var/lib/cwl/stga6239bc4-5147-4611-bb72-ae58477ca8c2/OceanDNA-b5779.fa --refList OceanDNA-b5779/target_genomes_gtdb.txt --output OceanDNA-b5779/fastani_result_gtdb.tsv --threads 1
[2023-03-15 04:47:10,140] [INFO] Task succeeded: fastANI
[2023-03-15 04:47:10,145] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 04:47:10,146] [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_013911625.1	s__UBA10364 sp013911625	98.859	267	590	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002430755.1	s__UBA10364 sp002430755	92.9205	357	590	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003385605.1	s__UBA10364 sp003385605	90.9581	552	590	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	99.63	99.63	0.71	0.71	2	-
GCA_011525035.1	s__UBA10364 sp011525035	90.7337	541	590	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012269745.1	s__UBA10364 sp012269745	84.8993	458	590	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623275.1	s__UBA10364 sp018623275	83.6218	306	590	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003545085.1	s__UBA10364 sp003545085	83.5165	340	590	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003023665.1	s__UBA10364 sp003023665	78.4784	166	590	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	98.70	98.70	0.79	0.79	2	-
--------------------------------------------------------------------------------
[2023-03-15 04:47:10,149] [INFO] GTDB search result was written to OceanDNA-b5779/result_gtdb.tsv
[2023-03-15 04:47:10,150] [INFO] ===== GTDB Search completed =====
[2023-03-15 04:47:10,153] [INFO] DFAST_QC result json was written to OceanDNA-b5779/dqc_result.json
[2023-03-15 04:47:10,153] [INFO] DFAST_QC completed!
[2023-03-15 04:47:10,153] [INFO] Total running time: 0h1m20s