[2023-03-18 05:53:16,840] [INFO] DFAST_QC pipeline started.
[2023-03-18 05:53:16,840] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 05:53:16,840] [INFO] DQC Reference Directory: /var/lib/cwl/stgf2ad85ee-fcf4-4f49-acf6-9618939ab0fc/dqc_reference
[2023-03-18 05:53:17,975] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 05:53:17,976] [INFO] Task started: Prodigal
[2023-03-18 05:53:17,976] [INFO] Running command: cat /var/lib/cwl/stg02cc38d8-a42c-498c-b3cf-1841c545d9ed/OceanDNA-a2109.fa | prodigal -d OceanDNA-a2109/cds.fna -a OceanDNA-a2109/protein.faa -g 11 -q > /dev/null
[2023-03-18 05:53:26,050] [INFO] Task succeeded: Prodigal
[2023-03-18 05:53:26,051] [INFO] Task started: HMMsearch
[2023-03-18 05:53:26,051] [INFO] Running command: hmmsearch --tblout OceanDNA-a2109/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf2ad85ee-fcf4-4f49-acf6-9618939ab0fc/dqc_reference/reference_markers.hmm OceanDNA-a2109/protein.faa > /dev/null
[2023-03-18 05:53:26,204] [INFO] Task succeeded: HMMsearch
[2023-03-18 05:53:26,204] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg02cc38d8-a42c-498c-b3cf-1841c545d9ed/OceanDNA-a2109.fa]
[2023-03-18 05:53:26,217] [INFO] Query marker FASTA was written to OceanDNA-a2109/markers.fasta
[2023-03-18 05:53:26,218] [INFO] Task started: Blastn
[2023-03-18 05:53:26,218] [INFO] Running command: blastn -query OceanDNA-a2109/markers.fasta -db /var/lib/cwl/stgf2ad85ee-fcf4-4f49-acf6-9618939ab0fc/dqc_reference/reference_markers.fasta -out OceanDNA-a2109/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:53:26,644] [INFO] Task succeeded: Blastn
[2023-03-18 05:53:26,644] [INFO] Selected 7 target genomes.
[2023-03-18 05:53:26,645] [INFO] Target genome list was writen to OceanDNA-a2109/target_genomes.txt
[2023-03-18 05:53:26,649] [INFO] Task started: fastANI
[2023-03-18 05:53:26,649] [INFO] Running command: fastANI --query /var/lib/cwl/stg02cc38d8-a42c-498c-b3cf-1841c545d9ed/OceanDNA-a2109.fa --refList OceanDNA-a2109/target_genomes.txt --output OceanDNA-a2109/fastani_result.tsv --threads 1
[2023-03-18 05:53:29,068] [INFO] Task succeeded: fastANI
[2023-03-18 05:53:29,068] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf2ad85ee-fcf4-4f49-acf6-9618939ab0fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 05:53:29,069] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf2ad85ee-fcf4-4f49-acf6-9618939ab0fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 05:53:29,069] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 05:53:29,069] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 05:53:29,069] [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 05:53:29,069] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2109/tc_result.tsv
[2023-03-18 05:53:29,069] [INFO] ===== Taxonomy check completed =====
[2023-03-18 05:53:29,069] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 05:53:29,069] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf2ad85ee-fcf4-4f49-acf6-9618939ab0fc/dqc_reference/checkm_data
[2023-03-18 05:53:29,072] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 05:53:29,076] [INFO] Task started: CheckM
[2023-03-18 05:53:29,076] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2109/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2109/checkm_input OceanDNA-a2109/checkm_result
[2023-03-18 05:53:54,793] [INFO] Task succeeded: CheckM
[2023-03-18 05:53:54,793] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 05:53:54,797] [INFO] ===== Completeness check finished =====
[2023-03-18 05:53:54,797] [INFO] ===== Start GTDB Search =====
[2023-03-18 05:53:54,798] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2109/markers.fasta)
[2023-03-18 05:53:54,798] [INFO] Task started: Blastn
[2023-03-18 05:53:54,799] [INFO] Running command: blastn -query OceanDNA-a2109/markers.fasta -db /var/lib/cwl/stgf2ad85ee-fcf4-4f49-acf6-9618939ab0fc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2109/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:53:55,210] [INFO] Task succeeded: Blastn
[2023-03-18 05:53:55,211] [INFO] Selected 10 target genomes.
[2023-03-18 05:53:55,211] [INFO] Target genome list was writen to OceanDNA-a2109/target_genomes_gtdb.txt
[2023-03-18 05:53:55,249] [INFO] Task started: fastANI
[2023-03-18 05:53:55,249] [INFO] Running command: fastANI --query /var/lib/cwl/stg02cc38d8-a42c-498c-b3cf-1841c545d9ed/OceanDNA-a2109.fa --refList OceanDNA-a2109/target_genomes_gtdb.txt --output OceanDNA-a2109/fastani_result_gtdb.tsv --threads 1
[2023-03-18 05:53:57,948] [INFO] Task succeeded: fastANI
[2023-03-18 05:53:57,952] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 05:53:57,952] [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_002729095.1	s__MGIIa-L1 sp002729095	77.0192	77	475	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	98.94	98.73	0.83	0.79	6	-
GCA_002688825.1	s__MGIIa-L1 sp002688825	76.775	61	475	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002172355.2	s__MGIIa-L1 sp002172355	76.6636	61	475	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.37	98.74	0.95	0.91	3	-
GCA_002726395.1	s__MGIIa-L1 sp002726395	76.5967	78	475	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.39	99.39	0.85	0.85	2	-
GCA_013329925.1	s__MGIIa-L1 sp8734u	76.5283	70	475	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	100.00	100.00	0.97	0.97	2	-
GCA_018667575.1	s__MGIIa-L1 sp018667575	76.3911	62	475	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.28	99.11	0.90	0.88	4	-
--------------------------------------------------------------------------------
[2023-03-18 05:53:57,953] [INFO] GTDB search result was written to OceanDNA-a2109/result_gtdb.tsv
[2023-03-18 05:53:57,953] [INFO] ===== GTDB Search completed =====
[2023-03-18 05:53:57,954] [INFO] DFAST_QC result json was written to OceanDNA-a2109/dqc_result.json
[2023-03-18 05:53:57,954] [INFO] DFAST_QC completed!
[2023-03-18 05:53:57,954] [INFO] Total running time: 0h0m41s