[2023-03-16 13:03:54,687] [INFO] DFAST_QC pipeline started.
[2023-03-16 13:03:54,687] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 13:03:54,687] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ca64467-4975-4e79-87d6-62dd6035c227/dqc_reference
[2023-03-16 13:03:55,979] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 13:03:55,980] [INFO] Task started: Prodigal
[2023-03-16 13:03:55,980] [INFO] Running command: cat /var/lib/cwl/stg528135d1-4e5d-4228-b4ba-154bcc15b01a/OceanDNA-b18960.fa | prodigal -d OceanDNA-b18960/cds.fna -a OceanDNA-b18960/protein.faa -g 11 -q > /dev/null
[2023-03-16 13:04:03,276] [INFO] Task succeeded: Prodigal
[2023-03-16 13:04:03,276] [INFO] Task started: HMMsearch
[2023-03-16 13:04:03,276] [INFO] Running command: hmmsearch --tblout OceanDNA-b18960/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ca64467-4975-4e79-87d6-62dd6035c227/dqc_reference/reference_markers.hmm OceanDNA-b18960/protein.faa > /dev/null
[2023-03-16 13:04:03,429] [INFO] Task succeeded: HMMsearch
[2023-03-16 13:04:03,430] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg528135d1-4e5d-4228-b4ba-154bcc15b01a/OceanDNA-b18960.fa]
[2023-03-16 13:04:03,442] [INFO] Query marker FASTA was written to OceanDNA-b18960/markers.fasta
[2023-03-16 13:04:03,442] [INFO] Task started: Blastn
[2023-03-16 13:04:03,442] [INFO] Running command: blastn -query OceanDNA-b18960/markers.fasta -db /var/lib/cwl/stg2ca64467-4975-4e79-87d6-62dd6035c227/dqc_reference/reference_markers.fasta -out OceanDNA-b18960/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 13:04:03,924] [INFO] Task succeeded: Blastn
[2023-03-16 13:04:03,925] [INFO] Selected 10 target genomes.
[2023-03-16 13:04:03,925] [INFO] Target genome list was writen to OceanDNA-b18960/target_genomes.txt
[2023-03-16 13:04:03,932] [INFO] Task started: fastANI
[2023-03-16 13:04:03,932] [INFO] Running command: fastANI --query /var/lib/cwl/stg528135d1-4e5d-4228-b4ba-154bcc15b01a/OceanDNA-b18960.fa --refList OceanDNA-b18960/target_genomes.txt --output OceanDNA-b18960/fastani_result.tsv --threads 1
[2023-03-16 13:04:08,435] [INFO] Task succeeded: fastANI
[2023-03-16 13:04:08,435] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ca64467-4975-4e79-87d6-62dd6035c227/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 13:04:08,435] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ca64467-4975-4e79-87d6-62dd6035c227/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 13:04:08,436] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 13:04:08,436] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 13:04:08,436] [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
--------------------------------------------------------------------------------
[2023-03-16 13:04:08,436] [INFO] DFAST Taxonomy check result was written to OceanDNA-b18960/tc_result.tsv
[2023-03-16 13:04:08,436] [INFO] ===== Taxonomy check completed =====
[2023-03-16 13:04:08,436] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 13:04:08,436] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ca64467-4975-4e79-87d6-62dd6035c227/dqc_reference/checkm_data
[2023-03-16 13:04:08,439] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 13:04:08,441] [INFO] Task started: CheckM
[2023-03-16 13:04:08,441] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b18960/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b18960/checkm_input OceanDNA-b18960/checkm_result
[2023-03-16 13:04:31,518] [INFO] Task succeeded: CheckM
[2023-03-16 13:04:31,518] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 13:04:31,520] [INFO] ===== Completeness check finished =====
[2023-03-16 13:04:31,520] [INFO] ===== Start GTDB Search =====
[2023-03-16 13:04:31,520] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b18960/markers.fasta)
[2023-03-16 13:04:31,520] [INFO] Task started: Blastn
[2023-03-16 13:04:31,521] [INFO] Running command: blastn -query OceanDNA-b18960/markers.fasta -db /var/lib/cwl/stg2ca64467-4975-4e79-87d6-62dd6035c227/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b18960/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 13:04:32,188] [INFO] Task succeeded: Blastn
[2023-03-16 13:04:32,189] [INFO] Selected 16 target genomes.
[2023-03-16 13:04:32,189] [INFO] Target genome list was writen to OceanDNA-b18960/target_genomes_gtdb.txt
[2023-03-16 13:04:32,760] [INFO] Task started: fastANI
[2023-03-16 13:04:32,760] [INFO] Running command: fastANI --query /var/lib/cwl/stg528135d1-4e5d-4228-b4ba-154bcc15b01a/OceanDNA-b18960.fa --refList OceanDNA-b18960/target_genomes_gtdb.txt --output OceanDNA-b18960/fastani_result_gtdb.tsv --threads 1
[2023-03-16 13:04:42,579] [INFO] Task succeeded: fastANI
[2023-03-16 13:04:42,585] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 13:04:42,585] [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_002715035.1	s__TCS55 sp002715035	94.379	237	402	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	85.8156	282	402	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	99.73	99.62	0.91	0.80	15	-
GCA_014382015.1	s__TCS55 sp014382015	83.4377	320	402	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	99.95	99.95	0.97	0.96	3	-
GCA_002704905.1	s__TCS55 sp002704905	77.755	52	402	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002716525.1	s__TCS55 sp002716525	77.5362	72	402	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	76.9365	90	402	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012964665.1	s__TCS55 sp012964665	76.8372	86	402	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	99.32	99.03	0.83	0.81	3	-
GCA_001577025.1	s__TCS55 sp001577025	76.3107	93	402	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	95.80	95.01	0.79	0.74	7	-
--------------------------------------------------------------------------------
[2023-03-16 13:04:42,585] [INFO] GTDB search result was written to OceanDNA-b18960/result_gtdb.tsv
[2023-03-16 13:04:42,585] [INFO] ===== GTDB Search completed =====
[2023-03-16 13:04:42,586] [INFO] DFAST_QC result json was written to OceanDNA-b18960/dqc_result.json
[2023-03-16 13:04:42,586] [INFO] DFAST_QC completed!
[2023-03-16 13:04:42,586] [INFO] Total running time: 0h0m48s