[2023-03-14 12:30:17,578] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:30:17,578] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:30:17,578] [INFO] DQC Reference Directory: /var/lib/cwl/stg07436bbc-b9e9-42c7-93cd-6715e7d0f125/dqc_reference
[2023-03-14 12:30:18,642] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:30:18,643] [INFO] Task started: Prodigal
[2023-03-14 12:30:18,643] [INFO] Running command: cat /var/lib/cwl/stgc26fe308-d100-4728-bb2b-a3b86c7cfc5b/OceanDNA-a2323.fa | prodigal -d OceanDNA-a2323/cds.fna -a OceanDNA-a2323/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:30:25,976] [INFO] Task succeeded: Prodigal
[2023-03-14 12:30:25,977] [INFO] Task started: HMMsearch
[2023-03-14 12:30:25,977] [INFO] Running command: hmmsearch --tblout OceanDNA-a2323/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg07436bbc-b9e9-42c7-93cd-6715e7d0f125/dqc_reference/reference_markers.hmm OceanDNA-a2323/protein.faa > /dev/null
[2023-03-14 12:30:26,130] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:30:26,131] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc26fe308-d100-4728-bb2b-a3b86c7cfc5b/OceanDNA-a2323.fa]
[2023-03-14 12:30:26,151] [INFO] Query marker FASTA was written to OceanDNA-a2323/markers.fasta
[2023-03-14 12:30:26,152] [INFO] Task started: Blastn
[2023-03-14 12:30:26,152] [INFO] Running command: blastn -query OceanDNA-a2323/markers.fasta -db /var/lib/cwl/stg07436bbc-b9e9-42c7-93cd-6715e7d0f125/dqc_reference/reference_markers.fasta -out OceanDNA-a2323/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:30:26,611] [INFO] Task succeeded: Blastn
[2023-03-14 12:30:26,613] [INFO] Selected 2 target genomes.
[2023-03-14 12:30:26,614] [INFO] Target genome list was writen to OceanDNA-a2323/target_genomes.txt
[2023-03-14 12:30:26,615] [INFO] Task started: fastANI
[2023-03-14 12:30:26,615] [INFO] Running command: fastANI --query /var/lib/cwl/stgc26fe308-d100-4728-bb2b-a3b86c7cfc5b/OceanDNA-a2323.fa --refList OceanDNA-a2323/target_genomes.txt --output OceanDNA-a2323/fastani_result.tsv --threads 1
[2023-03-14 12:30:27,515] [INFO] Task succeeded: fastANI
[2023-03-14 12:30:27,515] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg07436bbc-b9e9-42c7-93cd-6715e7d0f125/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:30:27,516] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg07436bbc-b9e9-42c7-93cd-6715e7d0f125/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:30:27,516] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:30:27,516] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 12:30:27,516] [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
--------------------------------------------------------------------------------
[2023-03-14 12:30:27,518] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2323/tc_result.tsv
[2023-03-14 12:30:27,518] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:30:27,518] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:30:27,519] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg07436bbc-b9e9-42c7-93cd-6715e7d0f125/dqc_reference/checkm_data
[2023-03-14 12:30:27,521] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:30:27,526] [INFO] Task started: CheckM
[2023-03-14 12:30:27,527] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2323/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2323/checkm_input OceanDNA-a2323/checkm_result
[2023-03-14 12:30:51,530] [INFO] Task succeeded: CheckM
[2023-03-14 12:30:51,531] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.22%
Contamintation: 1.77%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-14 12:30:51,541] [INFO] ===== Completeness check finished =====
[2023-03-14 12:30:51,541] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:30:51,541] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2323/markers.fasta)
[2023-03-14 12:30:51,542] [INFO] Task started: Blastn
[2023-03-14 12:30:51,542] [INFO] Running command: blastn -query OceanDNA-a2323/markers.fasta -db /var/lib/cwl/stg07436bbc-b9e9-42c7-93cd-6715e7d0f125/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2323/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:30:52,097] [INFO] Task succeeded: Blastn
[2023-03-14 12:30:52,099] [INFO] Selected 7 target genomes.
[2023-03-14 12:30:52,099] [INFO] Target genome list was writen to OceanDNA-a2323/target_genomes_gtdb.txt
[2023-03-14 12:30:52,105] [INFO] Task started: fastANI
[2023-03-14 12:30:52,106] [INFO] Running command: fastANI --query /var/lib/cwl/stgc26fe308-d100-4728-bb2b-a3b86c7cfc5b/OceanDNA-a2323.fa --refList OceanDNA-a2323/target_genomes_gtdb.txt --output OceanDNA-a2323/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:30:54,303] [INFO] Task succeeded: fastANI
[2023-03-14 12:30:54,308] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:30:54,308] [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	84.4866	352	432	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_002702945.1	s__MGIIa-L1 sp002702945	82.8614	341	432	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	98.55	98.53	0.86	0.86	3	-
GCA_002727485.1	s__MGIIa-L1 sp002727485	82.6642	233	432	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_002697705.1	s__MGIIa-L1 sp002697705	78.4292	152	432	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.07	99.07	0.77	0.77	2	-
GCA_002172355.2	s__MGIIa-L1 sp002172355	77.8709	167	432	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_009887195.1	s__MGIIa-L1 sp009887195	77.007	66	432	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	98.91	98.88	0.90	0.86	3	-
GCA_018659375.1	s__MGIIa-L1 sp018659375	76.8215	75	432	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.68	99.68	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-03-14 12:30:54,311] [INFO] GTDB search result was written to OceanDNA-a2323/result_gtdb.tsv
[2023-03-14 12:30:54,311] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:30:54,313] [INFO] DFAST_QC result json was written to OceanDNA-a2323/dqc_result.json
[2023-03-14 12:30:54,314] [INFO] DFAST_QC completed!
[2023-03-14 12:30:54,314] [INFO] Total running time: 0h0m37s