[2023-03-15 17:24:01,462] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:24:01,463] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:24:01,463] [INFO] DQC Reference Directory: /var/lib/cwl/stg28cac8c3-99c6-4166-93ac-7617ac5f8f77/dqc_reference
[2023-03-15 17:24:02,736] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:24:02,736] [INFO] Task started: Prodigal
[2023-03-15 17:24:02,736] [INFO] Running command: cat /var/lib/cwl/stg3a917513-2bee-4253-9738-80a71f72de52/OceanDNA-b18963.fa | prodigal -d OceanDNA-b18963/cds.fna -a OceanDNA-b18963/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:24:14,021] [INFO] Task succeeded: Prodigal
[2023-03-15 17:24:14,021] [INFO] Task started: HMMsearch
[2023-03-15 17:24:14,021] [INFO] Running command: hmmsearch --tblout OceanDNA-b18963/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28cac8c3-99c6-4166-93ac-7617ac5f8f77/dqc_reference/reference_markers.hmm OceanDNA-b18963/protein.faa > /dev/null
[2023-03-15 17:24:14,292] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:24:14,293] [INFO] Found 6/6 markers.
[2023-03-15 17:24:14,310] [INFO] Query marker FASTA was written to OceanDNA-b18963/markers.fasta
[2023-03-15 17:24:14,311] [INFO] Task started: Blastn
[2023-03-15 17:24:14,311] [INFO] Running command: blastn -query OceanDNA-b18963/markers.fasta -db /var/lib/cwl/stg28cac8c3-99c6-4166-93ac-7617ac5f8f77/dqc_reference/reference_markers.fasta -out OceanDNA-b18963/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:24:14,995] [INFO] Task succeeded: Blastn
[2023-03-15 17:24:14,996] [INFO] Selected 18 target genomes.
[2023-03-15 17:24:14,996] [INFO] Target genome list was writen to OceanDNA-b18963/target_genomes.txt
[2023-03-15 17:24:15,005] [INFO] Task started: fastANI
[2023-03-15 17:24:15,005] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a917513-2bee-4253-9738-80a71f72de52/OceanDNA-b18963.fa --refList OceanDNA-b18963/target_genomes.txt --output OceanDNA-b18963/fastani_result.tsv --threads 1
[2023-03-15 17:24:25,791] [INFO] Task succeeded: fastANI
[2023-03-15 17:24:25,791] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28cac8c3-99c6-4166-93ac-7617ac5f8f77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:24:25,791] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28cac8c3-99c6-4166-93ac-7617ac5f8f77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:24:25,792] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:24:25,792] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 17:24:25,792] [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 17:24:25,792] [INFO] DFAST Taxonomy check result was written to OceanDNA-b18963/tc_result.tsv
[2023-03-15 17:24:25,792] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:24:25,792] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:24:25,792] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28cac8c3-99c6-4166-93ac-7617ac5f8f77/dqc_reference/checkm_data
[2023-03-15 17:24:25,795] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:24:25,799] [INFO] Task started: CheckM
[2023-03-15 17:24:25,799] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b18963/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b18963/checkm_input OceanDNA-b18963/checkm_result
[2023-03-15 17:24:57,897] [INFO] Task succeeded: CheckM
[2023-03-15 17:24:57,897] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:24:57,899] [INFO] ===== Completeness check finished =====
[2023-03-15 17:24:57,899] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:24:57,899] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b18963/markers.fasta)
[2023-03-15 17:24:57,899] [INFO] Task started: Blastn
[2023-03-15 17:24:57,899] [INFO] Running command: blastn -query OceanDNA-b18963/markers.fasta -db /var/lib/cwl/stg28cac8c3-99c6-4166-93ac-7617ac5f8f77/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b18963/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:24:58,745] [INFO] Task succeeded: Blastn
[2023-03-15 17:24:58,865] [INFO] Selected 28 target genomes.
[2023-03-15 17:24:58,866] [INFO] Target genome list was writen to OceanDNA-b18963/target_genomes_gtdb.txt
[2023-03-15 17:24:58,897] [INFO] Task started: fastANI
[2023-03-15 17:24:58,897] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a917513-2bee-4253-9738-80a71f72de52/OceanDNA-b18963.fa --refList OceanDNA-b18963/target_genomes_gtdb.txt --output OceanDNA-b18963/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:25:09,089] [INFO] Task succeeded: fastANI
[2023-03-15 17:25:09,096] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 17:25:09,096] [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_002471845.1	s__TCS55 sp002471845	81.9011	366	631	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	99.96	99.93	0.96	0.96	5	-
GCA_002715035.1	s__TCS55 sp002715035	80.215	160	631	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	96.36	95.92	0.81	0.67	4	-
GCA_018674655.1	s__TCS55 sp018674655	79.1839	194	631	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	99.73	99.62	0.91	0.80	15	-
GCA_018647265.1	s__TCS55 sp018647265	79.0798	267	631	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	99.87	99.79	0.92	0.89	15	-
GCA_014382015.1	s__TCS55 sp014382015	78.1713	229	631	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	99.95	99.95	0.97	0.96	3	-
GCA_012964665.1	s__TCS55 sp012964665	77.7829	147	631	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	99.32	99.03	0.83	0.81	3	-
GCA_002716525.1	s__TCS55 sp002716525	77.4069	109	631	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845785.1	s__TCS55 sp016845785	77.3256	155	631	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001577025.1	s__TCS55 sp001577025	77.2686	136	631	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	95.80	95.01	0.79	0.74	7	-
GCA_002704905.1	s__TCS55 sp002704905	76.7604	71	631	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 17:25:09,096] [INFO] GTDB search result was written to OceanDNA-b18963/result_gtdb.tsv
[2023-03-15 17:25:09,096] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:25:09,097] [INFO] DFAST_QC result json was written to OceanDNA-b18963/dqc_result.json
[2023-03-15 17:25:09,097] [INFO] DFAST_QC completed!
[2023-03-15 17:25:09,097] [INFO] Total running time: 0h1m8s